Daily Papers

The complexity and heterogeneity of data in many real-world applications pose significant challenges for traditional machine learning and signal processing techniques. For instance, in medicine, effective analysis of diverse physiological signals is crucial for patient monitoring and clinical decision-making and yet highly challenging. We introduce MedTsLLM, a general multimodal large language model (LLM) framework that effectively integrates time series data and rich contextual information in the form of text to analyze physiological signals, performing three tasks with clinical relevance: semantic segmentation, boundary detection, and anomaly detection in time series. These critical tasks enable deeper analysis of physiological signals and can provide actionable insights for clinicians. We utilize a reprogramming layer to align embeddings of time series patches with a pretrained LLM's embedding space and make effective use of raw time series, in conjunction with textual context. Given the multivariate nature of medical datasets, we develop methods to handle multiple covariates. We additionally tailor the text prompt to include patient-specific information. Our model outperforms state-of-the-art baselines, including deep learning models, other LLMs, and clinical methods across multiple medical domains, specifically electrocardiograms and respiratory waveforms. MedTsLLM presents a promising step towards harnessing the power of LLMs for medical time series analysis that can elevate data-driven tools for clinicians and improve patient outcomes.

Transfer learning from pretrained language models recently became the dominant approach for solving many NLP tasks. A common approach to transfer learning for multiple tasks that maximize parameter sharing trains one or more task-specific layers on top of the language model. In this paper, we present an alternative approach based on adversarial reprogramming, which extends earlier work on automatic prompt generation. Adversarial reprogramming attempts to learn task-specific word embeddings that, when concatenated to the input text, instruct the language model to solve the specified task. Using up to 25K trainable parameters per task, this approach outperforms all existing methods with up to 25M trainable parameters on the public leaderboard of the GLUE benchmark. Our method, initialized with task-specific human-readable prompts, also works in a few-shot setting, outperforming GPT-3 on two SuperGLUE tasks with just 32 training samples.

Continual learning aims to emulate the human ability to continually accumulate knowledge over sequential tasks. The main challenge is to maintain performance on previously learned tasks after learning new tasks, i.e., to avoid catastrophic forgetting. We propose a Channel-wise Lightweight Reprogramming (CLR) approach that helps convolutional neural networks (CNNs) overcome catastrophic forgetting during continual learning. We show that a CNN model trained on an old task (or self-supervised proxy task) could be ``reprogrammed" to solve a new task by using our proposed lightweight (very cheap) reprogramming parameter. With the help of CLR, we have a better stability-plasticity trade-off to solve continual learning problems: To maintain stability and retain previous task ability, we use a common task-agnostic immutable part as the shared ``anchor" parameter set. We then add task-specific lightweight reprogramming parameters to reinterpret the outputs of the immutable parts, to enable plasticity and integrate new knowledge. To learn sequential tasks, we only train the lightweight reprogramming parameters to learn each new task. Reprogramming parameters are task-specific and exclusive to each task, which makes our method immune to catastrophic forgetting. To minimize the parameter requirement of reprogramming to learn new tasks, we make reprogramming lightweight by only adjusting essential kernels and learning channel-wise linear mappings from anchor parameters to task-specific domain knowledge. We show that, for general CNNs, the CLR parameter increase is less than 0.6\% for any new task. Our method outperforms 13 state-of-the-art continual learning baselines on a new challenging sequence of 53 image classification datasets. Code and data are available at https://github.com/gyhandy/Channel-wise-Lightweight-Reprogramming

This paper presents advancements in automated early-stage prediction of the success of reprogramming human induced pluripotent stem cells (iPSCs) as a potential source for regenerative cell therapies.The minuscule success rate of iPSC-reprogramming of around 0.01% to 0.1% makes it labor-intensive, time-consuming, and exorbitantly expensive to generate a stable iPSC line. Since that requires culturing of millions of cells and intense biological scrutiny of multiple clones to identify a single optimal clone. The ability to reliably predict which cells are likely to establish as an optimal iPSC line at an early stage of pluripotency would therefore be ground-breaking in rendering this a practical and cost-effective approach to personalized medicine. Temporal information about changes in cellular appearance over time is crucial for predicting its future growth outcomes. In order to generate this data, we first performed continuous time-lapse imaging of iPSCs in culture using an ultra-high resolution microscope. We then annotated the locations and identities of cells in late-stage images where reliable manual identification is possible. Next, we propagated these labels backwards in time using a semi-automated tracking system to obtain labels for early stages of growth. Finally, we used this data to train deep neural networks to perform automatic cell segmentation and classification. Our code and data are available at https://github.com/abhineet123/ipsc_prediction.

Deep Learning architectures, and in particular Transformers, are conventionally viewed as a composition of layers. These layers are actually often obtained as the sum of two contributions: a residual path that copies the input and the output of a Transformer block. As a consequence, the inner representations (i.e. the input of these blocks) can be interpreted as iterative refinement of a propagated latent representation. Under this lens, many works suggest that the inner space is shared across layers, meaning that tokens can be decoded at early stages. Mechanistic interpretability even goes further by conjecturing that some layers act as refinement layers. Following this path, we propose inference-time inner looping, which prolongs refinement in pretrained off-the-shelf language models by repeatedly re-applying a selected block range. Across multiple benchmarks, inner looping yields modest but consistent accuracy improvements. Analyses of the resulting latent trajectories suggest more stable state evolution and continued semantic refinement. Overall, our results suggest that additional refinement can be obtained through simple test-time looping, extending computation in frozen pretrained models.

We present a framework for using transformer networks as universal computers by programming them with specific weights and placing them in a loop. Our input sequence acts as a punchcard, consisting of instructions and memory for data read/writes. We demonstrate that a constant number of encoder layers can emulate basic computing blocks, including embedding edit operations, non-linear functions, function calls, program counters, and conditional branches. Using these building blocks, we emulate a small instruction-set computer. This allows us to map iterative algorithms to programs that can be executed by a looped, 13-layer transformer. We show how this transformer, instructed by its input, can emulate a basic calculator, a basic linear algebra library, and in-context learning algorithms that employ backpropagation. Our work highlights the versatility of the attention mechanism, and demonstrates that even shallow transformers can execute full-fledged, general-purpose programs.

In the era of foundation models with huge pre-training budgets, the downstream tasks have been shifted to the narrative of efficient and fast adaptation. For classification-based tasks in the domain of computer vision, the two most efficient approaches have been linear probing (LP) and visual prompting/reprogramming (VP); the former aims to learn a classifier in the form of a linear head on the features extracted by the pre-trained model, while the latter maps the input data to the domain of the source data on which the model was originally pre-trained on. Although extensive studies have demonstrated the differences between LP and VP in terms of downstream performance, we explore the capabilities of the two aforementioned methods via the sparsity axis: (a) Data sparsity: the impact of few-shot adaptation and (b) Model sparsity: the impact of lottery tickets (LT). We demonstrate that LT are not universal reprogrammers, i.e., for certain target datasets, reprogramming an LT yields significantly lower performance than the reprogrammed dense model although their corresponding upstream performance is similar. Further, we demonstrate that the calibration of dense models is always superior to that of their lottery ticket counterparts under both LP and VP regimes. Our empirical study opens a new avenue of research into VP for sparse models and encourages further understanding of the performance beyond the accuracy achieved by VP under constraints of sparsity. Code and logs can be accessed at https://github.com/landskape-ai/Reprogram_LT.

Memory layers use a trainable key-value lookup mechanism to add extra parameters to a model without increasing FLOPs. Conceptually, sparsely activated memory layers complement compute-heavy dense feed-forward layers, providing dedicated capacity to store and retrieve information cheaply. This work takes memory layers beyond proof-of-concept, proving their utility at contemporary scale. On downstream tasks, language models augmented with our improved memory layer outperform dense models with more than twice the computation budget, as well as mixture-of-expert models when matched for both compute and parameters. We find gains are especially pronounced for factual tasks. We provide a fully parallelizable memory layer implementation, demonstrating scaling laws with up to 128B memory parameters, pretrained to 1 trillion tokens, comparing to base models with up to 8B parameters.

We introduce Neural Organ Transplantation (NOT), a modular adaptation framework that enables trained transformer layers to function as reusable transferable checkpoints for domain adaptation. Unlike conventional fine-tuning approaches that tightly couple trained parameters to specific model instances and training data, NOT extracts contiguous layer subsets ("donor organs") from pre-trained models, trains them independently on domain-specific data, and saves them as standalone checkpoint files that can be transplanted into compatible recipient models without access to the original training data. Through experiments on three decoder-only transformer architectures spanning 124M to 20B parameters (GPT-2, TinyLlama, and GPT-OSS), we demonstrate that donor transplantation substantially outperforms existing adaptation methods, achieving an order-of-magnitude improvement in perplexity over LoRA while training significantly faster. The method exhibits position dependence, with early insertion positions yielding optimal results. Cross-domain transfer at billion-parameter scale reveals unexpected regularization benefits. These findings demonstrate that transformer middle layers can support efficient modular transfer for decoder-only architectures, enabling privacy-preserving expertise sharing through checkpoint distribution. We note that this approach is currently limited to decoder-only models; preliminary experiments on encoder-based architectures show reduced effectiveness.

The neurons of artificial neural networks were originally invented when much less was known about biological neurons than is known today. Our work explores a modification to the core neuron unit to make it more parallel to a biological neuron. The modification is made with the knowledge that biological dendrites are not simply passive activation funnels, but also compute complex non-linear functions as they transmit activation to the cell body. The paper explores a novel system of "Perforated" backpropagation empowering the artificial neurons of deep neural networks to achieve better performance coding for the same features they coded for in the original architecture. After an initial network training phase, additional "Dendrite Nodes" are added to the network and separately trained with a different objective: to correlate their output with the remaining error of the original neurons. The trained Dendrite Nodes are then frozen, and the original neurons are further trained, now taking into account the additional error signals provided by the Dendrite Nodes. The cycle of training the original neurons and then adding and training Dendrite Nodes can be repeated several times until satisfactory performance is achieved. Our algorithm was successfully added to modern state-of-the-art PyTorch networks across multiple domains, improving upon original accuracies and allowing for significant model compression without a loss in accuracy.

We introduce the Block-Recurrent Transformer, which applies a transformer layer in a recurrent fashion along a sequence, and has linear complexity with respect to sequence length. Our recurrent cell operates on blocks of tokens rather than single tokens during training, and leverages parallel computation within a block in order to make efficient use of accelerator hardware. The cell itself is strikingly simple. It is merely a transformer layer: it uses self-attention and cross-attention to efficiently compute a recurrent function over a large set of state vectors and tokens. Our design was inspired in part by LSTM cells, and it uses LSTM-style gates, but it scales the typical LSTM cell up by several orders of magnitude. Our implementation of recurrence has the same cost in both computation time and parameter count as a conventional transformer layer, but offers dramatically improved perplexity in language modeling tasks over very long sequences. Our model out-performs a long-range Transformer XL baseline by a wide margin, while running twice as fast. We demonstrate its effectiveness on PG19 (books), arXiv papers, and GitHub source code. Our code has been released as open source.

To understand the learning process in brains, biologically plausible algorithms have been explored by modeling the detailed neuron properties and dynamics. On the other hand, simplified multi-layer models of neural networks have shown great success on computational tasks such as image classification and speech recognition. However, the computational models that can achieve good accuracy for these learning applications are very different from the bio-plausible models. This paper studies whether a bio-plausible model of a in vitro living neural network can be used to perform machine learning tasks and achieve good inference accuracy. A novel two-layer bio-hardware hybrid neural network is proposed. The biological layer faithfully models variations of synapses, neurons, and network sparsity in in vitro living neural networks. The hardware layer is a computational fully-connected layer that tunes parameters to optimize for accuracy. Several techniques are proposed to improve the inference accuracy of the proposed hybrid neural network. For instance, an adaptive pre-processing technique helps the proposed neural network to achieve good learning accuracy for different living neural network sparsity. The proposed hybrid neural network with realistic neuron parameters and variations achieves a 98.3% testing accuracy for the handwritten digit recognition task on the full MNIST dataset.

Decoder-only transformers have become the standard architecture for large language models (LLMs) due to their strong performance. Recent studies suggest that, in pre-trained LLMs, early, middle, and late layers may serve distinct roles: Early layers focus on understanding the input context, middle layers handle task-specific processing, and late layers convert abstract representations into output tokens. We hypothesize that once representations have been processed by the early and middle layers, the resulting hidden states may encapsulate sufficient information to support the generation of multiple tokens using only the late layers, eliminating the need to repeatedly traverse the early and middle layers. We refer to this inference paradigm as Direct Multi-Token Decoding (DMTD). Unlike speculative decoding, our method introduces no additional parameters, auxiliary routines, or post-generation verification. Despite being trained on a limited dataset, a fine-tuned DMTD Qwen3-4B model has already demonstrated promising results, achieving up to a 2x speedup with only minor performance loss. Moreover, as shown in our scaling analysis, its performance is expected to further improve with larger training datasets.

We introduce a modern Hopfield network with continuous states and a corresponding update rule. The new Hopfield network can store exponentially (with the dimension of the associative space) many patterns, retrieves the pattern with one update, and has exponentially small retrieval errors. It has three types of energy minima (fixed points of the update): (1) global fixed point averaging over all patterns, (2) metastable states averaging over a subset of patterns, and (3) fixed points which store a single pattern. The new update rule is equivalent to the attention mechanism used in transformers. This equivalence enables a characterization of the heads of transformer models. These heads perform in the first layers preferably global averaging and in higher layers partial averaging via metastable states. The new modern Hopfield network can be integrated into deep learning architectures as layers to allow the storage of and access to raw input data, intermediate results, or learned prototypes. These Hopfield layers enable new ways of deep learning, beyond fully-connected, convolutional, or recurrent networks, and provide pooling, memory, association, and attention mechanisms. We demonstrate the broad applicability of the Hopfield layers across various domains. Hopfield layers improved state-of-the-art on three out of four considered multiple instance learning problems as well as on immune repertoire classification with several hundreds of thousands of instances. On the UCI benchmark collections of small classification tasks, where deep learning methods typically struggle, Hopfield layers yielded a new state-of-the-art when compared to different machine learning methods. Finally, Hopfield layers achieved state-of-the-art on two drug design datasets. The implementation is available at: https://github.com/ml-jku/hopfield-layers

Antibodies comprise the most versatile class of binding molecules, with numerous applications in biomedicine. Computational design of antibodies involves generating novel and diverse sequences, while maintaining structural consistency. Unique to antibodies, designing the complementarity-determining region (CDR), which determines the antigen binding affinity and specificity, creates its own unique challenges. Recent deep learning models have shown impressive results, however the limited number of known antibody sequence/structure pairs frequently leads to degraded performance, particularly lacking diversity in the generated sequences. In our work we address this challenge by leveraging Model Reprogramming (MR), which repurposes pretrained models on a source language to adapt to the tasks that are in a different language and have scarce data - where it may be difficult to train a high-performing model from scratch or effectively fine-tune an existing pre-trained model on the specific task. Specifically, we introduce ReprogBert in which a pretrained English language model is repurposed for protein sequence infilling - thus considers cross-language adaptation using less data. Results on antibody design benchmarks show that our model on low-resourced antibody sequence dataset provides highly diverse CDR sequences, up to more than a two-fold increase of diversity over the baselines, without losing structural integrity and naturalness. The generated sequences also demonstrate enhanced antigen binding specificity and virus neutralization ability. Code is available at https://github.com/IBM/ReprogBERT

This paper introduces a structured memory which can be easily integrated into a neural network. The memory is very large by design and significantly increases the capacity of the architecture, by up to a billion parameters with a negligible computational overhead. Its design and access pattern is based on product keys, which enable fast and exact nearest neighbor search. The ability to increase the number of parameters while keeping the same computational budget lets the overall system strike a better trade-off between prediction accuracy and computation efficiency both at training and test time. This memory layer allows us to tackle very large scale language modeling tasks. In our experiments we consider a dataset with up to 30 billion words, and we plug our memory layer in a state-of-the-art transformer-based architecture. In particular, we found that a memory augmented model with only 12 layers outperforms a baseline transformer model with 24 layers, while being twice faster at inference time. We release our code for reproducibility purposes.

Previous work has demonstrated that attention mechanisms are Turing complete. More recently, it has been shown that a looped 9-layer Transformer can function as a universal programmable computer. In contrast, the multi-layer perceptrons with ReLU activation (ReLU-MLP), one of the most fundamental components of neural networks, is known to be expressive; specifically, a two-layer neural network is a universal approximator given an exponentially large number of hidden neurons. However, it remains unclear whether a ReLU-MLP can be made into a universal programmable computer using a practical number of weights. In this work, we provide an affirmative answer that a looped 23-layer ReLU-MLP is capable of performing the basic necessary operations, more efficiently and effectively functioning as a programmable computer than a looped Transformer. This indicates simple modules have stronger expressive power than previously expected and have not been fully explored. Our work provides insights into the mechanisms of neural networks and demonstrates that complex tasks, such as functioning as a programmable computer, do not necessarily require advanced architectures like Transformers.

In this paper, we identify and characterize the emerging area of representation engineering (RepE), an approach to enhancing the transparency of AI systems that draws on insights from cognitive neuroscience. RepE places population-level representations, rather than neurons or circuits, at the center of analysis, equipping us with novel methods for monitoring and manipulating high-level cognitive phenomena in deep neural networks (DNNs). We provide baselines and an initial analysis of RepE techniques, showing that they offer simple yet effective solutions for improving our understanding and control of large language models. We showcase how these methods can provide traction on a wide range of safety-relevant problems, including honesty, harmlessness, power-seeking, and more, demonstrating the promise of top-down transparency research. We hope that this work catalyzes further exploration of RepE and fosters advancements in the transparency and safety of AI systems.

What is the computational model behind a Transformer? Where recurrent neural networks have direct parallels in finite state machines, allowing clear discussion and thought around architecture variants or trained models, Transformers have no such familiar parallel. In this paper we aim to change that, proposing a computational model for the transformer-encoder in the form of a programming language. We map the basic components of a transformer-encoder -- attention and feed-forward computation -- into simple primitives, around which we form a programming language: the Restricted Access Sequence Processing Language (RASP). We show how RASP can be used to program solutions to tasks that could conceivably be learned by a Transformer, and how a Transformer can be trained to mimic a RASP solution. In particular, we provide RASP programs for histograms, sorting, and Dyck-languages. We further use our model to relate their difficulty in terms of the number of required layers and attention heads: analyzing a RASP program implies a maximum number of heads and layers necessary to encode a task in a transformer. Finally, we see how insights gained from our abstraction might be used to explain phenomena seen in recent works.

Trainable layers such as convolutional building blocks are the standard network design choices by learning parameters to capture the global context through successive spatial operations. When designing an efficient network, trainable layers such as the depthwise convolution is the source of efficiency in the number of parameters and FLOPs, but there was little improvement to the model speed in practice. This paper argues that simple built-in parameter-free operations can be a favorable alternative to the efficient trainable layers replacing spatial operations in a network architecture. We aim to break the stereotype of organizing the spatial operations of building blocks into trainable layers. Extensive experimental analyses based on layer-level studies with fully-trained models and neural architecture searches are provided to investigate whether parameter-free operations such as the max-pool are functional. The studies eventually give us a simple yet effective idea for redesigning network architectures, where the parameter-free operations are heavily used as the main building block without sacrificing the model accuracy as much. Experimental results on the ImageNet dataset demonstrate that the network architectures with parameter-free operations could enjoy the advantages of further efficiency in terms of model speed, the number of the parameters, and FLOPs. Code and ImageNet pretrained models are available at https://github.com/naver-ai/PfLayer.

This article explores the adaptive relationship between Encoder Layers and Decoder Layers using the SOTA model Helsinki-NLP/opus-mt-de-en, which translates German to English. The specific method involves introducing a bias-free fully connected layer between the Encoder and Decoder, with different initializations of the layer's weights, and observing the outcomes of fine-tuning versus retraining. Four experiments were conducted in total. The results suggest that directly modifying the pre-trained model structure for fine-tuning yields suboptimal performance. However, upon observing the outcomes of the experiments with retraining, this structural adjustment shows significant potential.

The ability to dynamically adjust the computational load of neural models during inference in a resource aware manner is crucial for on-device processing scenarios, characterised by limited and time-varying computational resources. Early-exit architectures represent an elegant and effective solution, since they can process the input with a subset of their layers, exiting at intermediate branches (the upmost layers are hence removed from the model). From a different perspective, for automatic speech recognition applications there are memory-efficient neural architectures that apply variable frame rate analysis, through downsampling/upsampling operations in the middle layers, reducing the overall number of operations and improving significantly the performance on well established benchmarks. One example is the Zipformer. However, these architectures lack the modularity necessary to inject early-exit branches. With the aim of improving the performance in early-exit models, we propose introducing parallel layers in the architecture that process downsampled versions of their inputs. % in conjunction with standard processing layers. We show that in this way the speech recognition performance on standard benchmarks significantly improve, at the cost of a small increase in the overall number of model parameters but without affecting the inference time.

As one of the energy-efficient alternatives of conventional neural networks (CNNs), spiking neural networks (SNNs) have gained more and more interest recently. To train the deep models, some effective batch normalization (BN) techniques are proposed in SNNs. All these BNs are suggested to be used after the convolution layer as usually doing in CNNs. However, the spiking neuron is much more complex with the spatio-temporal dynamics. The regulated data flow after the BN layer will be disturbed again by the membrane potential updating operation before the firing function, i.e., the nonlinear activation. Therefore, we advocate adding another BN layer before the firing function to normalize the membrane potential again, called MPBN. To eliminate the induced time cost of MPBN, we also propose a training-inference-decoupled re-parameterization technique to fold the trained MPBN into the firing threshold. With the re-parameterization technique, the MPBN will not introduce any extra time burden in the inference. Furthermore, the MPBN can also adopt the element-wised form, while these BNs after the convolution layer can only use the channel-wised form. Experimental results show that the proposed MPBN performs well on both popular non-spiking static and neuromorphic datasets. Our code is open-sourced at https://github.com/yfguo91/MPBN{MPBN}.

Tool-augmented large language model (LLM) agents promise to unify scientific reasoning with computation, yet their deployment in high-stakes domains like drug discovery is bottlenecked by two critical barriers: unconstrained tool-use governance and poor long-horizon reliability. In dependency-heavy pharmaceutical pipelines, autonomous agents often drift into irreproducible trajectories, where early-stage hallucinations multiplicatively compound into downstream failures. To overcome this, we present Mozi, a dual-layer architecture that bridges the flexibility of generative AI with the deterministic rigor of computational biology. Layer A (Control Plane) establishes a governed supervisor--worker hierarchy that enforces role-based tool isolation, limits execution to constrained action spaces, and drives reflection-based replanning. Layer B (Workflow Plane) operationalizes canonical drug discovery stages -- from Target Identification to Lead Optimization -- as stateful, composable skill graphs. This layer integrates strict data contracts and strategic human-in-the-loop (HITL) checkpoints to safeguard scientific validity at high-uncertainty decision boundaries. Operating on the design principle of ``free-form reasoning for safe tasks, structured execution for long-horizon pipelines,'' Mozi provides built-in robustness mechanisms and trace-level audibility to completely mitigate error accumulation. We evaluate Mozi on PharmaBench, a curated benchmark for biomedical agents, demonstrating superior orchestration accuracy over existing baselines. Furthermore, through end-to-end therapeutic case studies, we demonstrate Mozi's ability to navigate massive chemical spaces, enforce stringent toxicity filters, and generate highly competitive in silico candidates, effectively transforming the LLM from a fragile conversationalist into a reliable, governed co-scientist.

Representation alignment (REPA) guides generative training by distilling representations from a strong, pretrained vision encoder to intermediate diffusion features. We investigate a fundamental question: what aspect of the target representation matters for generation, its global semantic information (e.g., measured by ImageNet-1K accuracy) or its spatial structure (i.e. pairwise cosine similarity between patch tokens)? Prevalent wisdom holds that stronger global semantic performance leads to better generation as a target representation. To study this, we first perform a large-scale empirical analysis across 27 different vision encoders and different model scales. The results are surprising; spatial structure, rather than global performance, drives the generation performance of a target representation. To further study this, we introduce two straightforward modifications, which specifically accentuate the transfer of spatial information. We replace the standard MLP projection layer in REPA with a simple convolution layer and introduce a spatial normalization layer for the external representation. Surprisingly, our simple method (implemented in <4 lines of code), termed iREPA, consistently improves convergence speed of REPA, across a diverse set of vision encoders, model sizes, and training variants (such as REPA, REPA-E, Meanflow, JiT etc). %, etc. Our work motivates revisiting the fundamental working mechanism of representational alignment and how it can be leveraged for improved training of generative models. The code and project page are available at https://end2end-diffusion.github.io/irepa

Despite advances in transformer-based language models (LMs), a fundamental question remains largely unanswered: Are all layers activated during inference? We investigate this question by detecting unactivated layers (which we refer to as Voids) using a non-trainable and parameter-free adaptive computation method called L2 Adaptive Computation (LAC). We adapt LAC from its original efficiency-focused application to trace activated layers during inference. This method monitors changes in the L2-norm of activations to identify voids. We analyze layer activation in instruction-tuned LMs across two phases: Prompt Processing (PP), where we trace activated layers for each token in the input prompts, and Response Generation (RG), where we trace activated layers for each generated token. We further demonstrate that distinct layers are activated during these two phases. To show the effectiveness of our method, we evaluated three distinct instruction-tuned LMs from the Llama, Mistral, and Qwen families on three benchmarks: MMLU, GPQA Diamond, and BoolQ. For example, on MMLU with a zero-shot setting, skipping voids in Qwen2.5-7B-Instruct resulted in an improvement from 69.24 to 71.29 while the model uses only 30% of the layers. Similarly, Mistral-7B-Instruct-v0.3 on GPQA Diamond improved from 13.88 to 18.36 when using 70% of the layers during both the PP and RG phases. These results show that not all layers contribute equally during inference, and that selectively skipping most of them can improve the performance of models on certain tasks.

In contrast to RNNs, which compress previous tokens into a single hidden state, Transformers can attend to all previous tokens directly. However, standard Transformers only use representations from the immediately preceding layer. In this paper, we show that this design choice causes representation collapse and leads to suboptimal performance. To address this issue, we introduce Layer-Integrated Memory (LIMe), a simple yet powerful approach that preserves the model's overall memory footprint while expanding its representational capacity by allowing access to hidden states from earlier layers. Through extensive experiments across various architectures and different lookup mechanisms, we demonstrate consistent performance improvements on a wide range of tasks. Moreover, our analysis of the learned representation dynamics and our exploration of depthwise circuits reveal how LIMe integrates information across layers, pointing to promising directions for future research.

Large language models (LLMs) currently suffer from parameter entanglement, where general reasoning capabilities (logic) and specific factual knowledge (facts) exist in a superposition state within shared weights. This coupling leads to the "memory wall," where computational capacity is squandered on simulating retrieval, often resulting in hallucinations. In this paper, we propose "digital metabolism," a thermodynamic hypothesis suggesting that targeted forgetting is necessary for distilling a pure neural logic core. To validate this hypothesis, we introduce the Regenerative Logic-Core Protocol (RLCP), a dual-stream training framework that renders specific factual dependencies linearly undecodable via deep-layer gradient reversal. Applying RLCP to Qwen2.5-0.5B, we observe a distinct phase transition: the model achieves near-zero retention of targeted factual associations (Accuracy < 7%) while exhibiting changes consistent with an emergent "structural crystallization" effect. Empirical analysis on GSM8K reveals that the "metabolized" model spontaneously adopts chain-of-thought (CoT) scaffolding, which we interpret as compensating for the loss of direct associative recall (shifting from O(1) recall to O(N) reasoning). While the causal mechanism underlying this behavioral shift requires further investigation, our findings provide a dynamic weight-level counterpart to architectural innovations like DeepSeek's Engram, paving the way for modular "Neural CPU + Symbolic RAM" architectures.

Recent years have seen the rise of Deep Learning (DL) techniques applied to source code. Researchers have exploited DL to automate several development and maintenance tasks, such as writing commit messages, generating comments and detecting vulnerabilities among others. One of the long lasting dreams of applying DL to source code is the possibility to automate non-trivial coding activities. While some steps in this direction have been taken (e.g., learning how to fix bugs), there is still a glaring lack of empirical evidence on the types of code changes that can be learned and automatically applied by DL. Our goal is to make this first important step by quantitatively and qualitatively investigating the ability of a Neural Machine Translation (NMT) model to learn how to automatically apply code changes implemented by developers during pull requests. We train and experiment with the NMT model on a set of 236k pairs of code components before and after the implementation of the changes provided in the pull requests. We show that, when applied in a narrow enough context (i.e., small/medium-sized pairs of methods before/after the pull request changes), NMT can automatically replicate the changes implemented by developers during pull requests in up to 36% of the cases. Moreover, our qualitative analysis shows that the model is capable of learning and replicating a wide variety of meaningful code changes, especially refactorings and bug-fixing activities. Our results pave the way for novel research in the area of DL on code, such as the automatic learning and applications of refactoring.

Chain-of-thought (CoT) prompting enables reasoning in language models but requires explicit verbalization of intermediate steps. Looped transformers offer an alternative by iteratively refining representations within hidden states. This parameter efficiency comes at a cost, as looped models lack the storage capacity of deeper models which use unique weights per layer. In this work, we investigate transformer models that feature both adaptive per-layer looping, where each transformer block learns to iterate its hidden state via a learned halting mechanism, and gated memory banks, that provide additional learned storage. We find that looping primarily benefits mathematical reasoning, while memory banks help recover performance on commonsense tasks compared to parameter and FLOP matched models. Combining both mechanisms yields a model that outperforms an iso-FLOP baseline, with three times the number of layers, across math benchmarks. Analysis of model internals reveals layer specialization: early layers learn to loop minimally and access memory sparingly, while later layers do both more heavily.

While scaling Transformer-based large language models (LLMs) has demonstrated promising performance across various tasks, it also introduces redundant architectures, posing efficiency challenges for real-world deployment. Despite some recognition of redundancy in LLMs, the variability of redundancy across different architectures in transformers, such as MLP and Attention layers, is under-explored. In this work, we investigate redundancy across different modules within Transformers, including Blocks, MLP, and Attention layers, using a similarity-based metric. Surprisingly, despite the critical role of attention layers in distinguishing transformers from other architectures, we found that a large portion of these layers exhibit excessively high similarity and can be pruned without degrading performance. For instance, Llama-2-70B achieved a 48.4\% speedup with only a 2.4\% performance drop by pruning half of the attention layers. Furthermore, by tracing model checkpoints throughout the training process, we observed that attention layer redundancy is inherent and consistent across training stages. Additionally, we further propose a method that jointly drops Attention and MLP layers, allowing us to more aggressively drop additional layers. For instance, when dropping 31 layers (Attention + MLP), Llama-2-13B still retains 90\% of the performance on the MMLU task. Our work provides valuable insights for future network architecture design. The code is released at: https://github.com/Shwai-He/LLM-Drop.

We propose RepMLP, a multi-layer-perceptron-style neural network building block for image recognition, which is composed of a series of fully-connected (FC) layers. Compared to convolutional layers, FC layers are more efficient, better at modeling the long-range dependencies and positional patterns, but worse at capturing the local structures, hence usually less favored for image recognition. We propose a structural re-parameterization technique that adds local prior into an FC to make it powerful for image recognition. Specifically, we construct convolutional layers inside a RepMLP during training and merge them into the FC for inference. On CIFAR, a simple pure-MLP model shows performance very close to CNN. By inserting RepMLP in traditional CNN, we improve ResNets by 1.8% accuracy on ImageNet, 2.9% for face recognition, and 2.3% mIoU on Cityscapes with lower FLOPs. Our intriguing findings highlight that combining the global representational capacity and positional perception of FC with the local prior of convolution can improve the performance of neural network with faster speed on both the tasks with translation invariance (e.g., semantic segmentation) and those with aligned images and positional patterns (e.g., face recognition). The code and models are available at https://github.com/DingXiaoH/RepMLP.

Recurrent neural networks (RNNs) are a cornerstone of sequence modeling across various scientific and industrial applications. Owing to their versatility, numerous RNN variants have been proposed over the past decade, aiming to improve the modeling of long-term dependencies and to address challenges such as vanishing and exploding gradients. However, no central library is available to test these variations, and reimplementing diverse architectures can be time-consuming and error-prone, limiting reproducibility and exploration. Here, we introduce three open-source libraries in Julia and Python that centralize numerous recurrent cell implementations and higher-level recurrent architectures. torchrecurrent, RecurrentLayers.jl, and LuxRecurrentLayers.jl offer a consistent framework for constructing and extending RNN models, providing built-in mechanisms for customization and experimentation. All packages are available under the MIT license and actively maintained on GitHub.

We introduce a new function-preserving transformation for efficient neural architecture search. This network transformation allows reusing previously trained networks and existing successful architectures that improves sample efficiency. We aim to address the limitation of current network transformation operations that can only perform layer-level architecture modifications, such as adding (pruning) filters or inserting (removing) a layer, which fails to change the topology of connection paths. Our proposed path-level transformation operations enable the meta-controller to modify the path topology of the given network while keeping the merits of reusing weights, and thus allow efficiently designing effective structures with complex path topologies like Inception models. We further propose a bidirectional tree-structured reinforcement learning meta-controller to explore a simple yet highly expressive tree-structured architecture space that can be viewed as a generalization of multi-branch architectures. We experimented on the image classification datasets with limited computational resources (about 200 GPU-hours), where we observed improved parameter efficiency and better test results (97.70% test accuracy on CIFAR-10 with 14.3M parameters and 74.6% top-1 accuracy on ImageNet in the mobile setting), demonstrating the effectiveness and transferability of our designed architectures.

We propose combining memory saving techniques with traditional U-Net architectures to increase the complexity of the models on the Brain Tumor Segmentation (BraTS) challenge. The BraTS challenge consists of a 3D segmentation of a 240x240x155x4 input image into a set of tumor classes. Because of the large volume and need for 3D convolutional layers, this task is very memory intensive. To address this, prior approaches use smaller cropped images while constraining the model's depth and width. Our 3D U-Net uses a reversible version of the mobile inverted bottleneck block defined in MobileNetV2, MnasNet and the more recent EfficientNet architectures to save activation memory during training. Using reversible layers enables the model to recompute input activations given the outputs of that layer, saving memory by eliminating the need to store activations during the forward pass. The inverted residual bottleneck block uses lightweight depthwise separable convolutions to reduce computation by decomposing convolutions into a pointwise convolution and a depthwise convolution. Further, this block inverts traditional bottleneck blocks by placing an intermediate expansion layer between the input and output linear 1x1 convolution, reducing the total number of channels. Given a fixed memory budget, with these memory saving techniques, we are able to train image volumes up to 3x larger, models with 25% more depth, or models with up to 2x the number of channels than a corresponding non-reversible network.

Deep learning-based code generation has completely transformed the way developers write programs today. Existing approaches to code generation have focused either on the Sequence-to-Sequence paradigm, which generates target code as a sequence of tokens, or the Sequence-to-Tree paradigm, which outputs code as a sequence of actions. While these two paradigms are intuitively complementary, their combination has not been previously explored. By comparing the code generated under these two paradigms, we find that integrating them holds significant potential. In this paper, we propose UniGenCoder for code-related generation tasks, which consists of a shared encoder, a shared decoder with a minimal set of additional parameters to unify two paradigms, and a selector that dynamically chooses optimal paradigm for each instance. Also, during the model training, we first perform the multi-task learning and distillation strategies to facilitate knowledge transfer between two paradigms, and then leverage contrastive learning to train the selector. Experimental results on the text-to-code and code-to-code generation tasks demonstrate the effectiveness of our proposed model. We release our code at https://github.com/DeepLearnXMU/UniGenCoder.

Few algorithms for supervised training of spiking neural networks exist that can deal with patterns of multiple spikes, and their computational properties are largely unexplored. We demonstrate in a set of simulations that the ReSuMe learning algorithm can be successfully applied to layered neural networks. Input and output patterns are encoded as spike trains of multiple precisely timed spikes, and the network learns to transform the input trains into target output trains. This is done by combining the ReSuMe learning algorithm with multiplicative scaling of the connections of downstream neurons. We show in particular that layered networks with one hidden layer can learn the basic logical operations, including Exclusive-Or, while networks without hidden layer cannot, mirroring an analogous result for layered networks of rate neurons. While supervised learning in spiking neural networks is not yet fit for technical purposes, exploring computational properties of spiking neural networks advances our understanding of how computations can be done with spike trains.

Recent advances in efficient sequence modeling have led to attention-free layers, such as Mamba, RWKV, and various gated RNNs, all featuring sub-quadratic complexity in sequence length and excellent scaling properties, enabling the construction of a new type of foundation models. In this paper, we present a unified view of these models, formulating such layers as implicit causal self-attention layers. The formulation includes most of their sub-components and is not limited to a specific part of the architecture. The framework compares the underlying mechanisms on similar grounds for different layers and provides a direct means for applying explainability methods. Our experiments show that our attention matrices and attribution method outperform an alternative and a more limited formulation that was recently proposed for Mamba. For the other architectures for which our method is the first to provide such a view, our method is effective and competitive in the relevant metrics compared to the results obtained by state-of-the-art transformer explainability methods. Our code is publicly available.

This study introduces BrainTransformers, an innovative Large Language Model (LLM) implemented using Spiking Neural Networks (SNN). Our key contributions include: (1) designing SNN-compatible Transformer components such as SNNMatmul, SNNSoftmax, and SNNSiLU; (2) implementing an SNN approximation of the SiLU activation function; and (3) developing a Synapsis module to simulate synaptic plasticity. Our 3-billion parameter model, BrainTransformers-3B-Chat, demonstrates competitive performance across various benchmarks, including MMLU (63.2), BBH (54.1), ARC-C (54.3), and GSM8K (76.3), while potentially offering improved energy efficiency and biological plausibility. The model employs a three-stage training approach, including SNN-specific neuronal synaptic plasticity training. This research opens new avenues for brain-like AI systems in natural language processing and neuromorphic computing. Future work will focus on hardware optimization, developing specialized SNN fine-tuning tools, and exploring practical applications in energy-efficient computing environments.

This paper presents VLCache, a cache reuse framework that exploits both Key-Value (KV) cache and encoder cache from prior multimodal inputs to eliminate costly recomputation when the same multimodal inputs recur. Unlike previous heuristic approaches, we formally identify the cumulative reuse error effect and demonstrate how to minimize the non-prefix cache reuse error effectively. We further analyze the varying importance of model layers and propose a dynamic, layer-aware recomputation strategy to balance accuracy and efficiency. Experimental results show that VLCache achieves an accuracy on par with full recomputation, while requiring only 2-5% of the tokens to compute, yielding 1.2x-16x TTFT speedups. The proposed VLCache pipeline has been integrated into SGLang, enabling significantly faster inference in practical deployments.

Recently, fine-tuning pre-trained code models such as CodeBERT on downstream tasks has achieved great success in many software testing and analysis tasks. While effective and prevalent, fine-tuning the pre-trained parameters incurs a large computational cost. In this paper, we conduct an extensive experimental study to explore what happens to layer-wise pre-trained representations and their encoded code knowledge during fine-tuning. We then propose efficient alternatives to fine-tune the large pre-trained code model based on the above findings. Our experimental study shows that (1) lexical, syntactic and structural properties of source code are encoded in the lower, intermediate, and higher layers, respectively, while the semantic property spans across the entire model. (2) The process of fine-tuning preserves most of the code properties. Specifically, the basic code properties captured by lower and intermediate layers are still preserved during fine-tuning. Furthermore, we find that only the representations of the top two layers change most during fine-tuning for various downstream tasks. (3) Based on the above findings, we propose Telly to efficiently fine-tune pre-trained code models via layer freezing. The extensive experimental results on five various downstream tasks demonstrate that training parameters and the corresponding time cost are greatly reduced, while performances are similar or better. Replication package including source code, datasets, and online Appendix is available at: https://github.com/DeepSoftwareAnalytics/Telly.

This work examines whether activating latent subspaces in language models (LLMs) can steer scientific code generation toward a specific programming language. Five causal LLMs were first evaluated on scientific coding prompts to quantify their baseline bias among four programming languages. A static neuron-attribution method, perturbing the highest activated MLP weight for a C++ or CPP token, proved brittle and exhibited limited generalization across prompt styles and model scales. To address these limitations, a gradient-refined adaptive activation steering framework (G-ACT) was developed: per-prompt activation differences are clustered into a small set of steering directions, and lightweight per-layer probes are trained and refined online to select the appropriate steering vector. In LLaMA-3.2 3B, this approach reliably biases generation towards the CPP language by increasing the average probe classification accuracy by 15% and the early layers (0-6) improving the probe classification accuracy by 61.5% compared to the standard ACT framework. For LLaMA-3.3 70B, where attention-head signals become more diffuse, targeted injections at key layers still improve language selection. Although per-layer probing introduces a modest inference overhead, it remains practical by steering only a subset of layers and enables reproducible model behavior. These results demonstrate a scalable, interpretable and efficient mechanism for concept-level control for practical agentic systems.

There has been a recent surge of interest in automating software engineering tasks using deep learning. This paper addresses the problem of code generation, where the goal is to generate target code given source code in a different language or a natural language description. Most state-of-the-art deep learning models for code generation use training strategies primarily designed for natural language. However, understanding and generating code requires a more rigorous comprehension of the code syntax and semantics. With this motivation, we develop an encoder-decoder Transformer model where both the encoder and decoder are explicitly trained to recognize the syntax and data flow in the source and target codes, respectively. We not only make the encoder structure-aware by leveraging the source code's syntax tree and data flow graph, but we also support the decoder in preserving the syntax and data flow of the target code by introducing two novel auxiliary tasks: AST (Abstract Syntax Tree) paths prediction and data flow prediction. To the best of our knowledge, this is the first work to introduce a structure-aware Transformer decoder that models both syntax and data flow to enhance the quality of generated code. The proposed StructCoder model achieves state-of-the-art performance on code translation and text-to-code generation tasks in the CodeXGLUE benchmark, and improves over baselines of similar size on the APPS code generation benchmark. Our code is publicly available at https://github.com/reddy-lab-code-research/StructCoder/.

We present AutoCompress, a transformer compression method motivated by an empirical finding: in small transformers, Layer 0 carries disproportionately high task-critical information, with an NTK-based importance score of 3.6 compared to a maximum of 0.054 for all other layers -- a gap of over 60x. Based on this finding, we propose Critical Layer Isolation (CLI), an architecture that protects Layer 0 at full dimensionality, compresses all intermediate layers through a learned bottleneck, and restores the full dimension at the final layer. Applied to GPT-2 Medium (354.8M parameters), CLI-GPT2 achieves 204.5 perplexity on WikiText-103 with only 143.8M parameters -- a 2.47x compression ratio and 59.5% parameter reduction. Crucially, an ablation study demonstrates that a uniform bottleneck baseline of comparable size achieves only 571.8 perplexity under identical training conditions, confirming that the architectural decision to protect Layer 0 -- rather than simply reducing model size -- is the primary driver of performance. Code and checkpoints are publicly available.

Transformers are mostly relying on softmax attention, which introduces quadratic complexity with respect to sequence length and remains a major bottleneck for efficient inference. Prior work on linear or hybrid attention typically replaces softmax attention uniformly across all layers, often leading to significant performance degradation or requiring extensive retraining to recover model quality. This work proposes LayerBoost, a layer-aware attention reduction method that selectively modifies the attention mechanism based on the sensitivity of individual transformer layers. It first performs a systematic sensitivity analysis on a pretrained model to identify layers that are critical for maintaining performance. Guided by this analysis, three distinct strategies can be applied: retaining standard softmax attention in highly sensitive layers, replacing it with linear sliding window attention in moderately sensitive layers, and removing attention entirely in layers that exhibit low sensitivity. To recover performance after these architectural modifications, we introduce a lightweight distillation-based healing phase requiring only 10M additional training tokens. LayerBoost reduces inference latency and improves throughput by up to 68% at high concurrency, while maintaining competitive model quality. It matches base model performance on several benchmarks, exhibits only minor degradations on others, and significantly outperforms state-of-the-art attention linearization methods. These efficiency gains make our method particularly well-suited for high-concurrency serving and hardware-constrained deployment scenarios, where inference cost and memory footprint are critical bottlenecks.

Retrofitting large language models (LLMs) with new behaviors typically requires full finetuning or distillation-costly steps that must be repeated for every architecture. In this work, we introduce Command-V, a backpropagation-free behavior transfer method that copies an existing residual activation adapter from a donor model and pastes its effect into a recipient model. Command-V profiles layer activations on a small prompt set, derives linear converters between corresponding layers, and applies the donor intervention in the recipient's activation space. This process does not require access to the original training data and needs minimal compute. In three case studies-safety-refusal enhancement, jailbreak facilitation, and automatic chain-of-thought reasoning--Command-V matches or exceeds the performance of direct finetuning while using orders of magnitude less compute. Our code and data are accessible at https://github.com/GithuBarry/Command-V/.

In this note (work in progress towards a full-length paper) we show that a family of sequence models based on recurrent linear layers~(including S4, S5, and the LRU) interleaved with position-wise multi-layer perceptrons~(MLPs) can approximate arbitrarily well any sufficiently regular non-linear sequence-to-sequence map. The main idea behind our result is to see recurrent layers as compression algorithms that can faithfully store information about the input sequence into an inner state, before it is processed by the highly expressive MLP.

Advancements in LLMs have recently unveiled challenges tied to computational efficiency and continual scalability due to their requirements of huge parameters, making the applications and evolution of these models on devices with limited computation resources and scenarios requiring various abilities increasingly cumbersome. Inspired by modularity within the human brain, there is a growing tendency to decompose LLMs into numerous functional modules, allowing for inference with part of modules and dynamic assembly of modules to tackle complex tasks, such as mixture-of-experts. To highlight the inherent efficiency and composability of the modular approach, we coin the term brick to represent each functional module, designating the modularized structure as configurable foundation models. In this paper, we offer a comprehensive overview and investigation of the construction, utilization, and limitation of configurable foundation models. We first formalize modules into emergent bricks - functional neuron partitions that emerge during the pre-training phase, and customized bricks - bricks constructed via additional post-training to improve the capabilities and knowledge of LLMs. Based on diverse functional bricks, we further present four brick-oriented operations: retrieval and routing, merging, updating, and growing. These operations allow for dynamic configuration of LLMs based on instructions to handle complex tasks. To verify our perspective, we conduct an empirical analysis on widely-used LLMs. We find that the FFN layers follow modular patterns with functional specialization of neurons and functional neuron partitions. Finally, we highlight several open issues and directions for future research. Overall, this paper aims to offer a fresh modular perspective on existing LLM research and inspire the future creation of more efficient and scalable foundational models.

The most important architectural problem in AI is not the size of the model but the absence of a layer that carries forward what the model has come to understand. Sessions end. Context windows fill. Memory APIs return flat facts that the model has to reinterpret from scratch on every read. The result is intelligence that is powerful per session and amnesiac across time. This position paper argues that the layer which fixes this, the continuity layer, is the most consequential piece of infrastructure the field has not yet built, and that the engineering work to build it has begun in public. The formal evaluation framework for the property described here is the ATANT benchmark (arXiv:2604.06710), published separately with evaluation results on a 250-story corpus; a companion paper (arXiv:2604.10981) positions this framework against existing memory, long-context, and agentic-memory benchmarks. The paper defines continuity as a system property with seven required characteristics, distinct from memory and from retrieval; describes a storage primitive (Decomposed Trace Convergence Memory) whose write-time decomposition and read-time reconstruction produce that property; maps the engineering architecture to the theological pattern of kenosis and the symbolic pattern of Alpha and Omega, and argues this mapping is structural rather than metaphorical; proposes a four-layer development arc from external SDK to hardware node to long-horizon human infrastructure; examines why the physics limits now constraining the model layer make the continuity layer newly consequential; and argues that the governance architecture (privacy implemented as physics rather than policy, founder-controlled class shares on non-negotiable architectural commitments) is inseparable from the product itself.

DL compiler's primary function is to translate DNN programs written in high-level DL frameworks such as PyTorch and TensorFlow into portable executables. These executables can then be flexibly executed by the deployed host programs. However, existing DL compilers rely on a tracing mechanism, which involves feeding a runtime input to a neural network program and tracing the program execution paths to generate the computational graph necessary for compilation. Unfortunately, this mechanism falls short when dealing with modern dynamic neural networks (DyNNs) that possess varying computational graphs depending on the inputs. Consequently, conventional DL compilers struggle to accurately compile DyNNs into executable code. To address this limitation, we propose \tool, a general approach that enables any existing DL compiler to successfully compile DyNNs. \tool tackles the dynamic nature of DyNNs by introducing a compilation mechanism that redistributes the control and data flow of the original DNN programs during the compilation process. Specifically, \tool develops program analysis and program transformation techniques to convert a dynamic neural network into multiple sub-neural networks. Each sub-neural network is devoid of conditional statements and is compiled independently. Furthermore, \tool synthesizes a host module that models the control flow of the DyNNs and facilitates the invocation of the sub-neural networks. Our evaluation demonstrates the effectiveness of \tool, achieving a 100\% success rate in compiling all dynamic neural networks. Moreover, the compiled executables generated by \tool exhibit significantly improved performance, running between 1.12times and 20.21times faster than the original DyNNs executed on general-purpose DL frameworks.

In practice, we usually need to build variable-sized models adapting for diverse resource constraints in different application scenarios, where weight initialization is an important step prior to training. The Learngene framework, introduced recently, firstly learns one compact part termed as learngene from a large well-trained model, after which learngene is expanded to initialize variable-sized models. In this paper, we start from analysing the importance of guidance for the expansion of well-trained learngene layers, inspiring the design of a simple but highly effective Learngene approach termed SWS (Stage-wise Weight Sharing), where both learngene layers and their learning process critically contribute to providing knowledge and guidance for initializing models at varying scales. Specifically, to learn learngene layers, we build an auxiliary model comprising multiple stages where the layer weights in each stage are shared, after which we train it through distillation. Subsequently, we expand these learngene layers containing stage information at their corresponding stage to initialize models of variable depths. Extensive experiments on ImageNet-1K demonstrate that SWS achieves consistent better performance compared to many models trained from scratch, while reducing around 6.6x total training costs. In some cases, SWS performs better only after 1 epoch tuning. When initializing variable-sized models adapting for different resource constraints, SWS achieves better results while reducing around 20x parameters stored to initialize these models and around 10x pre-training costs, in contrast to the pre-training and fine-tuning approach.

Large language models (LLMs) have shown impressive performance on language tasks but face challenges when deployed on resource-constrained devices due to their extensive parameters and reliance on dense multiplications, resulting in high memory demands and latency bottlenecks. Shift-and-add reparameterization offers a promising solution by replacing costly multiplications with hardware-friendly primitives in both the attention and multi-layer perceptron (MLP) layers of an LLM. However, current reparameterization techniques require training from scratch or full parameter fine-tuning to restore accuracy, which is resource-intensive for LLMs. To address this, we propose accelerating pretrained LLMs through post-training shift-and-add reparameterization, creating efficient multiplication-free models, dubbed ShiftAddLLM. Specifically, we quantize each weight matrix into binary matrices paired with group-wise scaling factors. The associated multiplications are reparameterized into (1) shifts between activations and scaling factors and (2) queries and adds according to the binary matrices. To reduce accuracy loss, we present a multi-objective optimization method to minimize both weight and output activation reparameterization errors. Additionally, based on varying sensitivity across layers to reparameterization, we develop an automated bit allocation strategy to further reduce memory usage and latency. Experiments on five LLM families and eight tasks consistently validate the effectiveness of ShiftAddLLM, achieving average perplexity improvements of 5.6 and 22.7 points at comparable or lower latency compared to the most competitive quantized LLMs at 3 and 2 bits, respectively, and more than 80% memory and energy reductions over the original LLMs. Codes and models are available at https://github.com/GATECH-EIC/ShiftAddLLM.

We investigate the origins of massive activations in large language models (LLMs) and identify a specific layer named the Massive Emergence Layer (ME Layer), that is consistently observed across model families, where massive activations first emerge and subsequently propagate to deeper layers through residual connections. We show that, within the ME Layer both the RMSNorm and the FFN parameters jointly contribute to the emergence of massive activations. Once formed, the massive activation token representation remains largely invariant across layers, reducing the diversity of hidden representations passed to the attention module. Motivated by this limitation, we propose a simple and effective method to reduce the rigidity of the massive activation token. Our approach consistently improves LLM performance across multiple tasks, including instruction following and math reasoning, in both training free and fine tuning settings. Moreover, we show that our method mitigates attention sinks by selectively weakening their influence, elucidating their origin at the hidden state level and shedding new light on principled mitigation strategies.

The computational overhead of Vision Transformers in practice stems fundamentally from their deep architectures, yet existing acceleration strategies have primarily targeted algorithmic-level optimizations such as token pruning and attention speedup. This leaves an underexplored research question: can we reduce the number of stacked transformer layers while maintaining comparable representational capacity? To answer this, we propose a branch-based structural reparameterization technique that operates during the training phase. Our approach leverages parallel branches within transformer blocks that can be systematically consolidated into streamlined single-path models suitable for inference deployment. The consolidation mechanism works by gradually merging branches at the entry points of nonlinear components, enabling both feed-forward networks (FFN) and multi-head self-attention (MHSA) modules to undergo exact mathematical reparameterization without inducing approximation errors at test time. When applied to ViT-Tiny, the framework successfully reduces the original 12-layer architecture to 6, 4, or as few as 3 layers while maintaining classification accuracy on ImageNet-1K. The resulting compressed models achieve inference speedups of up to 37% on mobile CPU platforms. Our findings suggest that the conventional wisdom favoring extremely deep transformer stacks may be unnecessarily restrictive, and point toward new opportunities for constructing efficient vision transformers.

Recent progress in large-scale language models has enabled breakthroughs in previously intractable computer programming tasks. Prior work in meta-learning and neural architecture search has led to substantial successes across various task domains, spawning myriad approaches for algorithmically optimizing the design and learning dynamics of deep learning models. At the intersection of these research areas, we implement a code-generating language model with the ability to modify its own source code. Self-programming AI algorithms have been of interest since the dawn of AI itself. Although various theoretical formulations of generalized self-programming AI have been posed, no such system has been successfully implemented to date under real-world computational constraints. Applying AI-based code generation to AI itself, we develop and experimentally validate the first practical implementation of a self-programming AI system. We empirically show that a self-programming AI implemented using a code generation model can successfully modify its own source code to improve performance and program sub-models to perform auxiliary tasks. Our model can self-modify various properties including model architecture, computational capacity, and learning dynamics.

Many engineering organizations are reimplementing and extending deep neural networks from the research community. We describe this process as deep learning model reengineering. Deep learning model reengineering - reusing, reproducing, adapting, and enhancing state-of-the-art deep learning approaches - is challenging for reasons including under-documented reference models, changing requirements, and the cost of implementation and testing. In addition, individual engineers may lack expertise in software engineering, yet teams must apply knowledge of software engineering and deep learning to succeed. Prior work has examined on DL systems from a "product" view, examining defects from projects regardless of the engineers' purpose. Our study is focused on reengineering activities from a "process" view, and focuses on engineers specifically engaged in the reengineering process. Our goal is to understand the characteristics and challenges of deep learning model reengineering. We conducted a case study of this phenomenon, focusing on the context of computer vision. Our results draw from two data sources: defects reported in open-source reeengineering projects, and interviews conducted with open-source project contributors and the leaders of a reengineering team. Our results describe how deep learning-based computer vision techniques are reengineered, analyze the distribution of defects in this process, and discuss challenges and practices. Integrating our quantitative and qualitative data, we proposed a novel reengineering workflow. Our findings inform several future directions, including: measuring additional unknown aspects of model reengineering; standardizing engineering practices to facilitate reengineering; and developing tools to support model reengineering and model reuse.

Current state-of-the-art machine translation systems are based on encoder-decoder architectures, that first encode the input sequence, and then generate an output sequence based on the input encoding. Both are interfaced with an attention mechanism that recombines a fixed encoding of the source tokens based on the decoder state. We propose an alternative approach which instead relies on a single 2D convolutional neural network across both sequences. Each layer of our network re-codes source tokens on the basis of the output sequence produced so far. Attention-like properties are therefore pervasive throughout the network. Our model yields excellent results, outperforming state-of-the-art encoder-decoder systems, while being conceptually simpler and having fewer parameters.

Implicit models separate the definition of a layer from the description of its solution process. While implicit layers allow features such as depth to adapt to new scenarios and inputs automatically, this adaptivity makes its computational expense challenging to predict. In this manuscript, we increase the "implicitness" of the DEQ by redefining the method in terms of an infinite time neural ODE, which paradoxically decreases the training cost over a standard neural ODE by 2-4x. Additionally, we address the question: is there a way to simultaneously achieve the robustness of implicit layers while allowing the reduced computational expense of an explicit layer? To solve this, we develop Skip and Skip Reg. DEQ, an implicit-explicit (IMEX) layer that simultaneously trains an explicit prediction followed by an implicit correction. We show that training this explicit predictor is free and even decreases the training time by 1.11-3.19x. Together, this manuscript shows how bridging the dichotomy of implicit and explicit deep learning can combine the advantages of both techniques.

We propose a new neural network design paradigm Reversible Column Network (RevCol). The main body of RevCol is composed of multiple copies of subnetworks, named columns respectively, between which multi-level reversible connections are employed. Such architectural scheme attributes RevCol very different behavior from conventional networks: during forward propagation, features in RevCol are learned to be gradually disentangled when passing through each column, whose total information is maintained rather than compressed or discarded as other network does. Our experiments suggest that CNN-style RevCol models can achieve very competitive performances on multiple computer vision tasks such as image classification, object detection and semantic segmentation, especially with large parameter budget and large dataset. For example, after ImageNet-22K pre-training, RevCol-XL obtains 88.2% ImageNet-1K accuracy. Given more pre-training data, our largest model RevCol-H reaches 90.0% on ImageNet-1K, 63.8% APbox on COCO detection minival set, 61.0% mIoU on ADE20k segmentation. To our knowledge, it is the best COCO detection and ADE20k segmentation result among pure (static) CNN models. Moreover, as a general macro architecture fashion, RevCol can also be introduced into transformers or other neural networks, which is demonstrated to improve the performances in both computer vision and NLP tasks. We release code and models at https://github.com/megvii-research/RevCol

We present a simple meta quantization approach that quantizes different layers of a large language model (LLM) at different bit levels, and is independent of the underlying quantization technique. Specifically, we quantize the most important layers to higher bit precision and less important layers to lower bits. We propose two effective strategies to measure the importance of layers within LLMs: the first measures the importance of a layer based on how different its output embeddings are from the input embeddings (higher is better); the second estimates the importance of a layer using the number of layer weights that are much larger than average (smaller is better). We show that quantizing different layers at varying bits according to our importance scores results in minimal performance drop with a far more compressed model size. Finally, we present several practical key takeaways from our variable layer-wise quantization experiments: (a) LLM performance under variable quantization remains close to the original model until 25-50% of layers are moved in lower quantization using our proposed ordering but only until 5-10% if moved using no specific ordering; (b) Adding layer importance to inherently dynamic quantization techniques can further improve their performance, showing that our approach is complementary to other dynamic quantization methods; (c) Quantizing LLMs to lower bits performs substantially better than pruning unless extreme quantization (2-bit) is used; and (d) Layer-wise quantization to lower bits works better in the case of larger LLMs with more layers compared to smaller LLMs with fewer layers. Our code is publicly available at https://github.com/RazvanDu/LayerwiseQuant/.

Recent works show that reducing the number of layers in a convolutional neural network can enhance efficiency while maintaining the performance of the network. Existing depth compression methods remove redundant non-linear activation functions and merge the consecutive convolution layers into a single layer. However, these methods suffer from a critical drawback; the kernel size of the merged layers becomes larger, significantly undermining the latency reduction gained from reducing the depth of the network. We show that this problem can be addressed by jointly pruning convolution layers and activation functions. To this end, we propose LayerMerge, a novel depth compression method that selects which activation layers and convolution layers to remove, to achieve a desired inference speed-up while minimizing performance loss. Since the corresponding selection problem involves an exponential search space, we formulate a novel surrogate optimization problem and efficiently solve it via dynamic programming. Empirical results demonstrate that our method consistently outperforms existing depth compression and layer pruning methods on various network architectures, both on image classification and generation tasks. We release the code at https://github.com/snu-mllab/LayerMerge.

We study the geometric structure of layer updates in deep language models. Rather than analyzing what information is encoded in intermediate representations, we ask how representations change from one layer to the next. We show that layerwise updates admit a decomposition into a dominant tokenwise component and a residual that is not captured by restricted tokenwise function classes. Across multiple architectures, including Transformers and state-space models, we find that the full layer update is almost perfectly aligned with the tokenwise component, while the residual exhibits substantially weaker alignment, larger angular deviation, and significantly lower projection onto the dominant tokenwise subspace. This indicates that the residual is not merely a small correction, but a geometrically distinct component of the transformation. This geometric separation has functional consequences: approximation error under the restricted tokenwise model is strongly associated with output perturbation, with Spearman correlations often exceeding 0.7 and reaching up to 0.95 in larger models. Together, these results suggest that most layerwise updates behave like structured reparameterizations along a dominant direction, while functionally significant computation is concentrated in a geometrically distinct residual component. Our framework provides a simple, architecture-agnostic method for probing the geometric and functional structure of layer updates in modern language models.

Deep feedforward and recurrent networks have achieved impressive results in many perception and language processing applications. This success is partially attributed to architectural innovations such as convolutional and long short-term memory networks. The main motivation for these architectural innovations is that they capture better domain knowledge, and importantly are easier to optimize than more basic architectures. Recently, more complex architectures such as Neural Turing Machines and Memory Networks have been proposed for tasks including question answering and general computation, creating a new set of optimization challenges. In this paper, we discuss a low-overhead and easy-to-implement technique of adding gradient noise which we find to be surprisingly effective when training these very deep architectures. The technique not only helps to avoid overfitting, but also can result in lower training loss. This method alone allows a fully-connected 20-layer deep network to be trained with standard gradient descent, even starting from a poor initialization. We see consistent improvements for many complex models, including a 72% relative reduction in error rate over a carefully-tuned baseline on a challenging question-answering task, and a doubling of the number of accurate binary multiplication models learned across 7,000 random restarts. We encourage further application of this technique to additional complex modern architectures.

Neural Code Intelligence -- leveraging deep learning to understand, generate, and optimize code -- holds immense potential for transformative impacts on the whole society. Bridging the gap between Natural Language and Programming Language, this domain has drawn significant attention from researchers in both research communities over the past few years. This survey presents a systematic and chronological review of the advancements in code intelligence, encompassing over 50 representative models and their variants, more than 20 categories of tasks, and an extensive coverage of over 680 related works. We follow the historical progression to trace the paradigm shifts across different research phases (e.g., from modeling code with recurrent neural networks to the era of Large Language Models). Concurrently, we highlight the major technical transitions in models, tasks, and evaluations spanning through different stages. For applications, we also observe a co-evolving shift. It spans from initial endeavors to tackling specific scenarios, through exploring a diverse array of tasks during its rapid expansion, to currently focusing on tackling increasingly complex and varied real-world challenges. Building on our examination of the developmental trajectories, we further investigate the emerging synergies between code intelligence and broader machine intelligence, uncovering new cross-domain opportunities and illustrating the substantial influence of code intelligence across various domains. Finally, we delve into both the opportunities and challenges associated with this field, alongside elucidating our insights on the most promising research directions. An ongoing, dynamically updated project and resources associated with this survey have been released at https://github.com/QiushiSun/NCISurvey.

This paper localizes the policy routing mechanism in alignment-trained language models. An intermediate-layer attention gate reads detected content and triggers deeper amplifier heads that boost the signal toward refusal. In smaller models the gate and amplifier are single heads; at larger scale they become bands of heads across adjacent layers. The gate contributes under 1% of output DLA, but interchange testing (p<0.001) and knockout cascade confirm it is causally necessary. Interchange screening at n>=120 detects the same motif in twelve models from six labs (2B to 72B), though specific heads differ by lab. Per-head ablation weakens up to 58x at 72B and misses gates that interchange identifies; interchange is the only reliable audit at scale. Modulating the detection-layer signal continuously controls policy from hard refusal through evasion to factual answering. On safety prompts the same intervention turns refusal into harmful guidance, showing the safety-trained capability is gated by routing rather than removed. Thresholds vary by topic and by input language, and the circuit relocates across generations within a family while behavioral benchmarks register no change. Routing is early-commitment: the gate commits at its own layer before deeper layers finish processing the input. Under an in-context substitution cipher, gate interchange necessity collapses 70 to 99% across three models and the model switches to puzzle-solving. Injecting the plaintext gate activation into the cipher forward pass restores 48% of refusals in Phi-4-mini, localizing the bypass to the routing interface. A second method, cipher contrast analysis, uses plain/cipher DLA differences to map the full cipher-sensitive routing circuit in O(3n) forward passes. Any encoding that defeats detection-layer pattern matching bypasses the policy regardless of whether deeper layers reconstruct the content.

While activation steering in large language models (LLMs) is a growing area of research, methods can often incur broader effects than desired. This motivates isolation of purer concept vectors to enable targeted interventions and understand LLM behavior at a more granular level. We present RepIt, a simple and data-efficient framework for isolating concept-specific representations. Across five frontier LLMs, RepIt enables precise interventions: it selectively suppresses refusal on targeted concepts while preserving refusal elsewhere, producing models that answer WMD-related questions while still scoring as safe on standard benchmarks. We further show that the corrective signal localizes to just 100-200 neurons and that robust target representations can be extracted from as few as a dozen examples on a single A6000. This efficiency raises a dual concern: manipulations can be performed with modest compute and data to extend to underrepresented data-scarce topics while evading existing benchmarks. By disentangling refusal vectors with RepIt, this work demonstrates that targeted interventions can counteract overgeneralization, laying the foundation for more granular control of model behavior.

Diffusion models excel at generating high-dimensional data but fall short in training efficiency and representation quality compared to self-supervised methods. We identify a key bottleneck: the underutilization of high-quality, semantically rich representations during training notably slows down convergence. Our systematic analysis reveals a critical representation processing region -- primarily in the early layers -- where semantic and structural pattern learning takes place before generation can occur. To address this, we propose Embedded Representation Warmup (ERW), a plug-and-play framework where in the first stage we get the ERW module serves as a warmup that initializes the early layers of the diffusion model with high-quality, pretrained representations. This warmup minimizes the burden of learning representations from scratch, thereby accelerating convergence and boosting performance. Our theoretical analysis demonstrates that ERW's efficacy depends on its precise integration into specific neural network layers -- termed the representation processing region -- where the model primarily processes and transforms feature representations for later generation. We further establish that ERW not only accelerates training convergence but also enhances representation quality: empirically, our method achieves a 40times acceleration in training speed compared to REPA, the current state-of-the-art methods. Code is available at https://github.com/LINs-lab/ERW.

Deep learning employs multi-layer neural networks trained via the backpropagation algorithm. This approach has achieved success across many domains and relies on adaptive gradient methods such as the Adam optimizer. Sequence modeling evolved from recurrent neural networks to attention-based models, culminating in the Transformer architecture. Transformers have achieved state-of-the-art performance in natural language processing (for example, BERT and GPT-3) and have been applied in computer vision and computational biology. However, theoretical understanding of these models remains limited. In this paper, we examine the mathematical foundations of deep learning and Transformers and present a novel theoretical result. We review key concepts from linear algebra, probability, and optimization that underpin deep learning, and we analyze the multi-head self-attention mechanism and the backpropagation algorithm in detail. Our main contribution is a universal approximation theorem for Transformers: we prove that a single-layer Transformer, comprising one self-attention layer followed by a position-wise feed-forward network with ReLU activation, can approximate any continuous sequence-to-sequence mapping on a compact domain to arbitrary precision. We provide a formal statement and a complete proof. Finally, we present case studies that demonstrate the practical implications of this result. Our findings advance the theoretical understanding of Transformer models and help bridge the gap between theory and practice.

Large Language Models (LLMs) have emerged as powerful tools, but their inherent safety risks - ranging from harmful content generation to broader societal harms - pose significant challenges. These risks can be amplified by the recent adversarial attacks, fine-tuning vulnerabilities, and the increasing deployment of LLMs in high-stakes environments. Existing safety-enhancing techniques, such as fine-tuning with human feedback or adversarial training, are still vulnerable as they address specific threats and often fail to generalize across unseen attacks, or require manual system-level defenses. This paper introduces RepBend, a novel approach that fundamentally disrupts the representations underlying harmful behaviors in LLMs, offering a scalable solution to enhance (potentially inherent) safety. RepBend brings the idea of activation steering - simple vector arithmetic for steering model's behavior during inference - to loss-based fine-tuning. Through extensive evaluation, RepBend achieves state-of-the-art performance, outperforming prior methods such as Circuit Breaker, RMU, and NPO, with up to 95% reduction in attack success rates across diverse jailbreak benchmarks, all with negligible reduction in model usability and general capabilities.

We introduce GateSkip, a simple residual-stream gating mechanism that enables token-wise layer skipping in decoder-only LMs. Each Attention/MLP branch is equipped with a sigmoid-linear gate that condenses the branch's output before it re-enters the residual stream. During inference we rank tokens by the gate values and skip low-importance ones using a per-layer budget. While early-exit or router-based Mixture-of-Depths models are known to be unstable and need extensive retraining, our smooth, differentiable gates fine-tune stably on top of pretrained models. On long-form reasoning, we save up to 15\% compute while retaining over 90\% of baseline accuracy. On instruction-tuned models we see accuracy gains at full compute and match baseline quality near 50\% savings. The learned gates give insight into transformer information flow (e.g., BOS tokens act as anchors), and the method combines easily with quantization, pruning, and self-speculative decoding.

Transformer layers, which use an alternating pattern of multi-head attention and multi-layer perceptron (MLP) layers, provide an effective tool for a variety of machine learning problems. As the transformer layers use residual connections to avoid the problem of vanishing gradients, they can be viewed as the numerical integration of a differential equation. In this extended abstract, we build upon this connection and propose a modification of the internal architecture of a transformer layer. The proposed model places the multi-head attention sublayer and the MLP sublayer parallel to each other. Our experiments show that this simple modification improves the performance of transformer networks in multiple tasks. Moreover, for the image classification task, we show that using neural ODE solvers with a sophisticated integration scheme further improves performance.

An important limitation to the development of Artificial Intelligence (AI)-based solutions for In Vitro Fertilization (IVF) is the absence of a public reference benchmark to train and evaluate deep learning (DL) models. In this work, we describe a fully annotated dataset of 704 videos of developing embryos, for a total of 337k images. We applied ResNet, LSTM, and ResNet-3D architectures to our dataset and demonstrate that they overperform algorithmic approaches to automatically annotate stage development phases. Altogether, we propose the first public benchmark that will allow the community to evaluate morphokinetic models. This is the first step towards deep learning-powered IVF. Of note, we propose highly detailed annotations with 16 different development phases, including early cell division phases, but also late cell divisions, phases after morulation, and very early phases, which have never been used before. We postulate that this original approach will help improve the overall performance of deep learning approaches on time-lapse videos of embryo development, ultimately benefiting infertile patients with improved clinical success rates (Code and data are available at https://gitlab.univ-nantes.fr/E144069X/bench_mk_pred.git).

As artificial intelligence models have exploded in scale and capability, understanding of their internal mechanisms remains a critical challenge. Inspired by the success of dynamical systems approaches in neuroscience, here we propose a novel framework for studying computations in deep learning systems. We focus on the residual stream (RS) in transformer models, conceptualizing it as a dynamical system evolving across layers. We find that activations of individual RS units exhibit strong continuity across layers, despite the RS being a non-privileged basis. Activations in the RS accelerate and grow denser over layers, while individual units trace unstable periodic orbits. In reduced-dimensional spaces, the RS follows a curved trajectory with attractor-like dynamics in the lower layers. These insights bridge dynamical systems theory and mechanistic interpretability, establishing a foundation for a "neuroscience of AI" that combines theoretical rigor with large-scale data analysis to advance our understanding of modern neural networks.

In this paper, we introduce a novel layer designed to be used as the output of pre-trained neural networks in the context of classification. Based on Associative Memories, this layer can help design Deep Neural Networks which support incremental learning and that can be (partially) trained in real time on embedded devices. Experiments on the ImageNet dataset and other different domain specific datasets show that it is possible to design more flexible and faster-to-train Neural Networks at the cost of a slight decrease in accuracy.

Recently, we have witnessed the rapid development of large language models, which have demonstrated excellent capabilities in the downstream task of code generation. However, despite their potential, LLM-based code generation still faces numerous technical and evaluation challenges, particularly when embedded in real-world development. In this paper, we present our vision for current research directions, and provide an in-depth analysis of existing studies on this task. We propose a six-layer vision framework that categorizes code generation process into distinct phases, namely Input Phase, Orchestration Phase, Development Phase, and Validation Phase. Additionally, we outline our vision workflow, which reflects on the currently prevalent frameworks. We systematically analyse the challenges faced by large language models, including those LLM-based agent frameworks, in code generation tasks. With these, we offer various perspectives and actionable recommendations in this area. Our aim is to provide guidelines for improving the reliability, robustness and usability of LLM-based code generation systems. Ultimately, this work seeks to address persistent challenges and to provide practical suggestions for a more pragmatic LLM-based solution for future code generation endeavors.

The input space of a neural network with ReLU-like activations is partitioned into multiple linear regions, each corresponding to a specific activation pattern of the included ReLU-like activations. We demonstrate that this partition exhibits the following encoding properties across a variety of deep learning models: (1) {\it determinism}: almost every linear region contains at most one training example. We can therefore represent almost every training example by a unique activation pattern, which is parameterized by a {\it neural code}; and (2) {\it categorization}: according to the neural code, simple algorithms, such as K-Means, K-NN, and logistic regression, can achieve fairly good performance on both training and test data. These encoding properties surprisingly suggest that {\it normal neural networks well-trained for classification behave as hash encoders without any extra efforts.} In addition, the encoding properties exhibit variability in different scenarios. {Further experiments demonstrate that {\it model size}, {\it training time}, {\it training sample size}, {\it regularization}, and {\it label noise} contribute in shaping the encoding properties, while the impacts of the first three are dominant.} We then define an {\it activation hash phase chart} to represent the space expanded by {model size}, training time, training sample size, and the encoding properties, which is divided into three canonical regions: {\it under-expressive regime}, {\it critically-expressive regime}, and {\it sufficiently-expressive regime}. The source code package is available at https://github.com/LeavesLei/activation-code.

Self-attention mechanism is the key of the Transformer but often criticized for its computation demands. Previous token pruning works motivate their methods from the view of computation redundancy but still need to load the full network and require same memory costs. This paper introduces a novel strategy that simplifies vision transformers and reduces computational load through the selective removal of non-essential attention layers, guided by entropy considerations. We identify that regarding the attention layer in bottom blocks, their subsequent MLP layers, i.e. two feed-forward layers, can elicit the same entropy quantity. Meanwhile, the accompanied MLPs are under-exploited since they exhibit smaller feature entropy compared to those MLPs in the top blocks. Therefore, we propose to integrate the uninformative attention layers into their subsequent counterparts by degenerating them into identical mapping, yielding only MLP in certain transformer blocks. Experimental results on ImageNet-1k show that the proposed method can remove 40% attention layer of DeiT-B, improving throughput and memory bound without performance compromise. Code is available at https://github.com/sihaoevery/lambda_vit.

We propose a new frontier: Neural Computers (NCs) -- an emerging machine form that unifies computation, memory, and I/O in a learned runtime state. Unlike conventional computers, which execute explicit programs, agents, which act over external execution environments, and world models, which learn environment dynamics, NCs aim to make the model itself the running computer. Our long-term goal is the Completely Neural Computer (CNC): the mature, general-purpose realization of this emerging machine form, with stable execution, explicit reprogramming, and durable capability reuse. As an initial step, we study whether early NC primitives can be learned solely from collected I/O traces, without instrumented program state. Concretely, we instantiate NCs as video models that roll out screen frames from instructions, pixels, and user actions (when available) in CLI and GUI settings. These implementations show that learned runtimes can acquire early interface primitives, especially I/O alignment and short-horizon control, while routine reuse, controlled updates, and symbolic stability remain open. We outline a roadmap toward CNCs around these challenges. If overcome, CNCs could establish a new computing paradigm beyond today's agents, world models, and conventional computers.

Language models are instruction-tuned to refuse harmful requests, but the mechanisms underlying this behavior remain poorly understood. Popular steering methods operate on the residual stream and degrade output coherence at high intervention strengths, limiting their practical use. We introduce contrastive neuron attribution (CNA), which identifies the 0.1% of MLP neurons whose activations most distinguish harmful from benign prompts, requiring only forward passes with no gradients or auxiliary training. In instruct models, ablating the discovered circuit reduces refusal rates by over 50% on a standard jailbreak benchmark while preserving fluency and non-degeneracy across all steering strengths. Applying CNA to matched base and instruct models across Llama and Qwen architectures (from 1B to 72B parameters), we find that base models contain similar late-layer discrimination structures but steering these neurons produces only content shifts, not behavioral change. These results demonstrate that neuron-level intervention enables reliable behavioral steering without the quality tradeoffs of residual-stream methods. More broadly, our findings suggest that alignment fine-tuning transforms pre-existing discrimination structure into a sparse, targetable refusal gate.

Large language models (LLMs) are increasingly used for code generation in fast, informal development workflows, often referred to as vibe coding, where speed and convenience are prioritized, and security requirements are rarely made explicit. In this setting, models frequently produce functionally correct but insecure code, creating a growing security risk. Existing approaches to improving code security rely on full-parameter fine-tuning or parameter-efficient adaptations, which are either costly and prone to catastrophic forgetting or operate at coarse granularity with limited interpretability and control. We present GoodVibe, a neuron-level framework for improving the security of code language models by default. GoodVibe is based on the key insight that security-relevant reasoning is localized to a small subset of neurons. We identify these neurons using gradient-based attribution from a supervised security task and perform neuron-selective fine-tuning that updates only this security-critical subspace. To further reduce training cost, we introduce activation-driven neuron clustering, enabling structured updates with minimal overhead. We evaluate GoodVibe on six LLMs across security-critical programming languages, including C++, Java, Swift, and Go. GoodVibe substantially improves the security of generated code while preserving general model utility, achieving up to a 2.5x improvement over base models, matching or exceeding full fine-tuning with over 4,700x fewer trainable parameters, and reducing training computation by more than 3.6x compared to the parameter-efficient baseline (LoRA). Our results demonstrate that neuron-level optimization offers an effective and scalable approach to securing code generation without sacrificing efficiency or generality.

Self-attention performs well in long context but has quadratic complexity. Existing RNN layers have linear complexity, but their performance in long context is limited by the expressive power of their hidden state. We propose a new class of sequence modeling layers with linear complexity and an expressive hidden state. The key idea is to make the hidden state a machine learning model itself, and the update rule a step of self-supervised learning. Since the hidden state is updated by training even on test sequences, our layers are called Test-Time Training (TTT) layers. We consider two instantiations: TTT-Linear and TTT-MLP, whose hidden state is a linear model and a two-layer MLP respectively. We evaluate our instantiations at the scale of 125M to 1.3B parameters, comparing with a strong Transformer and Mamba, a modern RNN. Both TTT-Linear and TTT-MLP match or exceed the baselines. Similar to Transformer, they can keep reducing perplexity by conditioning on more tokens, while Mamba cannot after 16k context. With preliminary systems optimization, TTT-Linear is already faster than Transformer at 8k context and matches Mamba in wall-clock time. TTT-MLP still faces challenges in memory I/O, but shows larger potential in long context, pointing to a promising direction for future research.

We develop a continual learning method for pretrained models that requires no access to old-task data, addressing a practical barrier in foundation model adaptation where pretraining distributions are often unavailable. Our key observation is that pretrained networks exhibit substantial geometric redundancy, and that this redundancy can be exploited in two complementary ways. First, redundant neurons provide a proxy for dominant pretraining-era feature directions, enabling the construction of approximately protected update subspaces directly from pretrained weights. Second, redundancy offers a natural bias for where to place plasticity: by restricting updates to a subset of redundant neurons and constraining the remaining degrees of freedom, we obtain update families with reduced functional drift on the old-data distribution and improved worst-case retention guarantees. These insights lead to PLATE (Plasticity-Tunable Efficient Adapters), a continual learning method requiring no past-task data that provides explicit control over the plasticity-retention trade-off. PLATE parameterizes each layer with a structured low-rank update ΔW = B A Q^top, where B and Q are computed once from pretrained weights and kept frozen, and only A is trained on the new task. The code is available at https://github.com/SalesforceAIResearch/PLATE.

Training large transformer models is one of the most important computational challenges of modern AI. In this paper, we show how to significantly accelerate training of large transformer models by reducing activation recomputation. Activation recomputation is commonly used to work around memory capacity constraints. Rather than storing activations for backpropagation, they are traditionally recomputed, which saves memory but adds redundant compute. In this work, we show most of this redundant compute is unnecessary because we can reduce memory consumption sufficiently without it. We present two novel yet very simple techniques: sequence parallelism and selective activation recomputation. In conjunction with tensor parallelism, these techniques almost eliminate the need to recompute activations. We evaluate our approach on language models up to one trillion parameters in scale and show that our method reduces activation memory by 5x, while reducing execution time overhead from activation recomputation by over 90%. For example, when training a 530B parameter GPT-3 style model on 2240 NVIDIA A100 GPUs, we achieve a Model Flops Utilization of 54.2%, which is 29% faster than the 42.1% we achieve using recomputation. Our implementation will be available in both Megatron-LM and NeMo-Megatron.

Auto-regressive Large Language Models (LLMs) demonstrate remarkable performance across different domains such as vision and language processing. However, due to sequential processing through a stack of transformer layers, autoregressive decoding faces significant computation/latency challenges, particularly in resource-constrained environments like mobile and edge devices. Existing approaches in literature that aim to improve latency via skipping layers have two distinct flavors - 1) Early exit, and 2) Input-agnostic heuristics where tokens exit at pre-determined layers irrespective of input sequence. Both the above strategies have limitations - the former cannot be applied to handle KV Caching necessary for speed-ups in modern framework and the latter does not capture the variation in layer importance across tasks or more generally, across input sequences. To address both limitations, we propose FiRST, an algorithm that reduces inference latency by using layer-specific routers to select a subset of transformer layers adaptively for each input sequence - the prompt (during the prefill stage) decides which layers will be skipped during decoding. FiRST preserves compatibility with KV caching enabling faster inference while being quality-aware. FiRST is model-agnostic and can be easily enabled on any pre-trained LLM. Our approach reveals that input adaptivity is critical - indeed, different task-specific middle layers play a crucial role in evolving hidden representations depending on tasks. Extensive experiments show that FiRST significantly reduces latency while outperforming other layer selection strategies in quality metics. It retains competitive performance to base model (without layer skipping) and in some cases, even improves upon it. FiRST is thus a promising and efficient solution for LLM deployment in low-resource environments.

This article proposes to auto-encode text at byte-level using convolutional networks with a recursive architecture. The motivation is to explore whether it is possible to have scalable and homogeneous text generation at byte-level in a non-sequential fashion through the simple task of auto-encoding. We show that non-sequential text generation from a fixed-length representation is not only possible, but also achieved much better auto-encoding results than recurrent networks. The proposed model is a multi-stage deep convolutional encoder-decoder framework using residual connections, containing up to 160 parameterized layers. Each encoder or decoder contains a shared group of modules that consists of either pooling or upsampling layers, making the network recursive in terms of abstraction levels in representation. Results for 6 large-scale paragraph datasets are reported, in 3 languages including Arabic, Chinese and English. Analyses are conducted to study several properties of the proposed model.

In the field of continual learning, models are designed to learn tasks one after the other. While most research has centered on supervised continual learning, there is a growing interest in unsupervised continual learning, which makes use of the vast amounts of unlabeled data. Recent studies have highlighted the strengths of unsupervised methods, particularly self-supervised learning, in providing robust representations. The improved transferability of those representations built with self-supervised methods is often associated with the role played by the multi-layer perceptron projector. In this work, we depart from this observation and reexamine the role of supervision in continual representation learning. We reckon that additional information, such as human annotations, should not deteriorate the quality of representations. Our findings show that supervised models when enhanced with a multi-layer perceptron head, can outperform self-supervised models in continual representation learning. This highlights the importance of the multi-layer perceptron projector in shaping feature transferability across a sequence of tasks in continual learning. The code is available on github: https://github.com/danielm1405/sl-vs-ssl-cl.

We propose spatially-adaptive normalization, a simple but effective layer for synthesizing photorealistic images given an input semantic layout. Previous methods directly feed the semantic layout as input to the deep network, which is then processed through stacks of convolution, normalization, and nonlinearity layers. We show that this is suboptimal as the normalization layers tend to ``wash away'' semantic information. To address the issue, we propose using the input layout for modulating the activations in normalization layers through a spatially-adaptive, learned transformation. Experiments on several challenging datasets demonstrate the advantage of the proposed method over existing approaches, regarding both visual fidelity and alignment with input layouts. Finally, our model allows user control over both semantic and style. Code is available at https://github.com/NVlabs/SPADE .

Self-replication is a key aspect of biological life that has been largely overlooked in Artificial Intelligence systems. Here we describe how to build and train self-replicating neural networks. The network replicates itself by learning to output its own weights. The network is designed using a loss function that can be optimized with either gradient-based or non-gradient-based methods. We also describe a method we call regeneration to train the network without explicit optimization, by injecting the network with predictions of its own parameters. The best solution for a self-replicating network was found by alternating between regeneration and optimization steps. Finally, we describe a design for a self-replicating neural network that can solve an auxiliary task such as MNIST image classification. We observe that there is a trade-off between the network's ability to classify images and its ability to replicate, but training is biased towards increasing its specialization at image classification at the expense of replication. This is analogous to the trade-off between reproduction and other tasks observed in nature. We suggest that a self-replication mechanism for artificial intelligence is useful because it introduces the possibility of continual improvement through natural selection.

Foundation models have transformed multimedia analysis by enabling robust and transferable representations across diverse modalities and tasks. However, their static deployment conflicts with growing societal and regulatory demands -- particularly the need to unlearn specific data upon request, as mandated by privacy frameworks such as the GDPR. Traditional unlearning approaches, including retraining, activation editing, or distillation, are often computationally expensive, fragile, and ill-suited for real-time or continuously evolving systems. In this paper, we propose a paradigm shift: rethinking unlearning not as a retroactive intervention but as a built-in capability. We introduce a prompt-based learning framework that unifies knowledge acquisition and removal within a single training phase. Rather than encoding information in model weights, our approach binds class-level semantics to dedicated prompt tokens. This design enables instant unlearning simply by removing the corresponding prompt -- without retraining, model modification, or access to original data. Experiments demonstrate that our framework preserves predictive performance on retained classes while effectively erasing forgotten ones. Beyond utility, our method exhibits strong privacy and security guarantees: it is resistant to membership inference attacks, and prompt removal prevents any residual knowledge extraction, even under adversarial conditions. This ensures compliance with data protection principles and safeguards against unauthorized access to forgotten information, making the framework suitable for deployment in sensitive and regulated environments. Overall, by embedding removability into the architecture itself, this work establishes a new foundation for designing modular, scalable and ethically responsive AI models.

Several studies have explored the mechanisms of large language models (LLMs) in coding tasks, but most have focused on programming languages (PLs) in a monolingual setting. In this paper, we investigate the relationship between multiple PLs and English in the concept space of LLMs. We perform a few-shot translation task on 21 PL pairs using two Llama-based models. By decoding the embeddings of intermediate layers during this task, we observe that the concept space is closer to English (including PL keywords) and assigns high probabilities to English tokens in the second half of the intermediate layers. We analyze neuron activations for 11 PLs and English, finding that while language-specific neurons are primarily concentrated in the bottom layers, those exclusive to each PL tend to appear in the top layers. For PLs that are highly aligned with multiple other PLs, identifying language-specific neurons is not feasible. These PLs also tend to have a larger keyword set than other PLs and are closer to the model's concept space regardless of the input/output PL in the translation task. Our findings provide insights into how LLMs internally represent PLs, revealing structural patterns in the model's concept space. Code is available at https://github.com/cisnlp/code-specific-neurons.

DNA foundation models have become transformative tools in bioinformatics and healthcare applications. Trained on vast genomic datasets, these models can be used to generate sequence embeddings, dense vector representations that capture complex genomic information. These embeddings are increasingly being shared via Embeddings-as-a-Service (EaaS) frameworks to facilitate downstream tasks, while supposedly protecting the privacy of the underlying raw sequences. However, as this practice becomes more prevalent, the security of these representations is being called into question. This study evaluates the resilience of DNA foundation models to model inversion attacks, whereby adversaries attempt to reconstruct sensitive training data from model outputs. In our study, the model's output for reconstructing the DNA sequence is a zero-shot embedding, which is then fed to a decoder. We evaluated the privacy of three DNA foundation models: DNABERT-2, Evo 2, and Nucleotide Transformer v2 (NTv2). Our results show that per-token embeddings allow near-perfect sequence reconstruction across all models. For mean-pooled embeddings, reconstruction quality degrades as sequence length increases, though it remains substantially above random baselines. Evo 2 and NTv2 prove to be most vulnerable, especially for shorter sequences with reconstruction similarities > 90%, while DNABERT-2's BPE tokenization provides the greatest resilience. We found that the correlation between embedding similarity and sequence similarity was a key predictor of reconstruction success. Our findings emphasize the urgent need for privacy-aware design in genomic foundation models prior to their widespread deployment in EaaS settings. Training code, model weights and evaluation pipeline are released on: https://github.com/not-a-feature/DNA-Embedding-Inversion.

Pre-trained models for programming languages have recently demonstrated great success on code intelligence. To support both code-related understanding and generation tasks, recent works attempt to pre-train unified encoder-decoder models. However, such encoder-decoder framework is sub-optimal for auto-regressive tasks, especially code completion that requires a decoder-only manner for efficient inference. In this paper, we present UniXcoder, a unified cross-modal pre-trained model for programming language. The model utilizes mask attention matrices with prefix adapters to control the behavior of the model and leverages cross-modal contents like AST and code comment to enhance code representation. To encode AST that is represented as a tree in parallel, we propose a one-to-one mapping method to transform AST in a sequence structure that retains all structural information from the tree. Furthermore, we propose to utilize multi-modal contents to learn representation of code fragment with contrastive learning, and then align representations among programming languages using a cross-modal generation task. We evaluate UniXcoder on five code-related tasks over nine datasets. To further evaluate the performance of code fragment representation, we also construct a dataset for a new task, called zero-shot code-to-code search. Results show that our model achieves state-of-the-art performance on most tasks and analysis reveals that comment and AST can both enhance UniXcoder.

The use of modern Natural Language Processing (NLP) techniques has shown to be beneficial for software engineering tasks, such as vulnerability detection and type inference. However, training deep NLP models requires significant computational resources. This paper explores techniques that aim at achieving the best usage of resources and available information in these models. We propose a generic approach, EarlyBIRD, to build composite representations of code from the early layers of a pre-trained transformer model. We empirically investigate the viability of this approach on the CodeBERT model by comparing the performance of 12 strategies for creating composite representations with the standard practice of only using the last encoder layer. Our evaluation on four datasets shows that several early layer combinations yield better performance on defect detection, and some combinations improve multi-class classification. More specifically, we obtain a +2 average improvement of detection accuracy on Devign with only 3 out of 12 layers of CodeBERT and a 3.3x speed-up of fine-tuning. These findings show that early layers can be used to obtain better results using the same resources, as well as to reduce resource usage during fine-tuning and inference.

We present LayerSkip, an end-to-end solution to speed-up inference of large language models (LLMs). First, during training we apply layer dropout, with low dropout rates for earlier layers and higher dropout rates for later layers, and an early exit loss where all transformer layers share the same exit. Second, during inference, we show that this training recipe increases the accuracy of early exit at earlier layers, without adding any auxiliary layers or modules to the model. Third, we present a novel self-speculative decoding solution where we exit at early layers and verify and correct with remaining layers of the model. Our proposed self-speculative decoding approach has less memory footprint than other speculative decoding approaches and benefits from shared compute and activations of the draft and verification stages. We run experiments on different Llama model sizes on different types of training: pretraining from scratch, continual pretraining, finetuning on specific data domain, and finetuning on specific task. We implement our inference solution and show speedups of up to 2.16x on summarization for CNN/DM documents, 1.82x on coding, and 2.0x on TOPv2 semantic parsing task. We open source our code and checkpoints at https://github.com/facebookresearch/LayerSkip.

Feed-forward layers constitute two-thirds of a transformer model's parameters, yet their role in the network remains under-explored. We show that feed-forward layers in transformer-based language models operate as key-value memories, where each key correlates with textual patterns in the training examples, and each value induces a distribution over the output vocabulary. Our experiments show that the learned patterns are human-interpretable, and that lower layers tend to capture shallow patterns, while upper layers learn more semantic ones. The values complement the keys' input patterns by inducing output distributions that concentrate probability mass on tokens likely to appear immediately after each pattern, particularly in the upper layers. Finally, we demonstrate that the output of a feed-forward layer is a composition of its memories, which is subsequently refined throughout the model's layers via residual connections to produce the final output distribution.

Transfer learning on edge is challenging due to on-device limited resources. Existing work addresses this issue by training a subset of parameters or adding model patches. Developed with inference in mind, Inverted Residual Blocks (IRBs) split a convolutional layer into depthwise and pointwise convolutions, leading to more stacking layers, e.g., convolution, normalization, and activation layers. Though they are efficient for inference, IRBs require that additional activation maps are stored in memory for training weights for convolution layers and scales for normalization layers. As a result, their high memory cost prohibits training IRBs on resource-limited edge devices, and making them unsuitable in the context of transfer learning. To address this issue, we present MobileTL, a memory and computationally efficient on-device transfer learning method for models built with IRBs. MobileTL trains the shifts for internal normalization layers to avoid storing activation maps for the backward pass. Also, MobileTL approximates the backward computation of the activation layer (e.g., Hard-Swish and ReLU6) as a signed function which enables storing a binary mask instead of activation maps for the backward pass. MobileTL fine-tunes a few top blocks (close to output) rather than propagating the gradient through the whole network to reduce the computation cost. Our method reduces memory usage by 46% and 53% for MobileNetV2 and V3 IRBs, respectively. For MobileNetV3, we observe a 36% reduction in floating-point operations (FLOPs) when fine-tuning 5 blocks, while only incurring a 0.6% accuracy reduction on CIFAR10. Extensive experiments on multiple datasets demonstrate that our method is Pareto-optimal (best accuracy under given hardware constraints) compared to prior work in transfer learning for edge devices.

Our work presents extensive empirical evidence that layer rotation, i.e. the evolution across training of the cosine distance between each layer's weight vector and its initialization, constitutes an impressively consistent indicator of generalization performance. In particular, larger cosine distances between final and initial weights of each layer consistently translate into better generalization performance of the final model. Interestingly, this relation admits a network independent optimum: training procedures during which all layers' weights reach a cosine distance of 1 from their initialization consistently outperform other configurations -by up to 30% test accuracy. Moreover, we show that layer rotations are easily monitored and controlled (helpful for hyperparameter tuning) and potentially provide a unified framework to explain the impact of learning rate tuning, weight decay, learning rate warmups and adaptive gradient methods on generalization and training speed. In an attempt to explain the surprising properties of layer rotation, we show on a 1-layer MLP trained on MNIST that layer rotation correlates with the degree to which features of intermediate layers have been trained.

Modern LLMs are increasingly deep, and depth correlates with performance, albeit with diminishing returns. However, do these models use their depth efficiently? Do they compose more features to create higher-order computations that are impossible in shallow models, or do they merely spread the same kinds of computation out over more layers? To address these questions, we analyze the residual stream of the Llama 3.1 and Qwen 3 family of models. We find: First, comparing the output of the sublayers to the residual stream reveals that layers in the second half contribute much less than those in the first half, with a clear phase transition between the two halves. Second, skipping layers in the second half has a much smaller effect on future computations and output predictions. Third, for multihop tasks, we are unable to find evidence that models are using increased depth to compose subresults in examples involving many hops. Fourth, we seek to directly address whether deeper models are using their additional layers to perform new kinds of computation. To do this, we train linear maps from the residual stream of a shallow model to a deeper one. We find that layers with the same relative depth map best to each other, suggesting that the larger model simply spreads the same computations out over its many layers. All this evidence suggests that deeper models are not using their depth to learn new kinds of computation, but only using the greater depth to perform more fine-grained adjustments to the residual. This may help explain why increasing scale leads to diminishing returns for stacked Transformer architectures.

Vision Transformer models exhibit immense power yet remain opaque to human understanding, posing challenges and risks for practical applications. While prior research has attempted to demystify these models through input attribution and neuron role analysis, there's been a notable gap in considering layer-level information and the holistic path of information flow across layers. In this paper, we investigate the significance of influential neuron paths within vision Transformers, which is a path of neurons from the model input to output that impacts the model inference most significantly. We first propose a joint influence measure to assess the contribution of a set of neurons to the model outcome. And we further provide a layer-progressive neuron locating approach that efficiently selects the most influential neuron at each layer trying to discover the crucial neuron path from input to output within the target model. Our experiments demonstrate the superiority of our method finding the most influential neuron path along which the information flows, over the existing baseline solutions. Additionally, the neuron paths have illustrated that vision Transformers exhibit some specific inner working mechanism for processing the visual information within the same image category. We further analyze the key effects of these neurons on the image classification task, showcasing that the found neuron paths have already preserved the model capability on downstream tasks, which may also shed some lights on real-world applications like model pruning. The project website including implementation code is available at https://foundation-model-research.github.io/NeuronPath/.

Deep implicit functions have been found to be an effective tool for efficiently encoding all manner of natural signals. Their attractiveness stems from their ability to compactly represent signals with little to no off-line training data. Instead, they leverage the implicit bias of deep networks to decouple hidden redundancies within the signal. In this paper, we explore the hypothesis that additional compression can be achieved by leveraging the redundancies that exist between layers. We propose to use a novel run-time decoder-only hypernetwork - that uses no offline training data - to better model this cross-layer parameter redundancy. Previous applications of hyper-networks with deep implicit functions have applied feed-forward encoder/decoder frameworks that rely on large offline datasets that do not generalize beyond the signals they were trained on. We instead present a strategy for the initialization of run-time deep implicit functions for single-instance signals through a Decoder-Only randomly projected Hypernetwork (D'OH). By directly changing the dimension of a latent code to approximate a target implicit neural architecture, we provide a natural way to vary the memory footprint of neural representations without the costly need for neural architecture search on a space of alternative low-rate structures.

Code large language models (LLMs) enhance programming by understanding and generating code across languages, offering intelligent feedback, bug detection, and code updates through reflection, improving development efficiency and accessibility. While benchmarks (e.g. HumanEval/LiveCodeBench) evaluate code generation and real-world relevance, previous works ignore the scenario of modifying code in repositories. Considering challenges remaining in improving reflection capabilities and avoiding data contamination in dynamic benchmarks, we introduce LiveRepoReflection, a challenging benchmark for evaluating code understanding and generation in multi-file repository contexts, featuring 1,888 rigorously filtered test cases across 6 programming languages to ensure diversity, correctness, and high difficulty. Further, we create RepoReflection-Instruct, a large-scale, quality-filtered instruction-tuning dataset derived from diverse sources, used to train RepoReflectionCoder through a two-turn dialogue process involving code generation and error-driven repair. The leaderboard evaluates over 40 LLMs to reflect the model performance of repository-based code reflection.

Controlling undesirable Large Language Model (LLM) behaviors, such as the generation of unsafe content or failing to adhere to safety guidelines, often relies on costly fine-tuning. Activation steering provides an alternative for inference-time control, but existing methods typically lack fine-grained, adaptive mechanisms. We introduce a novel approach using a lightweight, trainable controller network integrated during inference. This controller network observes specific intermediate LLM activations and predicts both a global scaling factor and layer-specific weights. The predicted global scaling factor and layer-specific weights then dynamically modulate the intensity of a steering patch, derived from a pre-computed "refusal direction" vector, applied across the LLM's layers during generation. Trained on activations from both harmful and benign prompts, our controller learns to discriminatively apply nuanced, layer-aware interventions, activating steering primarily for harmful inputs. Experiments using safety benchmarks like ToxicChat & In-The-Wild Jailbreak Prompts demonstrate that our weighted steering controller significantly increases refusal rates compared to the base LLM, achieving targeted behavioral modification without altering the original model parameters. Our experiments with Llama-3.1-8B, Llama-3.2-1B & Mistral-7B show our approach outperforms existing methods, presenting an efficient and adaptive method for fine-grained control over LLM behavior at inference time.

The problem of automatically generating a computer program from some specification has been studied since the early days of AI. Recently, two competing approaches for automatic program learning have received significant attention: (1) neural program synthesis, where a neural network is conditioned on input/output (I/O) examples and learns to generate a program, and (2) neural program induction, where a neural network generates new outputs directly using a latent program representation. Here, for the first time, we directly compare both approaches on a large-scale, real-world learning task. We additionally contrast to rule-based program synthesis, which uses hand-crafted semantics to guide the program generation. Our neural models use a modified attention RNN to allow encoding of variable-sized sets of I/O pairs. Our best synthesis model achieves 92% accuracy on a real-world test set, compared to the 34% accuracy of the previous best neural synthesis approach. The synthesis model also outperforms a comparable induction model on this task, but we more importantly demonstrate that the strength of each approach is highly dependent on the evaluation metric and end-user application. Finally, we show that we can train our neural models to remain very robust to the type of noise expected in real-world data (e.g., typos), while a highly-engineered rule-based system fails entirely.

From extracting features to generating text, the outputs of large language models (LLMs) typically rely on their final layers, following the conventional wisdom that earlier layers capture only low-level cues. However, our analysis shows that intermediate layers can encode even richer representations, often improving performance on a wide range of downstream tasks. To explain and quantify these hidden-layer properties, we propose a unified framework of representation quality metrics based on information theory, geometry, and invariance to input perturbations. Our framework highlights how each model layer balances information compression and signal preservation, revealing why mid-depth embeddings can exceed the last layer's performance. Through extensive experiments on 32 text-embedding tasks and comparisons across model architectures (transformers, state-space models) and domains (language, vision), we demonstrate that intermediate layers consistently provide stronger features. These findings challenge the standard focus on final-layer embeddings and open new directions for model analysis and optimization, including strategic use of mid-layer representations for more robust and accurate AI systems.

Transfer learning has become a central paradigm in modern machine learning, yet it suffers from the long-standing problem of negative transfer, where leveraging source representations can harm rather than help performance on the target task. Although empirical remedies have been proposed, there remains little theoretical understanding of how to reliably avoid negative transfer. In this paper, we investigate a simple yet remarkably effective strategy: augmenting frozen, pretrained source-side features with a trainable target-side encoder that adapts target features to capture residual signals overlooked by models pretrained on the source data. We show this residual feature integration strategy is sufficient to provably prevent negative transfer, by establishing theoretical guarantees that it has no worse convergence rate than training from scratch under the informative class of target distributions up to logarithmic factors, and that the convergence rate can transition seamlessly from nonparametric to near-parametric when source representations are informative. To our knowledge, this is the first theoretical work that ensures protection against negative transfer. We carry out extensive numerical experiments across image, text and tabular benchmarks, and empirically verify that the method consistently safeguards performance under distribution shift, label noise, semantic perturbation, and class imbalance. We additionally demonstrate that this residual integration mechanism uniquely supports adapt-time multimodality extension, enabling a pretrained single-cell foundation model to incorporate spatial signals for lymph-node anatomical classification despite the source model being trained without them. Our study thus advances the theory of safe transfer learning, and provides a principled approach that is simple, robust, architecture-agnostic, and broadly applicable.

Modern recurrent layers are emerging as a promising path toward edge deployment of foundation models, especially in the context of large language models (LLMs). Compressing the whole input sequence in a finite-dimensional representation enables recurrent layers to model long-range dependencies while maintaining a constant inference cost for each token and a fixed memory requirement. However, the practical deployment of LLMs in resource-limited environments often requires further model compression, such as quantization and pruning. While these techniques are well-established for attention-based models, their effects on recurrent layers remain underexplored. In this preliminary work, we focus on post-training quantization for recurrent LLMs and show that Mamba models exhibit the same pattern of outlier channels observed in attention-based LLMs. We show that the reason for the difficulty of quantizing SSMs is caused by activation outliers, similar to those observed in transformer-based LLMs. We report baseline results for post-training quantization of Mamba that do not take into account the activation outliers and suggest first steps for outlier-aware quantization.

We present a novel approach to adjust global image properties such as colour, saturation, and luminance using human-interpretable image enhancement curves, inspired by the Photoshop curves tool. Our method, dubbed neural CURve Layers (CURL), is designed as a multi-colour space neural retouching block trained jointly in three different colour spaces (HSV, CIELab, RGB) guided by a novel multi-colour space loss. The curves are fully differentiable and are trained end-to-end for different computer vision problems including photo enhancement (RGB-to-RGB) and as part of the image signal processing pipeline for image formation (RAW-to-RGB). To demonstrate the effectiveness of CURL we combine this global image transformation block with a pixel-level (local) image multi-scale encoder-decoder backbone network. In an extensive experimental evaluation we show that CURL produces state-of-the-art image quality versus recently proposed deep learning approaches in both objective and perceptual metrics, setting new state-of-the-art performance on multiple public datasets. Our code is publicly available at: https://github.com/sjmoran/CURL.

GCC and LLVM underpin much of modern software infrastructure, relying on distinct Intermediate Representations (IRs) to drive optimizations and code generation. However, the semantic and structural differences between these IRs create significant barriers for cross-toolchain interaction, limiting the reuse of compiler frontends, backends, and optimization pipelines across programming languages and compilation ecosystems. Traditional rule-based translators have attempted to bridge this gap, but their complexity and maintenance cost have hindered practical adoption. In this context, Large Language Models (LLMs) appear to be an emerging technology that offers a data-driven alternative, capable of learning complex mappings between heterogeneous compiler IRs directly from sufficiently representative examples. To explore this approach, this paper presents IRIS-14B, a 14-billion-parameter transformer model fine-tuned to translate GIMPLE (as emitted by GCC) to LLVM IR (as emitted by LLVM). The model is trained on paired IRs extracted from C sources and evaluated on the GIMPLE-to-LLVM IR transformation applied to IRs derived from real-world C code and competitive programming problems. To the best of our knowledge, IRIS-14B is the first model trained explicitly for IR-to-IR translation. It outperforms the accuracy of widely used models, including the largest state-of-the-art open models available today, ranging from 13 to 1,000 billion parameters, by up to 44 percentage points. The proposed transformation supports the integration of LLMs as complementary components within hybrid neuro-symbolic compiler architectures, where models such as IRIS-14B act as interoperability layers enabling cross-toolchain workflows without modifying existing compiler passes, while traditional compiler infrastructure continues to perform deterministic compilation and optimization.

Large language and vision models (LLVMs) have been driven by the generalization power of large language models (LLMs) and the advent of visual instruction tuning. Along with scaling them up directly, these models enable LLVMs to showcase powerful vision language (VL) performances by covering diverse tasks via natural language instructions. However, existing open-source LLVMs that perform comparably to closed-source LLVMs such as GPT-4V are often considered too large (e.g., 26B, 34B, and 110B parameters), having a larger number of layers. These large models demand costly, high-end resources for both training and inference. To address this issue, we present a new efficient LLVM family with 1.8B, 3.8B, and 7B LLM model sizes, Traversal of Layers (TroL), which enables the reuse of layers in a token-wise manner. This layer traversing technique simulates the effect of looking back and retracing the answering stream while increasing the number of forward propagation layers without physically adding more layers. We demonstrate that TroL employs a simple layer traversing approach yet efficiently outperforms the open-source LLVMs with larger model sizes and rivals the performances of the closed-source LLVMs with substantial sizes.

Code intelligence leverages machine learning techniques to extract knowledge from extensive code corpora, with the aim of developing intelligent tools to improve the quality and productivity of computer programming. Currently, there is already a thriving research community focusing on code intelligence, with efforts ranging from software engineering, machine learning, data mining, natural language processing, and programming languages. In this paper, we conduct a comprehensive literature review on deep learning for code intelligence, from the aspects of code representation learning, deep learning techniques, and application tasks. We also benchmark several state-of-the-art neural models for code intelligence, and provide an open-source toolkit tailored for the rapid prototyping of deep-learning-based code intelligence models. In particular, we inspect the existing code intelligence models under the basis of code representation learning, and provide a comprehensive overview to enhance comprehension of the present state of code intelligence. Furthermore, we publicly release the source code and data resources to provide the community with a ready-to-use benchmark, which can facilitate the evaluation and comparison of existing and future code intelligence models (https://xcodemind.github.io). At last, we also point out several challenging and promising directions for future research.

Adapting Deep Learning (DL) techniques to automate non-trivial coding activities, such as code documentation and defect detection, has been intensively studied recently. Learning to predict code changes is one of the popular and essential investigations. Prior studies have shown that DL techniques such as Neural Machine Translation (NMT) can benefit meaningful code changes, including bug fixing and code refactoring. However, NMT models may encounter bottleneck when modeling long sequences, thus are limited in accurately predicting code changes. In this work, we design a Transformer-based approach, considering that Transformer has proven effective in capturing long-term dependencies. Specifically, we propose a novel model named DTrans. For better incorporating the local structure of code, i.e., statement-level information in this paper, DTrans is designed with dynamically relative position encoding in the multi-head attention of Transformer. Experiments on benchmark datasets demonstrate that DTrans can more accurately generate patches than the state-of-the-art methods, increasing the performance by at least 5.45\%-46.57\% in terms of the exact match metric on different datasets. Moreover, DTrans can locate the lines to change with 1.75\%-24.21\% higher accuracy than the existing methods.

Model extraction is a growing concern for the security of AI systems. For deep neural network models, the architecture is the most important information an adversary aims to recover. Being a sequence of repeated computation blocks, neural network models deployed on edge-devices will generate distinctive side-channel leakages. The latter can be exploited to extract critical information when targeted platforms are physically accessible. By combining theoretical knowledge about deep learning practices and analysis of a widespread implementation library (ARM CMSIS-NN), our purpose is to answer this critical question: how far can we extract architecture information by simply examining an EM side-channel trace? For the first time, we propose an extraction methodology for traditional MLP and CNN models running on a high-end 32-bit microcontroller (Cortex-M7) that relies only on simple pattern recognition analysis. Despite few challenging cases, we claim that, contrary to parameters extraction, the complexity of the attack is relatively low and we highlight the urgent need for practicable protections that could fit the strong memory and latency requirements of such platforms.

The foundation of reproducible science lies in protocols that are precise, logically ordered, and executable. The autonomous generation of these protocols through natural language queries could greatly improve the efficiency of the reproduction process. However, current leading large language models (LLMs) often generate incomplete or inconsistent protocols, limiting their utility. To address this limitation, we first introduce SciRecipe, a large-scale dataset of over 12K structured protocols spanning 27 biological subfields and encompassing both comprehension and problem-solving tasks. To further improve protocol generation, we propose the "Sketch-and-Fill" paradigm, which separates analysis, structuring, and expression to ensure each step is explicit and verifiable. Complementing this, the structured component-based reward mechanism evaluates step granularity, action order, and semantic fidelity, aligning model optimization with experimental reliability. Building on these components, we develop Thoth, trained through a staged Knowledge-to-Action process that progresses from knowledge acquisition to operational reasoning and ultimately to robust, executable protocol generation. Across multiple benchmarks, Thoth consistently surpasses both proprietary and open-source LLMs, achieving significant improvements in step alignment, logical sequencing, and semantic accuracy. Our approach paves the way for reliable scientific assistants that bridge knowledge with experimental execution. All data, code, and models will be released publicly.

Transformer models have demonstrated high accuracy in numerous applications but have high complexity and lack sequential processing capability making them ill-suited for many streaming applications at the edge where devices are heavily resource-constrained. Thus motivated, many researchers have proposed reformulating the transformer models as RNN modules which modify the self-attention computation with explicit states. However, these approaches often incur significant performance degradation. The ultimate goal is to develop a model that has the following properties: parallel training, streaming and low-cost inference, and SOTA performance. In this paper, we propose a new direction to achieve this goal. We show how architectural modifications to a recurrent model can help push its performance toward Transformer models while retaining its sequential processing capability. Specifically, inspired by the recent success of Legendre Memory Units (LMU) in sequence learning tasks, we propose LMUFormer, which augments the LMU with convolutional patch embedding and convolutional channel mixer. Moreover, we present a spiking version of this architecture, which introduces the benefit of states within the patch embedding and channel mixer modules while simultaneously reducing the computing complexity. We evaluated our architectures on multiple sequence datasets. In comparison to SOTA transformer-based models within the ANN domain on the SCv2 dataset, our LMUFormer demonstrates comparable performance while necessitating a remarkable 53 times reduction in parameters and a substantial 65 times decrement in FLOPs. Additionally, owing to our model's proficiency in real-time data processing, we can achieve a 32.03% reduction in sequence length, all while incurring an inconsequential decline in performance. Our code is publicly available at https://github.com/zeyuliu1037/LMUFormer.git.

Electroencephalography (EEG) foundation models hold significant promise for universal Brain-Computer Interfaces (BCIs). However, existing approaches often rely on end-to-end fine-tuning and exhibit limited efficacy under frozen-probing protocols, lacking the intrinsic universality required for broad generalization. This limitation stems from adapting general-purpose sequence architectures that overlook the biophysical and dynamical principles of neural activity. To bridge this gap, we propose DeeperBrain, a neuro-grounded foundation model integrating domain-specific inductive biases into its model design and learning objectives. Architecturally, DeeperBrain incorporates a volume conduction-aware channel encoding to model spatial mixing via 3D geometry, and a neurodynamics-aware temporal encoding capturing slow adaptations using oscillatory and exponential bases. For pretraining, we introduce a dual-objective strategy combining Masked EEG Reconstruction (MER) for local fidelity and Neurodynamics Statistics Prediction (NSP). NSP enforces alignment with macroscopic brain states by predicting interpretable order parameters, including spectral power, functional connectivity, cross-frequency coupling, and dynamic complexity. Extensive experiments demonstrate that DeeperBrain achieves state-of-the-art or highly competitive performance under end-to-end fine-tuning. Crucially, it maintains superior efficacy under a rigorous frozen-probing protocol, verifying that embedding neuroscientific first principles endows learned representations with the intrinsic universality essential for universal BCI. The code will be publicly available.

We introduce directional routing, a lightweight mechanism that gives each transformer attention head learned suppression directions controlled by a shared router, at 3.9% parameter cost. We train a 433M-parameter model alongside an identical baseline in a single run, then trace the resulting circuits through mechanistic interpretability. Routing becomes the model's dominant computational pathway. Disabling it collapses factual recall to near-zero probability across all 8 test prompts and drops induction accuracy from 93.4% to 0.0%. Knocking out individual attention heads has negligible effect: the primary mover head's removal actually increases target probability, and induction heads retain 98.6% accuracy without their strongest member. The coordination mechanism is irreplaceable; the components it coordinates are not. The model also self-organizes, without explicit pressure, into two regimes: domain-adaptive routing in early layers and fixed syntactic pruning in late layers, where the least-varying layer is the most critical (+42.6 PPL when disabled). Routing reduces perplexity 31-56% relative to the baseline, though downstream multiple-choice benchmarks do not yet reflect these gains.

The ability to remove features from the input of machine learning models is very important to understand and interpret model predictions. However, this is non-trivial for vision models since masking out parts of the input image typically causes large distribution shifts. This is because the baseline color used for masking (typically grey or black) is out of distribution. Furthermore, the shape of the mask itself can contain unwanted signals which can be used by the model for its predictions. Recently, there has been some progress in mitigating this issue (called missingness bias) in image masking for vision transformers. In this work, we propose a new masking method for CNNs we call layer masking in which the missingness bias caused by masking is reduced to a large extent. Intuitively, layer masking applies a mask to intermediate activation maps so that the model only processes the unmasked input. We show that our method (i) is able to eliminate or minimize the influence of the mask shape or color on the output of the model, and (ii) is much better than replacing the masked region by black or grey for input perturbation based interpretability techniques like LIME. Thus, layer masking is much less affected by missingness bias than other masking strategies. We also demonstrate how the shape of the mask may leak information about the class, thus affecting estimates of model reliance on class-relevant features derived from input masking. Furthermore, we discuss the role of data augmentation techniques for tackling this problem, and argue that they are not sufficient for preventing model reliance on mask shape. The code for this project is publicly available at https://github.com/SriramB-98/layer_masking

In this work, we present a learning-based approach to chip placement, one of the most complex and time-consuming stages of the chip design process. Unlike prior methods, our approach has the ability to learn from past experience and improve over time. In particular, as we train over a greater number of chip blocks, our method becomes better at rapidly generating optimized placements for previously unseen chip blocks. To achieve these results, we pose placement as a Reinforcement Learning (RL) problem and train an agent to place the nodes of a chip netlist onto a chip canvas. To enable our RL policy to generalize to unseen blocks, we ground representation learning in the supervised task of predicting placement quality. By designing a neural architecture that can accurately predict reward across a wide variety of netlists and their placements, we are able to generate rich feature embeddings of the input netlists. We then use this architecture as the encoder of our policy and value networks to enable transfer learning. Our objective is to minimize PPA (power, performance, and area), and we show that, in under 6 hours, our method can generate placements that are superhuman or comparable on modern accelerator netlists, whereas existing baselines require human experts in the loop and take several weeks.

Ensuring faithful interpretability in large language models is imperative for trustworthy and reliable AI. A key obstacle is self-repair, a phenomenon where networks compensate for reduced signal in one component by amplifying others, masking the true importance of the ablated component. While prior work attributes self-repair to layer normalization and back-up components that compensate for ablated components, we identify a novel form occurring within the attention mechanism, where softmax redistribution conceals the influence of important attention scores. This leads traditional ablation and gradient-based methods to underestimate the significance of all components contributing to these attention scores. We introduce Gradient Interaction Modifications (GIM), a technique that accounts for self-repair during backpropagation. Extensive experiments across multiple large language models (Gemma 2B/9B, LLAMA 1B/3B/8B, Qwen 1.5B/3B) and diverse tasks demonstrate that GIM significantly improves faithfulness over existing circuit identification and feature attribution methods. Our work is a significant step toward better understanding the inner mechanisms of LLMs, which is crucial for improving them and ensuring their safety. Our code is available at https://github.com/JoakimEdin/gim.

The Transformer architecture is widely used in natural language processing. Despite its success, the design principle of the Transformer remains elusive. In this paper, we provide a novel perspective towards understanding the architecture: we show that the Transformer can be mathematically interpreted as a numerical Ordinary Differential Equation (ODE) solver for a convection-diffusion equation in a multi-particle dynamic system. In particular, how words in a sentence are abstracted into contexts by passing through the layers of the Transformer can be interpreted as approximating multiple particles' movement in the space using the Lie-Trotter splitting scheme and the Euler's method. Given this ODE's perspective, the rich literature of numerical analysis can be brought to guide us in designing effective structures beyond the Transformer. As an example, we propose to replace the Lie-Trotter splitting scheme by the Strang-Marchuk splitting scheme, a scheme that is more commonly used and with much lower local truncation errors. The Strang-Marchuk splitting scheme suggests that the self-attention and position-wise feed-forward network (FFN) sub-layers should not be treated equally. Instead, in each layer, two position-wise FFN sub-layers should be used, and the self-attention sub-layer is placed in between. This leads to a brand new architecture. Such an FFN-attention-FFN layer is "Macaron-like", and thus we call the network with this new architecture the Macaron Net. Through extensive experiments, we show that the Macaron Net is superior to the Transformer on both supervised and unsupervised learning tasks. The reproducible codes and pretrained models can be found at https://github.com/zhuohan123/macaron-net