Daily Papers

The rapid scaling of Protein Language Models (PLMs) has unlocked unprecedented accuracy in protein structure prediction and design, but the quadratic memory growth of the Key-Value (KV) cache during inference remains a prohibitive barrier for single-GPU deployment and high-throughput generation. While 8-bit quantization is now standard, 3-bit quantization remains elusive due to severe numerical outliers in activations. This paper presents TurboESM, an adaptation of Google's TurboQuant to the PLM domain. We solve the fundamental incompatibility between Rotary Position Embeddings (RoPE) and orthogonal transformations by deriving a RoPE-first rotation pipeline. We introduce a head-wise SVD calibration method tailored to the amino acid activation manifold, a dual look-up table (LUT) strategy for asymmetric K/V distributions, and a 1-bit Quantized Johnson-Lindenstrauss (QJL) residual correction. All experiments are conducted on ESM-2 650M, where our implementation achieves a 7.1x memory reduction (330 MB to 47 MB) while maintaining cosine similarity > 0.96 in autoregressive decoding across diverse protein families, including short peptides, transmembrane helices, enzyme active site fragments, and intrinsically disordered regions. We further implement a Triton-based fused decode attention kernel that eliminates intermediate dequantization memory allocations, achieving a 1.96x speedup over the PyTorch two-step path for the KV fetch operation alone; however, TurboESM incurs a prefill overhead of 21-27 ms relative to the original model due to KV quantization and packing, making it most suitable for memory-bound scenarios rather than latency-critical short-sequence workloads. Analysis reveals that PLMs exhibit sharper outlier profiles than large language models (LLMs) due to amino acid vocabulary sparsity, and our method effectively addresses these distributions.

Sparsity in the structure of Neural Networks can lead to less energy consumption, less memory usage, faster computation times on convenient hardware, and automated machine learning. If sparsity gives rise to certain kinds of structure, it can explain automatically obtained features during learning. We provide insights into experiments in which we show how sparsity can be achieved through prior initialization, pruning, and during learning, and answer questions on the relationship between the structure of Neural Networks and their performance. This includes the first work of inducing priors from network theory into Recurrent Neural Networks and an architectural performance prediction during a Neural Architecture Search. Within our experiments, we show how magnitude class blinded pruning achieves 97.5% on MNIST with 80% compression and re-training, which is 0.5 points more than without compression, that magnitude class uniform pruning is significantly inferior to it and how a genetic search enhanced with performance prediction achieves 82.4% on CIFAR10. Further, performance prediction for Recurrent Networks learning the Reber grammar shows an R^2 of up to 0.81 given only structural information.

We introduce a protein language model for determining the complete sequence of a peptide based on measurement of a limited set of amino acids. To date, protein sequencing relies on mass spectrometry, with some novel edman degregation based platforms able to sequence non-native peptides. Current protein sequencing techniques face limitations in accurately identifying all amino acids, hindering comprehensive proteome analysis. Our method simulates partial sequencing data by selectively masking amino acids that are experimentally difficult to identify in protein sequences from the UniRef database. This targeted masking mimics real-world sequencing limitations. We then modify and finetune a ProtBert derived transformer-based model, for a new downstream task predicting these masked residues, providing an approximation of the complete sequence. Evaluating on three bacterial Escherichia species, we achieve per-amino-acid accuracy up to 90.5% when only four amino acids ([KCYM]) are known. Structural assessment using AlphaFold and TM-score validates the biological relevance of our predictions. The model also demonstrates potential for evolutionary analysis through cross-species performance. This integration of simulated experimental constraints with computational predictions offers a promising avenue for enhancing protein sequence analysis, potentially accelerating advancements in proteomics and structural biology by providing a probabilistic reconstruction of the complete protein sequence from limited experimental data.

Exploiting sparsity underlying neural networks has become one of the most potential methodologies to reduce the memory footprint, I/O cost, and computation workloads during inference. And the degree of sparsity one can exploit has become higher as larger model sizes have been considered along with the trend of pre-training giant models. On the other hand, compared with quantization that has been a widely supported option, acceleration through high-degree sparsity is not supported in most computing platforms. In this work, we introduce the first commercial hardware platform supporting high-degree sparsity acceleration up to 32 times -- S4. Combined with state-of-the-art sparse pruning techniques, we demonstrate several-times practical inference speedup on S4 over mainstream inference platforms such as Nvidia T4. We also show that in practice a sparse model of larger size can achieve both higher accuracy and higher throughput on S4 than a dense model of smaller size.

N:M Structured sparsity has garnered significant interest as a result of relatively modest overhead and improved efficiency. Additionally, this form of sparsity holds considerable appeal for reducing the memory footprint owing to their modest representation overhead. There have been efforts to develop training recipes for N:M structured sparsity, they primarily focus on low-sparsity regions (sim50\%). Nonetheless, performance of models trained using these approaches tends to decline when confronted with high-sparsity regions (>80\%). In this work, we study the effectiveness of existing sparse training recipes at high-sparsity regions and argue that these methods fail to sustain the model quality on par with low-sparsity regions. We demonstrate that the significant factor contributing to this disparity is the presence of elevated levels of induced noise in the gradient magnitudes. To mitigate this undesirable effect, we employ decay mechanisms to progressively restrict the flow of gradients towards pruned elements. Our approach improves the model quality by up to 2% and 5% in vision and language models at high sparsity regime, respectively. We also evaluate the trade-off between model accuracy and training compute cost in terms of FLOPs. At iso-training FLOPs, our method yields better performance compared to conventional sparse training recipes, exhibiting an accuracy improvement of up to 2%. The source code is available at https://github.com/abhibambhaniya/progressive_gradient_flow_nm_sparsity.

The sparsity of labelled data is an obstacle to the development of Relation Extraction models and the completion of databases in various biomedical areas. While being of high interest in drug-discovery, the natural-products literature, reporting the identification of potential bioactive compounds from organisms, is a concrete example of such an overlooked topic. To mark the start of this new task, we created the first curated evaluation dataset and extracted literature items from the LOTUS database to build training sets. To this end, we developed a new sampler inspired by diversity metrics in ecology, named Greedy Maximum Entropy sampler, or GME-sampler (https://github.com/idiap/gme-sampler). The strategic optimization of both balance and diversity of the selected items in the evaluation set is important given the resource-intensive nature of manual curation. After quantifying the noise in the training set, in the form of discrepancies between the input abstracts text and the expected output labels, we explored different strategies accordingly. Framing the task as an end-to-end Relation Extraction, we evaluated the performance of standard fine-tuning as a generative task and few-shot learning with open Large Language Models (LLaMA 7B-65B). In addition to their evaluation in few-shot settings, we explore the potential of open Large Language Models (Vicuna-13B) as synthetic data generator and propose a new workflow for this purpose. All evaluated models exhibited substantial improvements when fine-tuned on synthetic abstracts rather than the original noisy data. We provide our best performing (f1-score=59.0) BioGPT-Large model for end-to-end RE of natural-products relationships along with all the generated synthetic data and the evaluation dataset. See more details at https://github.com/idiap/abroad-re.

Reinforcement learning (RL) yields substantial improvements in large language models (LLMs) downstream task performance and alignment with human values. Surprisingly, such large gains result from updating only a small subnetwork comprising just 5 percent to 30 percent of the parameters, with the rest effectively unchanged. We refer to this phenomenon as parameter update sparsity induced by RL. It is observed across all 7 widely used RL algorithms (e.g., PPO, GRPO, DPO) and all 10 LLMs from different families in our experiments. This sparsity is intrinsic and occurs without any explicit sparsity promoting regularizations or architectural constraints. Finetuning the subnetwork alone recovers the test accuracy, and, remarkably, produces a model nearly identical to the one obtained via full finetuning. The subnetworks from different random seeds, training data, and even RL algorithms show substantially greater overlap than expected by chance. Our analysis suggests that this sparsity is not due to updating only a subset of layers, instead, nearly all parameter matrices receive similarly sparse updates. Moreover, the updates to almost all parameter matrices are nearly full-rank, suggesting RL updates a small subset of parameters that nevertheless span almost the full subspaces that the parameter matrices can represent. We conjecture that the this update sparsity can be primarily attributed to training on data that is near the policy distribution, techniques that encourage the policy to remain close to the pretrained model, such as the KL regularization and gradient clipping, have limited impact.

Recent works have successfully demonstrated that sparse deep reinforcement learning agents can be competitive against their dense counterparts. This opens up opportunities for reinforcement learning applications in fields where inference time and memory requirements are cost-sensitive or limited by hardware. Until now, dense-to-sparse methods have relied on hand-designed sparsity schedules that are not synchronized with the agent's learning pace. Crucially, the final sparsity level is chosen as a hyperparameter, which requires careful tuning as setting it too high might lead to poor performances. In this work, we address these shortcomings by crafting a dense-to-sparse algorithm that we name Eau De Q-Network (EauDeQN). To increase sparsity at the agent's learning pace, we consider multiple online networks with different sparsity levels, where each online network is trained from a shared target network. At each target update, the online network with the smallest loss is chosen as the next target network, while the other networks are replaced by a pruned version of the chosen network. We evaluate the proposed approach on the Atari 2600 benchmark and the MuJoCo physics simulator, showing that EauDeQN reaches high sparsity levels while keeping performances high.

Sparse autoencoders (SAEs) have emerged as a powerful tool for interpreting neural networks by extracting the concepts represented in their activations. However, choosing the size of the SAE dictionary (i.e. number of learned concepts) creates a tension: as dictionary size increases to capture more relevant concepts, sparsity incentivizes features to be split or absorbed into more specific features, leaving high-level features missing or warped. We introduce Matryoshka SAEs, a novel variant that addresses these issues by simultaneously training multiple nested dictionaries of increasing size, forcing the smaller dictionaries to independently reconstruct the inputs without using the larger dictionaries. This organizes features hierarchically - the smaller dictionaries learn general concepts, while the larger dictionaries learn more specific concepts, without incentive to absorb the high-level features. We train Matryoshka SAEs on Gemma-2-2B and TinyStories and find superior performance on sparse probing and targeted concept erasure tasks, more disentangled concept representations, and reduced feature absorption. While there is a minor tradeoff with reconstruction performance, we believe Matryoshka SAEs are a superior alternative for practical tasks, as they enable training arbitrarily large SAEs while retaining interpretable features at different levels of abstraction.

With growing size of Neural Networks (NNs), model sparsification to reduce the computational cost and memory demand for model inference has become of vital interest for both research and production. While many sparsification methods have been proposed and successfully applied on individual models, to the best of our knowledge their behavior and robustness has not yet been studied on large populations of models. With this paper, we address that gap by applying two popular sparsification methods on populations of models (so called model zoos) to create sparsified versions of the original zoos. We investigate the performance of these two methods for each zoo, compare sparsification layer-wise, and analyse agreement between original and sparsified populations. We find both methods to be very robust with magnitude pruning able outperform variational dropout with the exception of high sparsification ratios above 80%. Further, we find sparsified models agree to a high degree with their original non-sparsified counterpart, and that the performance of original and sparsified model is highly correlated. Finally, all models of the model zoos and their sparsified model twins are publicly available: modelzoos.cc.

Sparse Autoencoders (SAEs) have emerged as a promising approach to decompose the activations of Large Language Models (LLMs) into human-interpretable latents. In this paper, we pose two questions. First, to what extent do SAEs extract monosemantic and interpretable latents? Second, to what extent does varying the sparsity or the size of the SAE affect monosemanticity / interpretability? By investigating these questions in the context of a simple first-letter identification task where we have complete access to ground truth labels for all tokens in the vocabulary, we are able to provide more detail than prior investigations. Critically, we identify a problematic form of feature-splitting we call feature absorption where seemingly monosemantic latents fail to fire in cases where they clearly should. Our investigation suggests that varying SAE size or sparsity is insufficient to solve this issue, and that there are deeper conceptual issues in need of resolution.

Obtaining versions of deep neural networks that are both highly-accurate and highly-sparse is one of the main challenges in the area of model compression, and several high-performance pruning techniques have been investigated by the community. Yet, much less is known about the interaction between sparsity and the standard stochastic optimization techniques used for training sparse networks, and most existing work uses standard dense schedules and hyperparameters for training sparse networks. In this work, we examine the impact of high sparsity on model training using the standard computer vision and natural language processing sparsity benchmarks. We begin by showing that using standard dense training recipes for sparse training is suboptimal, and results in under-training. We provide new approaches for mitigating this issue for both sparse pre-training of vision models (e.g. ResNet50/ImageNet) and sparse fine-tuning of language models (e.g. BERT/GLUE), achieving state-of-the-art results in both settings in the high-sparsity regime, and providing detailed analyses for the difficulty of sparse training in both scenarios. Our work sets a new threshold in terms of the accuracies that can be achieved under high sparsity, and should inspire further research into improving sparse model training, to reach higher accuracies under high sparsity, but also to do so efficiently.

As deep learning models grow, sparsity is becoming an increasingly critical component of deep neural networks, enabling improved performance and reduced storage. However, existing frameworks offer poor support for sparsity. Specialized sparsity engines focus exclusively on sparse inference, while general frameworks primarily focus on sparse tensors in classical formats and neglect the broader sparsification pipeline necessary for using sparse models, especially during training. Further, existing frameworks are not easily extensible: adding a new sparse tensor format or operator is challenging and time-consuming. To address this, we propose STen, a sparsity programming model and interface for PyTorch, which incorporates sparsity layouts, operators, and sparsifiers, in an efficient, customizable, and extensible framework that supports virtually all sparsification methods. We demonstrate this by developing a high-performance grouped n:m sparsity layout for CPU inference at moderate sparsity. STen brings high performance and ease of use to the ML community, making sparsity easily accessible.

Sparse neural networks have shown similar or better generalization performance than their dense counterparts while having higher parameter efficiency. This has motivated a number of works to learn or search for high performing sparse networks. While reports of task performance or efficiency gains are impressive, standard baselines are lacking leading to poor comparability and unreliable reproducibility across methods. In this work, we propose Random Search as a baseline algorithm for finding good sparse configurations and study its performance. We apply Random Search on the node space of an overparameterized network with the goal of finding better initialized sparse sub-networks that are positioned more advantageously in the loss landscape. We record the post-training performances of the found sparse networks and at various levels of sparsity, and compare against both their fully connected parent networks and random sparse configurations at the same sparsity levels. First, we demonstrate performance at different levels of sparsity and highlight that a significant level of performance can still be preserved even when the network is highly sparse. Second, we observe that for this sparse architecture search task, initialized sparse networks found by Random Search neither perform better nor converge more efficiently than their random counterparts. Thus we conclude that Random Search may be viewed as a reasonable neutral baseline for sparsity search methods.

This article does not propose any novel algorithm or new hardware for sparsity. Instead, it aims to serve the "common good" for the increasingly prosperous Sparse Neural Network (SNN) research community. We attempt to summarize some most common confusions in SNNs, that one may come across in various scenarios such as paper review/rebuttal and talks - many drawn from the authors' own bittersweet experiences! We feel that doing so is meaningful and timely, since the focus of SNN research is notably shifting from traditional pruning to more diverse and profound forms of sparsity before, during, and after training. The intricate relationships between their scopes, assumptions, and approaches lead to misunderstandings, for non-experts or even experts in SNNs. In response, we summarize ten Q\&As of SNNs from many key aspects, including dense vs. sparse, unstructured sparse vs. structured sparse, pruning vs. sparse training, dense-to-sparse training vs. sparse-to-sparse training, static sparsity vs. dynamic sparsity, before-training/during-training vs. post-training sparsity, and many more. We strive to provide proper and generically applicable answers to clarify those confusions to the best extent possible. We hope our summary provides useful general knowledge for people who want to enter and engage with this exciting community; and also provides some "mind of ease" convenience for SNN researchers to explain their work in the right contexts. At the very least (and perhaps as this article's most insignificant target functionality), if you are writing/planning to write a paper or rebuttal in the field of SNNs, we hope some of our answers could help you!

Despite their recent popularity and well-known advantages, dense retrievers still lag behind sparse methods such as BM25 in their ability to reliably match salient phrases and rare entities in the query and to generalize to out-of-domain data. It has been argued that this is an inherent limitation of dense models. We rebut this claim by introducing the Salient Phrase Aware Retriever (SPAR), a dense retriever with the lexical matching capacity of a sparse model. We show that a dense Lexical Model {\Lambda} can be trained to imitate a sparse one, and SPAR is built by augmenting a standard dense retriever with {\Lambda}. Empirically, SPAR shows superior performance on a range of tasks including five question answering datasets, MS MARCO passage retrieval, as well as the EntityQuestions and BEIR benchmarks for out-of-domain evaluation, exceeding the performance of state-of-the-art dense and sparse retrievers. The code and models of SPAR are available at: https://github.com/facebookresearch/dpr-scale/tree/main/spar

Growing evidence indicates that only a sparse subset from a pool of sensory neurons is active for the encoding of visual stimuli at any instant in time. Traditionally, to replicate such biological sparsity, generative models have been using the ell_1 norm as a penalty due to its convexity, which makes it amenable to fast and simple algorithmic solvers. In this work, we use biological vision as a test-bed and show that the soft thresholding operation associated to the use of the ell_1 norm is highly suboptimal compared to other functions suited to approximating ell_q with 0 leq q < 1 (including recently proposed Continuous Exact relaxations), both in terms of performance and in the production of features that are akin to signatures of the primary visual cortex. We show that ell_1 sparsity produces a denser code or employs a pool with more neurons, i.e. has a higher degree of overcompleteness, in order to maintain the same reconstruction error as the other methods considered. For all the penalty functions tested, a subset of the neurons develop orientation selectivity similarly to V1 neurons. When their code is sparse enough, the methods also develop receptive fields with varying functionalities, another signature of V1. Compared to other methods, soft thresholding achieves this level of sparsity at the expense of much degraded reconstruction performance, that more likely than not is not acceptable in biological vision. Our results indicate that V1 uses a sparsity inducing regularization that is closer to the ell_0 pseudo-norm rather than to the ell_1 norm.

Hamiltonian matrix prediction is pivotal in computational chemistry, serving as the foundation for determining a wide range of molecular properties. While SE(3) equivariant graph neural networks have achieved remarkable success in this domain, their substantial computational cost--driven by high-order tensor product (TP) operations--restricts their scalability to large molecular systems with extensive basis sets. To address this challenge, we introduce SPHNet, an efficient and scalable equivariant network, that incorporates adaptive SParsity into Hamiltonian prediction. SPHNet employs two innovative sparse gates to selectively constrain non-critical interaction combinations, significantly reducing tensor product computations while maintaining accuracy. To optimize the sparse representation, we develop a Three-phase Sparsity Scheduler, ensuring stable convergence and achieving high performance at sparsity rates of up to 70%. Extensive evaluations on QH9 and PubchemQH datasets demonstrate that SPHNet achieves state-of-the-art accuracy while providing up to a 7x speedup over existing models. Beyond Hamiltonian prediction, the proposed sparsification techniques also hold significant potential for improving the efficiency and scalability of other SE(3) equivariant networks, further broadening their applicability and impact. Our code can be found at https://github.com/microsoft/SPHNet.

Large language models (LLMs) have revolutionized Natural Language Processing (NLP), but their size creates computational bottlenecks. We introduce a novel approach to create accurate, sparse foundational versions of performant LLMs that achieve full accuracy recovery for fine-tuning tasks at up to 70% sparsity. We achieve this for the LLaMA-2 7B model by combining the SparseGPT one-shot pruning method and sparse pretraining of those models on a subset of the SlimPajama dataset mixed with a Python subset of The Stack dataset. We exhibit training acceleration due to sparsity on Cerebras CS-3 chips that closely matches theoretical scaling. In addition, we establish inference acceleration of up to 3x on CPUs by utilizing Neural Magic's DeepSparse engine and 1.7x on GPUs through Neural Magic's nm-vllm engine. The above gains are realized via sparsity alone, thus enabling further gains through additional use of quantization. Specifically, we show a total speedup on CPUs for sparse-quantized LLaMA models of up to 8.6x. We demonstrate these results across diverse, challenging tasks, including chat, instruction following, code generation, arithmetic reasoning, and summarization to prove their generality. This work paves the way for rapidly creating smaller and faster LLMs without sacrificing accuracy.

Large pre-trained transformers are show-stealer in modern-day deep learning, and it becomes crucial to comprehend the parsimonious patterns that exist within them as they grow in scale. With exploding parameter counts, Lottery Ticket Hypothesis (LTH) and its variants, have lost their pragmatism in sparsifying them due to high computation and memory bottleneck of repetitive train-prune-retrain routine of iterative magnitude pruning (IMP) which worsens with increasing model size. This paper comprehensively studies induced sparse patterns across multiple large pre-trained vision and language transformers. We propose the existence of -- essential sparsity defined with a sharp dropping point beyond which the performance declines much faster w.r.t the rise of sparsity level, when we directly remove weights with the smallest magnitudes in one-shot without re-training. We also find essential sparsity to hold valid for N:M sparsity patterns as well as on modern-scale large language models (Vicuna-7B). We also present an intriguing emerging phenomenon of abrupt sparsification during the pre-training of BERT, i.e., BERT suddenly becomes heavily sparse in pre-training after certain iterations. Moreover, our observations also indicate a counter-intuitive finding that BERT trained with a larger amount of pre-training data tends to have a better ability to condense knowledge in comparatively relatively fewer parameters. Lastly, we investigate the effect of the pre-training loss on essential sparsity and discover that self-supervised learning (SSL) objectives trigger stronger emergent sparsification properties than supervised learning (SL). Our codes are available at https://github.com/VITA-Group/essential_sparsity.

With the blossom of large language models (LLMs), inference efficiency becomes increasingly important. Various approximation methods are proposed to reduce the cost at inference time. Contextual Sparsity (CS) is appealing for its training-free nature and its ability to reach a higher compression ratio seemingly without quality degradation. However, after a comprehensive evaluation of contextual sparsity methods on various complex generation tasks, we find that although CS succeeds in prompt-understanding tasks, CS significantly degrades the model performance for reasoning, deduction, and knowledge-based tasks. Despite the gap in end-to-end accuracy, we observed that sparse models often share general problem-solving logic and require only a few token corrections to recover the original model performance. This paper introduces Sirius, an efficient correction mechanism, which significantly recovers CS models quality on reasoning tasks while maintaining its efficiency gain. Sirius is evaluated on 6 models with 8 difficult generation tasks in reasoning, math, and coding and shows consistent effectiveness and efficiency. Also, we carefully develop a system implementation for Sirius and show that Sirius achieves roughly 20% reduction in latency for 8B model on-chip and 35% reduction for 70B model offloading. We open-source our implementation of Sirius at https://github.com/Infini-AI-Lab/Sirius.git.

With the dramatically increased number of parameters in language models, sparsity methods have received ever-increasing research focus to compress and accelerate the models. While most research focuses on how to accurately retain appropriate weights while maintaining the performance of the compressed model, there are challenges in the computational overhead and memory footprint of sparse training when compressing large-scale language models. To address this problem, we propose a Parameter-efficient Sparse Training (PST) method to reduce the number of trainable parameters during sparse-aware training in downstream tasks. Specifically, we first combine the data-free and data-driven criteria to efficiently and accurately measure the importance of weights. Then we investigate the intrinsic redundancy of data-driven weight importance and derive two obvious characteristics i.e., low-rankness and structuredness. Based on that, two groups of small matrices are introduced to compute the data-driven importance of weights, instead of using the original large importance score matrix, which therefore makes the sparse training resource-efficient and parameter-efficient. Experiments with diverse networks (i.e., BERT, RoBERTa and GPT-2) on dozens of datasets demonstrate PST performs on par or better than previous sparsity methods, despite only training a small number of parameters. For instance, compared with previous sparsity methods, our PST only requires 1.5% trainable parameters to achieve comparable performance on BERT.

Identifying a small molecule from its mass spectrum is the primary open problem in computational metabolomics. This is typically cast as information retrieval: an unknown spectrum is matched against spectra predicted computationally from a large database of chemical structures. However, current approaches to spectrum prediction model the output space in ways that force a tradeoff between capturing high resolution mass information and tractable learning. We resolve this tradeoff by casting spectrum prediction as a mapping from an input molecular graph to a probability distribution over molecular formulas. We discover that a large corpus of mass spectra can be closely approximated using a fixed vocabulary constituting only 2% of all observed formulas. This enables efficient spectrum prediction using an architecture similar to graph classification - GrAFF-MS - achieving significantly lower prediction error and orders-of-magnitude faster runtime than state-of-the-art methods.

Neural networks can be significantly compressed by pruning, yielding sparse models with reduced storage and computational demands while preserving predictive performance. Model soups (Wortsman et al., 2022) enhance generalization and out-of-distribution (OOD) performance by averaging the parameters of multiple models into a single one, without increasing inference time. However, achieving both sparsity and parameter averaging is challenging as averaging arbitrary sparse models reduces the overall sparsity due to differing sparse connectivities. This work addresses these challenges by demonstrating that exploring a single retraining phase of Iterative Magnitude Pruning (IMP) with varied hyperparameter configurations such as batch ordering or weight decay yields models suitable for averaging, sharing identical sparse connectivity by design. Averaging these models significantly enhances generalization and OOD performance over their individual counterparts. Building on this, we introduce Sparse Model Soups (SMS), a novel method for merging sparse models by initiating each prune-retrain cycle with the averaged model from the previous phase. SMS preserves sparsity, exploits sparse network benefits, is modular and fully parallelizable, and substantially improves IMP's performance. We further demonstrate that SMS can be adapted to enhance state-of-the-art pruning-during-training approaches.

We consider the problem of accurate sparse finetuning of large language models (LLMs), that is, finetuning pretrained LLMs on specialized tasks, while inducing sparsity in their weights. On the accuracy side, we observe that standard loss-based finetuning may fail to recover accuracy, especially at high sparsities. To address this, we perform a detailed study of distillation-type losses, determining an L2-based distillation approach we term SquareHead which enables accurate recovery even at higher sparsities, across all model types. On the practical efficiency side, we show that sparse LLMs can be executed with speedups by taking advantage of sparsity, for both CPU and GPU runtimes. While the standard approach is to leverage sparsity for computational reduction, we observe that in the case of memory-bound LLMs sparsity can also be leveraged for reducing memory bandwidth. We exhibit end-to-end results showing speedups due to sparsity, while recovering accuracy, on T5 (language translation), Whisper (speech translation), and open GPT-type (MPT for text generation). For MPT text generation, we show for the first time that sparse finetuning can reach 75% sparsity without accuracy drops, provide notable end-to-end speedups for both CPU and GPU inference, and highlight that sparsity is also compatible with quantization approaches. Models and software for reproducing our results are provided in Section 6.

Open-domain question answering can be formulated as a phrase retrieval problem, in which we can expect huge scalability and speed benefit but often suffer from low accuracy due to the limitation of existing phrase representation models. In this paper, we aim to improve the quality of each phrase embedding by augmenting it with a contextualized sparse representation (Sparc). Unlike previous sparse vectors that are term-frequency-based (e.g., tf-idf) or directly learned (only few thousand dimensions), we leverage rectified self-attention to indirectly learn sparse vectors in n-gram vocabulary space. By augmenting the previous phrase retrieval model (Seo et al., 2019) with Sparc, we show 4%+ improvement in CuratedTREC and SQuAD-Open. Our CuratedTREC score is even better than the best known retrieve & read model with at least 45x faster inference speed.

Recent works have explored the use of weight sparsity to improve the training efficiency (test accuracy w.r.t training FLOPs) of deep neural networks (DNNs). These works aim to reduce training FLOPs but training with sparse weights often leads to accuracy loss or requires longer training schedules, making the resulting training efficiency less clear. In contrast, we focus on using sparsity to increase accuracy while using the same FLOPs as the dense model and show training efficiency gains through higher accuracy. In this work, we introduce Sparse-IFT, a family of Sparse Iso-FLOP Transformations which are used as drop-in replacements for dense layers to improve their representational capacity and FLOP efficiency. Each transformation is parameterized by a single hyperparameter (sparsity level) and provides a larger search space to find optimal sparse masks. Without changing any training hyperparameters, replacing dense layers with Sparse-IFT leads to significant improvements across computer vision (CV) and natural language processing (NLP) tasks, including ResNet-18 on ImageNet (+3.5%) and GPT-3 Small on WikiText-103 (-0.4 PPL), both matching larger dense model variants that use 2x or more FLOPs. To our knowledge, this is the first work to demonstrate the use of sparsity for improving the accuracy of dense models via a simple-to-use set of sparse transformations. Code is available at: https://github.com/CerebrasResearch/Sparse-IFT.

Overparameterized neural networks generalize well but are expensive to train. Ideally, one would like to reduce their computational cost while retaining their generalization benefits. Sparse model training is a simple and promising approach to achieve this, but there remain challenges as existing methods struggle with accuracy loss, slow training runtime, or difficulty in sparsifying all model components. The core problem is that searching for a sparsity mask over a discrete set of sparse matrices is difficult and expensive. To address this, our main insight is to optimize over a continuous superset of sparse matrices with a fixed structure known as products of butterfly matrices. As butterfly matrices are not hardware efficient, we propose simple variants of butterfly (block and flat) to take advantage of modern hardware. Our method (Pixelated Butterfly) uses a simple fixed sparsity pattern based on flat block butterfly and low-rank matrices to sparsify most network layers (e.g., attention, MLP). We empirically validate that Pixelated Butterfly is 3x faster than butterfly and speeds up training to achieve favorable accuracy--efficiency tradeoffs. On the ImageNet classification and WikiText-103 language modeling tasks, our sparse models train up to 2.5x faster than the dense MLP-Mixer, Vision Transformer, and GPT-2 medium with no drop in accuracy.

State-of-the-art Learned Sparse Retrieval (LSR) models, such as Splade, typically employ a Language Modeling (LM) head to project latent hidden states into a lexically-anchored logit matrix. This intermediate matrix is subsequently transformed into a sparse lexical representation through element-wise operations (ReLU, Log1P) and max-pooling over the sequence dimension. Despite its effectiveness, the LM head creates a massive memory bottleneck due to the sheer size of the vocabulary (V), which can range from 30,000 to over 250,000 tokens in recent models. Materializing this matrix creates a significant memory bottleneck, limiting model scaling. The resulting I/O overhead between operators further throttles throughput and runtime performance. In this paper, we propose Sparton, a fast memory-efficient Triton kernel tailored for the LM head in LSR models. Sparton utilizes a fused approach that integrates the tiled matrix multiplication, ReLU, Log1P, and max-reduction into a single GPU kernel. By performing an early online reduction directly on raw logit tiles, Sparton avoids materializing the full logit matrix in memory. Our experiments demonstrate that the Sparton kernel, in isolation, achieves up to a 4.8x speedup and an order-of-magnitude reduction in peak memory usage compared to PyTorch baselines. Integrated into Splade (|V| ~ 30k), Sparton enables a 33% larger batch size and 14% faster training with no effectiveness loss. On a multilingual backbone (|V| ~ 250k), these gains jump to a 26x larger batch size and 2.5x faster training.

Recently, the study of linear misspecified bandits has generated intriguing implications of the hardness of learning in bandits and reinforcement learning (RL). In particular, Du et al. (2020) show that even if a learner is given linear features in R^d that approximate the rewards in a bandit or RL with a uniform error of varepsilon, searching for an O(varepsilon)-optimal action requires pulling at least Omega(exp(d)) queries. Furthermore, Lattimore et al. (2020) show that a degraded O(varepsilond)-optimal solution can be learned within poly(d/varepsilon) queries. Yet it is unknown whether a structural assumption on the ground-truth parameter, such as sparsity, could break the varepsilond barrier. In this paper, we address this question by showing that algorithms can obtain O(varepsilon)-optimal actions by querying O(varepsilon^{-s}d^s) actions, where s is the sparsity parameter, removing the exp(d)-dependence. We then establish information-theoretical lower bounds, i.e., Omega(exp(s)), to show that our upper bound on sample complexity is nearly tight if one demands an error O(s^{delta}varepsilon) for 0<delta<1. For deltageq 1, we further show that poly(s/varepsilon) queries are possible when the linear features are "good" and even in general settings. These results provide a nearly complete picture of how sparsity can help in misspecified bandit learning and provide a deeper understanding of when linear features are "useful" for bandit and reinforcement learning with misspecification.

The growing demand for long-context inference capabilities in Large Language Models (LLMs) has intensified the computational and memory bottlenecks inherent to the standard attention mechanism. To address this challenge, we introduce BLASST, a drop-in sparse attention method that dynamically prunes the attention matrix without any pre-computation or proxy scores. Our method uses a fixed threshold and existing information from online softmax to identify negligible attention scores, skipping softmax computation, Value block loading, and the subsequent matrix multiplication. This fits seamlessly into existing FlashAttention kernel designs with negligible latency overhead. The approach is applicable to both prefill and decode stages across all attention variants (MHA, GQA, MQA, and MLA), providing a unified solution for accelerating long-context inference. We develop an automated calibration procedure that reveals a simple inverse relationship between optimal threshold and context length, enabling robust deployment across diverse scenarios. Maintaining high accuracy, we demonstrate a 1.62x speedup for prefill at 74.7% sparsity and a 1.48x speedup for decode at 73.2% sparsity on modern GPUs. Furthermore, we explore sparsity-aware training as a natural extension, showing that models can be trained to be inherently more robust to sparse attention patterns, pushing the accuracy-sparsity frontier even further.

Protein design, a grand challenge of the day, involves optimization on a fitness landscape, and leading methods adopt a model-based approach where a model is trained on a training set (protein sequences and fitness) and proposes candidates to explore next. These methods are challenged by sparsity of high-fitness samples in the training set, a problem that has been in the literature. A less recognized but equally important problem stems from the distribution of training samples in the design space: leading methods are not designed for scenarios where the desired optimum is in a region that is not only poorly represented in training data, but also relatively far from the highly represented low-fitness regions. We show that this problem of "separation" in the design space is a significant bottleneck in existing model-based optimization tools and propose a new approach that uses a novel VAE as its search model to overcome the problem. We demonstrate its advantage over prior methods in robustly finding improved samples, regardless of the imbalance and separation between low- and high-fitness training samples. Our comprehensive benchmark on real and semi-synthetic protein datasets as well as solution design for physics-informed neural networks, showcases the generality of our approach in discrete and continuous design spaces. Our implementation is available at https://github.com/sabagh1994/PGVAE.

Sparse linear regression is one of the most basic questions in machine learning and statistics. Here, we are given as input a design matrix X in R^{N times d} and measurements or labels {y} in R^N where {y} = {X} {w}^* + {xi}, and {xi} is the noise in the measurements. Importantly, we have the additional constraint that the unknown signal vector {w}^* is sparse: it has k non-zero entries where k is much smaller than the ambient dimension. Our goal is to output a prediction vector {w} that has small prediction error: 1{N}cdot |{X} {w}^* - {X} {w}|^2_2. Information-theoretically, we know what is best possible in terms of measurements: under most natural noise distributions, we can get prediction error at most epsilon with roughly N = O(k log d/epsilon) samples. Computationally, this currently needs d^{Omega(k)} run-time. Alternately, with N = O(d), we can get polynomial-time. Thus, there is an exponential gap (in the dependence on d) between the two and we do not know if it is possible to get d^{o(k)} run-time and o(d) samples. We give the first generic positive result for worst-case design matrices {X}: For any {X}, we show that if the support of {w}^* is chosen at random, we can get prediction error epsilon with N = poly(k, log d, 1/epsilon) samples and run-time poly(d,N). This run-time holds for any design matrix {X} with condition number up to 2^{poly(d)}. Previously, such results were known for worst-case {w}^*, but only for random design matrices from well-behaved families, matrices that have a very low condition number (poly(log d); e.g., as studied in compressed sensing), or those with special structural properties.

Term-based sparse representations dominate the first-stage text retrieval in industrial applications, due to its advantage in efficiency, interpretability, and exact term matching. In this paper, we study the problem of transferring the deep knowledge of the pre-trained language model (PLM) to Term-based Sparse representations, aiming to improve the representation capacity of bag-of-words(BoW) method for semantic-level matching, while still keeping its advantages. Specifically, we propose a novel framework SparTerm to directly learn sparse text representations in the full vocabulary space. The proposed SparTerm comprises an importance predictor to predict the importance for each term in the vocabulary, and a gating controller to control the term activation. These two modules cooperatively ensure the sparsity and flexibility of the final text representation, which unifies the term-weighting and expansion in the same framework. Evaluated on MSMARCO dataset, SparTerm significantly outperforms traditional sparse methods and achieves state of the art ranking performance among all the PLM-based sparse models.

Sparse autoencoders (SAEs) are a useful tool for uncovering human-interpretable features in the activations of large language models (LLMs). While some expect SAEs to find the true underlying features used by a model, our research shows that SAEs trained on the same model and data, differing only in the random seed used to initialize their weights, identify different sets of features. For example, in an SAE with 131K latents trained on a feedforward network in Llama 3 8B, only 30% of the features were shared across different seeds. We observed this phenomenon across multiple layers of three different LLMs, two datasets, and several SAE architectures. While ReLU SAEs trained with the L1 sparsity loss showed greater stability across seeds, SAEs using the state-of-the-art TopK activation function were more seed-dependent, even when controlling for the level of sparsity. Our results suggest that the set of features uncovered by an SAE should be viewed as a pragmatically useful decomposition of activation space, rather than an exhaustive and universal list of features "truly used" by the model.

Large language models have become the cornerstone of natural language processing, but their use comes with substantial costs in terms of compute and memory resources. Sparsification provides a solution to alleviate these resource constraints, and recent works have shown that trained models can be sparsified post-hoc. Existing sparsification techniques face challenges as they need additional data structures and offer constrained speedup with current hardware. In this paper we present SliceGPT, a new post-training sparsification scheme which replaces each weight matrix with a smaller (dense) matrix, reducing the embedding dimension of the network. Through extensive experimentation, we show that SliceGPT can remove up to 25% of the model parameters (including embeddings) for LLAMA2-70B, OPT 66B and Phi-2 models while maintaining 99%, 99% and 90% zero-shot task performance of the dense model respectively. Our sliced models run on fewer GPUs and run faster without any additional code optimization: on 24GB consumer GPUs we reduce the total compute for inference on LLAMA2-70B to 64% of that of the dense model; on 40GB A100 GPUs we reduce it to 66%. We offer a new insight, computational invariance in transformer networks, which enables SliceGPT and we hope it will inspire and enable future avenues to reduce memory and computation demands for pre-trained models. Code is available at: https://github.com/microsoft/TransformerCompression

Sparse neural networks are a key factor in developing resource-efficient machine learning applications. We propose the novel and powerful sparse learning method Adaptive Regularized Training (ART) to compress dense into sparse networks. Instead of the commonly used binary mask during training to reduce the number of model weights, we inherently shrink weights close to zero in an iterative manner with increasing weight regularization. Our method compresses the pre-trained model knowledge into the weights of highest magnitude. Therefore, we introduce a novel regularization loss named HyperSparse that exploits the highest weights while conserving the ability of weight exploration. Extensive experiments on CIFAR and TinyImageNet show that our method leads to notable performance gains compared to other sparsification methods, especially in extremely high sparsity regimes up to 99.8 percent model sparsity. Additional investigations provide new insights into the patterns that are encoded in weights with high magnitudes.

This paper introduces Sparsified Late Interaction for Multi-vector (SLIM) retrieval with inverted indexes. Multi-vector retrieval methods have demonstrated their effectiveness on various retrieval datasets, and among them, ColBERT is the most established method based on the late interaction of contextualized token embeddings of pre-trained language models. However, efficient ColBERT implementations require complex engineering and cannot take advantage of off-the-shelf search libraries, impeding their practical use. To address this issue, SLIM first maps each contextualized token vector to a sparse, high-dimensional lexical space before performing late interaction between these sparse token embeddings. We then introduce an efficient two-stage retrieval architecture that includes inverted index retrieval followed by a score refinement module to approximate the sparsified late interaction, which is fully compatible with off-the-shelf lexical search libraries such as Lucene. SLIM achieves competitive accuracy on MS MARCO Passages and BEIR compared to ColBERT while being much smaller and faster on CPUs. To our knowledge, we are the first to explore using sparse token representations for multi-vector retrieval. Source code and data are integrated into the Pyserini IR toolkit.

Optimal transport (OT) theory focuses, among all maps T:R^drightarrow R^d that can morph a probability measure onto another, on those that are the ``thriftiest'', i.e. such that the averaged cost c(x, T(x)) between x and its image T(x) be as small as possible. Many computational approaches have been proposed to estimate such Monge maps when c is the ell_2^2 distance, e.g., using entropic maps [Pooladian'22], or neural networks [Makkuva'20, Korotin'20]. We propose a new model for transport maps, built on a family of translation invariant costs c(x, y):=h(x-y), where h:=1{2}|cdot|_2^2+tau and tau is a regularizer. We propose a generalization of the entropic map suitable for h, and highlight a surprising link tying it with the Bregman centroids of the divergence D_h generated by h, and the proximal operator of tau. We show that choosing a sparsity-inducing norm for tau results in maps that apply Occam's razor to transport, in the sense that the displacement vectors Delta(x):= T(x)-x they induce are sparse, with a sparsity pattern that varies depending on x. We showcase the ability of our method to estimate meaningful OT maps for high-dimensional single-cell transcription data, in the 34000-d space of gene counts for cells, without using dimensionality reduction, thus retaining the ability to interpret all displacements at the gene level.

Recently, it has been observed that when representations are learnt in a way that encourages sparsity, improved performance is obtained on classification tasks. These methods involve combinations of activation functions, sampling steps and different kinds of penalties. To investigate the effectiveness of sparsity by itself, we propose the k-sparse autoencoder, which is an autoencoder with linear activation function, where in hidden layers only the k highest activities are kept. When applied to the MNIST and NORB datasets, we find that this method achieves better classification results than denoising autoencoders, networks trained with dropout, and RBMs. k-sparse autoencoders are simple to train and the encoding stage is very fast, making them well-suited to large problem sizes, where conventional sparse coding algorithms cannot be applied.

Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the analysis of protein composition in biological samples. Despite the development of various deep learning methods for identifying amino acid sequences (peptides) responsible for observed spectra, challenges persist in de novo peptide sequencing. Firstly, prior methods struggle to identify amino acids with post-translational modifications (PTMs) due to their lower frequency in training data compared to canonical amino acids, further resulting in decreased peptide-level identification precision. Secondly, diverse types of noise and missing peaks in mass spectra reduce the reliability of training data (peptide-spectrum matches, PSMs). To address these challenges, we propose AdaNovo, a novel framework that calculates conditional mutual information (CMI) between the spectrum and each amino acid/peptide, using CMI for adaptive model training. Extensive experiments demonstrate AdaNovo's state-of-the-art performance on a 9-species benchmark, where the peptides in the training set are almost completely disjoint from the peptides of the test sets. Moreover, AdaNovo excels in identifying amino acids with PTMs and exhibits robustness against data noise. The supplementary materials contain the official code.

Sparsity in Deep Neural Networks (DNNs) has been widely studied to compress and accelerate the models on resource-constrained environments. It can be generally categorized into unstructured fine-grained sparsity that zeroes out multiple individual weights distributed across the neural network, and structured coarse-grained sparsity which prunes blocks of sub-networks of a neural network. Fine-grained sparsity can achieve a high compression ratio but is not hardware friendly and hence receives limited speed gains. On the other hand, coarse-grained sparsity cannot concurrently achieve both apparent acceleration on modern GPUs and decent performance. In this paper, we are the first to study training from scratch an N:M fine-grained structured sparse network, which can maintain the advantages of both unstructured fine-grained sparsity and structured coarse-grained sparsity simultaneously on specifically designed GPUs. Specifically, a 2:4 sparse network could achieve 2x speed-up without performance drop on Nvidia A100 GPUs. Furthermore, we propose a novel and effective ingredient, sparse-refined straight-through estimator (SR-STE), to alleviate the negative influence of the approximated gradients computed by vanilla STE during optimization. We also define a metric, Sparse Architecture Divergence (SAD), to measure the sparse network's topology change during the training process. Finally, We justify SR-STE's advantages with SAD and demonstrate the effectiveness of SR-STE by performing comprehensive experiments on various tasks. Source codes and models are available at https://github.com/NM-sparsity/NM-sparsity.

Speculative decoding accelerates autoregressive language model inference by verifying multiple draft tokens in parallel. However, the verification stage often becomes the dominant computational bottleneck, especially for long-context inputs and mixture-of-experts (MoE) models. Existing sparsification methods are designed primarily for standard token-by-token autoregressive decoding to remove substantial computational redundancy in LLMs. This work systematically adopts different sparse methods on the verification stage of the speculative decoding and identifies structured redundancy across multiple dimensions. Based on these observations, we propose a sparse verification framework that jointly sparsifies attention, FFN, and MoE components during the verification stage to reduce the dominant computation cost. The framework further incorporates an inter-draft token and inter-layer retrieval reuse strategy to further reduce redundant computation without introducing additional training. Extensive experiments across summarization, question answering, and mathematical reasoning datasets demonstrate that the proposed methods achieve favorable efficiency-accuracy trade-offs, while maintaining stable acceptance length.

Random masks define surprisingly effective sparse neural network models, as has been shown empirically. The resulting sparse networks can often compete with dense architectures and state-of-the-art lottery ticket pruning algorithms, even though they do not rely on computationally expensive prune-train iterations and can be drawn initially without significant computational overhead. We offer a theoretical explanation of how random masks can approximate arbitrary target networks if they are wider by a logarithmic factor in the inverse sparsity 1 / log(1/sparsity). This overparameterization factor is necessary at least for 3-layer random networks, which elucidates the observed degrading performance of random networks at higher sparsity. At moderate to high sparsity levels, however, our results imply that sparser networks are contained within random source networks so that any dense-to-sparse training scheme can be turned into a computationally more efficient sparse-to-sparse one by constraining the search to a fixed random mask. We demonstrate the feasibility of this approach in experiments for different pruning methods and propose particularly effective choices of initial layer-wise sparsity ratios of the random source network. As a special case, we show theoretically and experimentally that random source networks also contain strong lottery tickets.

Sparse Autoencoders (SAEs) have proven to be powerful tools for interpreting neural networks by decomposing hidden representations into disentangled, interpretable features via sparsity constraints. However, conventional SAEs are constrained by the fixed sparsity level chosen during training; meeting different sparsity requirements therefore demands separate models and increases the computational footprint during both training and evaluation. We introduce a novel training objective, HierarchicalTopK, which trains a single SAE to optimise reconstructions across multiple sparsity levels simultaneously. Experiments with Gemma-2 2B demonstrate that our approach achieves Pareto-optimal trade-offs between sparsity and explained variance, outperforming traditional SAEs trained at individual sparsity levels. Further analysis shows that HierarchicalTopK preserves high interpretability scores even at higher sparsity. The proposed objective thus closes an important gap between flexibility and interpretability in SAE design.

Activation sparsity can enable practical inference speedups in large language models (LLMs) by reducing the compute and memory-movement required for matrix multiplications during the forward pass. However, existing methods face limitations that inhibit widespread adoption. Some approaches are tailored towards older models with ReLU-based sparsity, while others require extensive continued pre-training on up to hundreds of billions of tokens. This paper describes TEAL, a simple training-free method that applies magnitude-based activation sparsity to hidden states throughout the entire model. TEAL achieves 40-50% model-wide sparsity with minimal performance degradation across Llama-2, Llama-3, and Mistral families, with sizes varying from 7B to 70B. We improve existing sparse kernels and demonstrate wall-clock decoding speed-ups of up to 1.53times and 1.8times at 40% and 50% model-wide sparsity. TEAL is compatible with weight quantization, enabling further efficiency gains.

In this work, we investigate how Large Language Models (LLMs) adapt their internal representations when encountering inputs of increasing difficulty, quantified as the degree of out-of-distribution (OOD) shift. We reveal a consistent and quantifiable phenomenon: as task difficulty increases, whether through harder reasoning questions, longer contexts, or adding answer choices, the last hidden states of LLMs become substantially sparser. In short, \textit{the farther the shift, the sparser the representations}. This sparsity--difficulty relation is observable across diverse models and domains, suggesting that language models respond to unfamiliar or complex inputs by concentrating computation into specialized subspaces in the last hidden state. Through a series of controlled analyses with a learning dynamic explanation, we demonstrate that this sparsity is not incidental but an adaptive mechanism for stabilizing reasoning under OOD. Leveraging this insight, we design Sparsity-Guided Curriculum In-Context Learning (SG-ICL), a strategy that explicitly uses representation sparsity to schedule few-shot demonstrations, leading to considerable performance enhancements. Our study provides new mechanistic insights into how LLMs internalize OOD challenges. The source code is available at the URL: https://github.com/MingyuJ666/sparsityLLM.

Large Language Models (LLMs) have become pivotal in advancing the field of artificial intelligence, yet their immense sizes pose significant challenges for both fine-tuning and deployment. Current post-training pruning methods, while reducing the sizes of LLMs, often fail to maintain their original performance. To address these challenges, this paper introduces SPP, a Sparsity-Preserved Parameter-efficient fine-tuning method. Different from existing post-training pruning approaches that struggle with performance retention, SPP proposes to employ lightweight learnable column and row matrices to optimize sparse LLM weights, keeping the structure and sparsity of pruned pre-trained models intact. By element-wise multiplication and residual addition, SPP ensures the consistency of model sparsity pattern and ratio during both training and weight-merging processes. We demonstrate the effectiveness of SPP by applying it to the LLaMA and LLaMA-2 model families with recent post-training pruning methods. Our results show that SPP significantly enhances the performance of models with different sparsity patterns (i.e. unstructured and N:M sparsity), especially for those with high sparsity ratios (e.g. 75%), making it a promising solution for the efficient fine-tuning of sparse LLMs. Code will be made available at https://github.com/Lucky-Lance/SPP.

Predicting protein function from amino acid sequence remains a central challenge in data-scarce (low-N) regimes, limiting machine learning-guided protein design when only small amounts of assay-labeled sequence-function data are available. Protein language models (pLMs) have advanced the field by providing evolutionary-informed embeddings and sparse autoencoders (SAEs) have enabled decomposition of these embeddings into interpretable latent variables that capture structural and functional features. However, the effectiveness of SAEs for low-N function prediction and protein design has not been systematically studied. Herein, we evaluate SAEs trained on fine-tuned ESM2 embeddings across diverse fitness extrapolation and protein engineering tasks. We show that SAEs, with as few as 24 sequences, consistently outperform or compete with their ESM2 baselines in fitness prediction, indicating that their sparse latent space encodes compact and biologically meaningful representations that generalize more effectively from limited data. Moreover, steering predictive latents exploits biological motifs in pLM representations, yielding top-fitness variants in 83% of cases compared to designing with ESM2 alone.

We introduce, Q-Sparse, a simple yet effective approach to training sparsely-activated large language models (LLMs). Q-Sparse enables full sparsity of activations in LLMs which can bring significant efficiency gains in inference. This is achieved by applying top-K sparsification to the activations and the straight-through-estimator to the training. The key results from this work are, (1) Q-Sparse can achieve results comparable to those of baseline LLMs while being much more efficient at inference time; (2) We present an inference-optimal scaling law for sparsely-activated LLMs; (3) Q-Sparse is effective in different settings, including training-from-scratch, continue-training of off-the-shelf LLMs, and finetuning; (4) Q-Sparse works for both full-precision and 1-bit LLMs (e.g., BitNet b1.58). Particularly, the synergy of BitNet b1.58 and Q-Sparse (can be equipped with MoE) provides the cornerstone and a clear path to revolutionize the efficiency, including cost and energy consumption, of future LLMs.

The demand for efficient processing of deep neural networks (DNNs) on embedded devices is a significant challenge limiting their deployment. Exploiting sparsity in the network's feature maps is one of the ways to reduce its inference latency. It is known that unstructured sparsity results in lower accuracy degradation with respect to structured sparsity but the former needs extensive inference engine changes to get latency benefits. To tackle this challenge, we propose a solution to induce semi-structured activation sparsity exploitable through minor runtime modifications. To attain high speedup levels at inference time, we design a sparse training procedure with awareness of the final position of the activations while computing the General Matrix Multiplication (GEMM). We extensively evaluate the proposed solution across various models for image classification and object detection tasks. Remarkably, our approach yields a speed improvement of 1.25 times with a minimal accuracy drop of 1.1% for the ResNet18 model on the ImageNet dataset. Furthermore, when combined with a state-of-the-art structured pruning method, the resulting models provide a good latency-accuracy trade-off, outperforming models that solely employ structured pruning techniques.

Activation sparsity denotes the existence of substantial weakly-contributed elements within activation outputs that can be eliminated, benefiting many important applications concerned with large language models (LLMs). Although promoting greater activation sparsity within LLMs deserves deep studies, existing works lack comprehensive and quantitative research on the correlation between activation sparsity and potentially influential factors. In this paper, we present a comprehensive study on the quantitative scaling properties and influential factors of the activation sparsity within decoder-only Transformer-based LLMs. Specifically, we propose PPL-p% sparsity, a precise and performance-aware activation sparsity metric that is applicable to any activation function. Through extensive experiments, we find several important phenomena. Firstly, different activation functions exhibit comparable performance but opposite training-time sparsity trends. The activation ratio (i.e., 1-sparsity ratio) evolves as a convergent increasing power-law and decreasing logspace power-law with the amount of training data for SiLU-activated and ReLU-activated LLMs, respectively. These demonstrate that ReLU is more efficient as the activation function than SiLU and can leverage more training data to improve activation sparsity. Secondly, the activation ratio linearly increases with the width-depth ratio below a certain bottleneck point, indicating the potential advantage of a deeper architecture at a fixed parameter scale. Finally, at similar width-depth ratios, we surprisingly find that the limit value of activation sparsity varies weakly with the parameter scale, i.e., the activation patterns within LLMs are insensitive to the parameter scale. These empirical laws towards LLMs with greater activation sparsity have important implications for making LLMs more efficient and interpretable.

We introduce Nerva, a fast neural network library under development in C++. It supports sparsity by using the sparse matrix operations of Intel's Math Kernel Library (MKL), which eliminates the need for binary masks. We show that Nerva significantly decreases training time and memory usage while reaching equivalent accuracy to PyTorch. We run static sparse experiments with an MLP on CIFAR-10. On high sparsity levels like 99%, the runtime is reduced by a factor of 4times compared to a PyTorch model using masks. Similar to other popular frameworks such as PyTorch and Keras, Nerva offers a Python interface for users to work with.

Sparse expert models are a thirty-year old concept re-emerging as a popular architecture in deep learning. This class of architecture encompasses Mixture-of-Experts, Switch Transformers, Routing Networks, BASE layers, and others, all with the unifying idea that each example is acted on by a subset of the parameters. By doing so, the degree of sparsity decouples the parameter count from the compute per example allowing for extremely large, but efficient models. The resulting models have demonstrated significant improvements across diverse domains such as natural language processing, computer vision, and speech recognition. We review the concept of sparse expert models, provide a basic description of the common algorithms, contextualize the advances in the deep learning era, and conclude by highlighting areas for future work.

Large language models (LLMs) deliver impressive performance but incur prohibitive memory and compute costs at deployment. Model pruning is an effective way to reduce these overheads, yet existing approaches face challenges: unstructured sparsity, where nonzeros can appear anywhere, preserves accuracy but yields irregular access patterns that prevent GPU acceleration, while semi-structured 2:4 sparsity is hardware-friendly but enforces a rigid 50% pattern that degrades model quality. To bridge this gap, we introduce PATCH, a hybrid sparsity framework that enables a continuous sparsity ratio between 0% and 50%. PATCH partitions weight matrices into tiles, assigning each tile to be either dense or 2:4 sparse via a learnable mask selection mechanism. This design provides fine-grained control over accuracy-acceleration tradeoffs and supports non-uniform sparsity across layers, leading to superior overall quality. Across models from 0.5B to 8B parameters, PATCH consistently narrows the gap to dense accuracy while delivering practical speedups. For instance, on LLaMA-2 7B with an A6000 GPU, PATCH achieves 1.18x-1.38x end-to-end speedup over dense baselines while improving accuracy by 0.37%-2.96% compared to the state-of-the-art 2:4 pruning method, MaskLLM.

We explore leveraging corpus-specific vocabularies that improve both efficiency and effectiveness of learned sparse retrieval systems. We find that pre-training the underlying BERT model on the target corpus, specifically targeting different vocabulary sizes incorporated into the document expansion process, improves retrieval quality by up to 12% while in some scenarios decreasing latency by up to 50%. Our experiments show that adopting corpus-specific vocabulary and increasing vocabulary size decreases average postings list length which in turn reduces latency. Ablation studies show interesting interactions between custom vocabularies, document expansion techniques, and sparsification objectives of sparse models. Both effectiveness and efficiency improvements transfer to different retrieval approaches such as uniCOIL and SPLADE and offer a simple yet effective approach to providing new efficiency-effectiveness trade-offs for learned sparse retrieval systems.

With the latest advances in deep learning, there has been a lot of focus on the online learning paradigm due to its relevance in practical settings. Although many methods have been investigated for optimal learning settings in scenarios where the data stream is continuous over time, sparse networks training in such settings have often been overlooked. In this paper, we explore the problem of training a neural network with a target sparsity in a particular case of online learning: the anytime learning at macroscale paradigm (ALMA). We propose a novel way of progressive pruning, referred to as Anytime Progressive Pruning (APP); the proposed approach significantly outperforms the baseline dense and Anytime OSP models across multiple architectures and datasets under short, moderate, and long-sequence training. Our method, for example, shows an improvement in accuracy of approx 7% and a reduction in the generalization gap by approx 22%, while being approx 1/3 rd the size of the dense baseline model in few-shot restricted imagenet training. We further observe interesting nonmonotonic transitions in the generalization gap in the high number of megabatches-based ALMA. The code and experiment dashboards can be accessed at https://github.com/landskape-ai/Progressive-Pruning and https://wandb.ai/landskape/APP, respectively.

The inference process for large language models is slow and memory-intensive, with one of the most critical bottlenecks being excessive Key-Value (KV) cache accesses. This paper introduces "Double Sparsity," a novel post-training sparse attention technique designed to alleviate this bottleneck by reducing KV cache access. Double Sparsity combines token sparsity, which focuses on utilizing only the important tokens for computing self-attention, with channel sparsity, an approach that uses important feature channels for identifying important tokens. Our key insight is that the pattern of channel sparsity is relatively static, allowing us to use offline calibration to make it efficient at runtime, thereby enabling accurate and efficient identification of important tokens. Moreover, this method can be combined with offloading to achieve significant memory usage reduction. Experimental results demonstrate that Double Sparsity can achieve 1{16} token and channel sparsity with minimal impact on accuracy across various tasks, including wiki-2 perplexity, key-value retrieval, and long context benchmarks with models including Llama-2-7B, Llama-2-70B, and Mixtral-8x7B. It brings up to a 14.1times acceleration in attention operations and a 1.9times improvement in end-to-end inference on GPUs. With offloading, it achieves a decoding speed acceleration of 16.3times compared to state-of-the-art solutions at a sequence length of 256K. Our code is publicly available at https://github.com/andy-yang-1/DoubleSparse.

Dynamic Sparse Training (DST) methods achieve state-of-the-art results in sparse neural network training, matching the generalization of dense models while enabling sparse training and inference. Although the resulting models are highly sparse and theoretically less computationally expensive, achieving speedups with unstructured sparsity on real-world hardware is challenging. In this work, we propose a sparse-to-sparse DST method, Structured RigL (SRigL), to learn a variant of fine-grained structured N:M sparsity by imposing a constant fan-in constraint. Using our empirical analysis of existing DST methods at high sparsity, we additionally employ a neuron ablation method which enables SRigL to achieve state-of-the-art sparse-to-sparse structured DST performance on a variety of Neural Network (NN) architectures. We demonstrate reduced real-world timings on CPU for online inference -- 3.6x/2x faster at 90% sparsity than equivalent dense/unstructured sparse layers, respectively. Our source code is available at https://github.com/calgaryml/condensed-sparsity

Activation sparsity refers to the existence of considerable weakly-contributed elements among activation outputs. As a prevalent property of the models using the ReLU activation function, it has been proven a promising paradigm to boost model inference efficiency. Nevertheless, most large language models (LLMs) adopt activation functions without intrinsic activation sparsity (e.g., GELU and Swish). Some recent efforts have explored introducing ReLU or its variants as the substitutive activation function to help LLMs achieve activation sparsity and inference acceleration, but few can simultaneously obtain high sparsity and comparable model performance. This paper introduces an effective sparsification method named "ProSparse" to push LLMs for higher activation sparsity without decreasing model performance. Specifically, after substituting the activation function of LLMs with ReLU, ProSparse adopts progressive sparsity regularization with a factor smoothly increasing along sine curves in multiple stages. This can enhance activation sparsity and alleviate performance degradation by avoiding radical shifts in activation distribution. With ProSparse, we obtain high sparsity of 89.32% and 88.80% for LLaMA2-7B and LLaMA2-13B, respectively, achieving comparable performance to their original Swish-activated versions. Our inference acceleration experiments further demonstrate the practical acceleration brought by higher activation sparsity.

With increasing demands for efficiency, information retrieval has developed a branch of sparse retrieval, further advancing towards inference-free retrieval where the documents are encoded during indexing time and there is no model-inference for queries. Existing sparse retrieval models rely on FLOPS regularization for sparsification, while this mechanism was originally designed for Siamese encoders, it is considered to be suboptimal in inference-free scenarios which is asymmetric. Previous attempts to adapt FLOPS for inference-free scenarios have been limited to rule-based methods, leaving the potential of sparsification approaches for inference-free retrieval models largely unexplored. In this paper, we explore ell_0 inspired sparsification manner for inference-free retrievers. Through comprehensive out-of-domain evaluation on the BEIR benchmark, our method achieves state-of-the-art performance among inference-free sparse retrieval models and is comparable to leading Siamese sparse retrieval models. Furthermore, we provide insights into the trade-off between retrieval effectiveness and computational efficiency, demonstrating practical value for real-world applications.

Deploying large language models (LLMs) for long-context inference remains challenging due to their substantial memory and computational demands. While techniques such as Key-Value (KV) cache compression are designed to reduce memory usage, they often neglect the structured sparsity inherent in the relationship between hidden states and their corresponding KV cache. In this work, we explore the role of uncertainty as a potential indicator of sparsity within LLMs. We propose UNComp, an uncertainty-aware framework that leverages truncated matrix entropy to identify areas of low information content, thereby revealing sparsity patterns that can be used for adaptive compression. Unlike traditional methods that apply uniform compression, UNComp dynamically adjusts its approach to compression, guided by uncertainty measures that reflect the importance of various model components. Our analysis shows that sparsity patterns, when derived from uncertainty estimates, can be exploited to reveal special long-range dependencies, such as retrieval heads and retrieval layers. This perspective not only enhances our understanding of how compression can be optimized but also provides new insights into the inherent sparsity of LLMs during long-context inference. By focusing on uncertainty to analyze the sparsity pattern in detail, UNComp reduces the KV cache size to 4.74% of the original, achieves a 6% prefill speedup, and improves throughput by 6.4x - not only delivering strong lossless compression performance, but also validating the effectiveness of the underlying theoretical tool. We release the code at https://github.com/menik1126/UNComp.

We introduce a new type of foundational model for parsing human anatomy in medical images that works for different modalities. It supports supervised or unsupervised training and can perform matching, registration, classification, or segmentation with or without user interaction. We achieve this by training a neural network estimator that maps query locations to atlas coordinates via regression. Efficiency is improved by sparsely sampling the input, enabling response times of less than 1 ms without additional accelerator hardware. We demonstrate the utility of the algorithm in both CT and MRI modalities.

Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the high-throughput analysis of protein composition in biological tissues. Many deep learning methods have been developed for de novo peptide sequencing task, i.e., predicting the peptide sequence for the observed mass spectrum. However, two key challenges seriously hinder the further advancement of this important task. Firstly, since there is no consensus for the evaluation datasets, the empirical results in different research papers are often not comparable, leading to unfair comparison. Secondly, the current methods are usually limited to amino acid-level or peptide-level precision and recall metrics. In this work, we present the first unified benchmark NovoBench for de novo peptide sequencing, which comprises diverse mass spectrum data, integrated models, and comprehensive evaluation metrics. Recent impressive methods, including DeepNovo, PointNovo, Casanovo, InstaNovo, AdaNovo and pi-HelixNovo are integrated into our framework. In addition to amino acid-level and peptide-level precision and recall, we evaluate the models' performance in terms of identifying post-tranlational modifications (PTMs), efficiency and robustness to peptide length, noise peaks and missing fragment ratio, which are important influencing factors while seldom be considered. Leveraging this benchmark, we conduct a large-scale study of current methods, report many insightful findings that open up new possibilities for future development.

Sparse autoencoders (SAEs) are useful for detecting and steering interpretable features in neural networks, with particular potential for understanding complex multimodal representations. Given their ability to uncover interpretable features, SAEs are particularly valuable for analyzing large-scale vision-language models (e.g., CLIP and SigLIP), which are fundamental building blocks in modern systems yet remain challenging to interpret and control. However, current SAE methods are limited by optimizing both reconstruction quality and sparsity simultaneously, as they rely on either activation suppression or rigid sparsity constraints. To this end, we introduce Matryoshka SAE (MSAE), a new architecture that learns hierarchical representations at multiple granularities simultaneously, enabling a direct optimization of both metrics without compromise. MSAE establishes a new state-of-the-art Pareto frontier between reconstruction quality and sparsity for CLIP, achieving 0.99 cosine similarity and less than 0.1 fraction of variance unexplained while maintaining ~80% sparsity. Finally, we demonstrate the utility of MSAE as a tool for interpreting and controlling CLIP by extracting over 120 semantic concepts from its representation to perform concept-based similarity search and bias analysis in downstream tasks like CelebA.

Sparse linear models are one of several core tools for interpretable machine learning, a field of emerging importance as predictive models permeate decision-making in many domains. Unfortunately, sparse linear models are far less flexible as functions of their input features than black-box models like deep neural networks. With this capability gap in mind, we study a not-uncommon situation where the input features dichotomize into two groups: explanatory features, which are candidates for inclusion as variables in an interpretable model, and contextual features, which select from the candidate variables and determine their effects. This dichotomy leads us to the contextual lasso, a new statistical estimator that fits a sparse linear model to the explanatory features such that the sparsity pattern and coefficients vary as a function of the contextual features. The fitting process learns this function nonparametrically via a deep neural network. To attain sparse coefficients, we train the network with a novel lasso regularizer in the form of a projection layer that maps the network's output onto the space of ell_1-constrained linear models. An extensive suite of experiments on real and synthetic data suggests that the learned models, which remain highly transparent, can be sparser than the regular lasso without sacrificing the predictive power of a standard deep neural network.

Sparse autoencoders (SAEs) have emerged as powerful techniques for interpretability of large language models (LLMs), aiming to decompose hidden states into meaningful semantic features. While several SAE variants have been proposed, there remains no principled framework to derive SAEs from the original dictionary learning formulation. In this work, we introduce such a framework by unrolling the proximal gradient method for sparse coding. We show that a single-step update naturally recovers common SAE variants, including ReLU, JumpReLU, and TopK. Through this lens, we reveal a fundamental limitation of existing SAEs: their sparsity-inducing regularizers enforce non-negativity, preventing a single feature from representing bidirectional concepts (e.g., male vs. female). This structural constraint fragments semantic axes into separate, redundant features, limiting representational completeness. To address this issue, we propose AbsTopK SAE, a new variant derived from the ell_0 sparsity constraint that applies hard thresholding over the largest-magnitude activations. By preserving both positive and negative activations, AbsTopK uncovers richer, bidirectional conceptual representations. Comprehensive experiments across four LLMs and seven probing and steering tasks show that AbsTopK improves reconstruction fidelity, enhances interpretability, and enables single features to encode contrasting concepts. Remarkably, AbsTopK matches or even surpasses the Difference-in-Mean method, a supervised approach that requires labeled data for each concept and has been shown in prior work to outperform SAEs.

With the rapid growth of artificial intelligence (AI) in healthcare, there has been a significant increase in the generation and storage of sensitive medical data. This abundance of data, in turn, has propelled the advancement of medical AI technologies. However, concerns about unauthorized data exploitation, such as training commercial AI models, often deter researchers from making their invaluable datasets publicly available. In response to the need to protect this hard-to-collect data while still encouraging medical institutions to share it, one promising solution is to introduce imperceptible noise into the data. This method aims to safeguard the data against unauthorized training by inducing degradation in model generalization. Although existing methods have shown commendable data protection capabilities in general domains, they tend to fall short when applied to biomedical data, mainly due to their failure to account for the sparse nature of medical images. To address this problem, we propose the Sparsity-Aware Local Masking (SALM) method, a novel approach that selectively perturbs significant pixel regions rather than the entire image as previous strategies have done. This simple-yet-effective approach significantly reduces the perturbation search space by concentrating on local regions, thereby improving both the efficiency and effectiveness of data protection for biomedical datasets characterized by sparse features. Besides, we have demonstrated that SALM maintains the essential characteristics of the data, ensuring its clinical utility remains uncompromised. Our extensive experiments across various datasets and model architectures demonstrate that SALM effectively prevents unauthorized training of deep-learning models and outperforms previous state-of-the-art data protection methods.

We explore the impact of parameter sparsity on the scaling behavior of Transformers trained on massive datasets (i.e., "foundation models"), in both vision and language domains. In this setting, we identify the first scaling law describing the relationship between weight sparsity, number of non-zero parameters, and amount of training data, which we validate empirically across model and data scales; on ViT/JFT-4B and T5/C4. These results allow us to characterize the "optimal sparsity", the sparsity level which yields the best performance for a given effective model size and training budget. For a fixed number of non-zero parameters, we identify that the optimal sparsity increases with the amount of data used for training. We also extend our study to different sparsity structures (such as the hardware-friendly n:m pattern) and strategies (such as starting from a pretrained dense model). Our findings shed light on the power and limitations of weight sparsity across various parameter and computational settings, offering both theoretical understanding and practical implications for leveraging sparsity towards computational efficiency improvements.

The growing computational demands of large language models (LLMs) make efficient inference and activation strategies increasingly critical. While recent approaches, such as Mixture-of-Experts (MoE), leverage selective activation but require specialized training, training-free sparse activation methods offer broader applicability and superior resource efficiency through their plug-and-play design. However, many existing methods rely solely on hidden state magnitudes to determine activation, resulting in high approximation errors and suboptimal inference accuracy. To address these limitations, we propose WINA (Weight Informed Neuron Activation), a novel, simple, and training-free sparse activation framework that jointly considers hidden state magnitudes and the column-wise ell_2-norms of weight matrices. We show that this leads to a sparsification strategy that obtains optimal approximation error bounds with theoretical guarantees tighter than existing techniques. Empirically, WINA also outperforms state-of-the-art methods (e.g., TEAL) by up to 2.94% in average performance at the same sparsity levels, across a diverse set of LLM architectures and datasets. These results position WINA as a new performance frontier for training-free sparse activation in LLM inference, advancing training-free sparse activation methods and setting a robust baseline for efficient inference. The source code is available at https://github.com/microsoft/wina.

We propose a novel Two-Stage framework for Structured Pruning (2SSP) for pruning Large Language Models (LLMs), which combines two different strategies of pruning, namely Width and Depth Pruning. The first stage (Width Pruning) removes entire neurons, hence their corresponding rows and columns, aiming to preserve the connectivity among the pruned structures in the intermediate state of the Feed-Forward Networks in each Transformer block. This is done based on an importance score measuring the impact of each neuron over the output magnitude. The second stage (Depth Pruning), instead, removes entire Attention submodules. This is done by applying an iterative process that removes the Attention submodules with the minimum impact on a given metric of interest (in our case, perplexity). We also propose a novel mechanism to balance the sparsity rate of the two stages w.r.t. to the desired global sparsity. We test 2SSP on four LLM families and three sparsity rates (25\%, 37.5\%, and 50\%), measuring the resulting perplexity over three language modeling datasets as well as the performance over six downstream tasks. Our method consistently outperforms five state-of-the-art competitors over three language modeling and six downstream tasks, with an up to two-order-of-magnitude gain in terms of pruning time. The code is available at available at https://github.com/FabrizioSandri/2SSP.

We present ROCKET, a training-free model compression method that achieves state-of-the-art performance in comparison with factorization, structured-sparsification and dynamic compression baselines. Operating under a global compression budget, ROCKET comprises two key innovations: First, it formulates layer-wise compression allocation as a multi-choice knapsack problem, selecting the optimal compression level for each layer to minimize total reconstruction error while adhering to a target model size. Second, it introduces a single-step sparse matrix factorization inspired by dictionary learning: using only a small calibration set, it sparsifies weight coefficients based on activation-weights sensitivity and then updates the dictionary in closed form via least squares bypassing iterative optimization, sparse coding, or backpropagation entirely. ROCKET consistently outperforms existing compression approaches across different model architectures at 20-50\% compression rates. Notably, it retains over 90\% of the original model's performance at 30\% compression without any fine-tuning. Moreover, when applying a light fine-tuning phase, recovery is substantially enhanced: for instance, compressing Qwen3-14B to an 8B-parameter model and healing it with just 30 million tokens yields performance nearly on par with the original Qwen3-8B. The code for ROCKET is at github.com/mts-ai/ROCKET/tree/main.

Semi-structured N:M sparsity and low-bit quantization (e.g., 1.58-bit BitNet) are two promising approaches for improving the efficiency of large language models (LLMs), yet they have largely been studied in isolation. In this work, we investigate their interaction and show that 1.58-bit BitNet is naturally more compatible with N:M sparsity than full-precision models. To study this effect, we propose Sparse-BitNet, a unified framework that jointly applies 1.58-bit quantization and dynamic N:M sparsification while ensuring stable training for the first time. Across multiple model scales and training regimes (sparse pretraining and dense-to-sparse schedules), 1.58-bit BitNet consistently exhibits smaller performance degradation than full-precision baselines at the same sparsity levels and can tolerate higher structured sparsity before accuracy collapse. Moreover, using our custom sparse tensor core, Sparse-BitNet achieves substantial speedups in both training and inference, reaching up to 1.30X. These results highlight that combining extremely low-bit quantization with semi-structured N:M sparsity is a promising direction for efficient LLMs. Code available at https://github.com/AAzdi/Sparse-BitNet

Recent advances in large language models (LLMs) have opened new opportunities for academic literature retrieval. However, existing systems often rely on rigid pipelines and exhibit limited reasoning capabilities. We introduce SPAR, a multi-agent framework that incorporates RefChain-based query decomposition and query evolution to enable more flexible and effective search. To facilitate systematic evaluation, we also construct SPARBench, a challenging benchmark with expert-annotated relevance labels. Experimental results demonstrate that SPAR substantially outperforms strong baselines, achieving up to +56% F1 on AutoScholar and +23% F1 on SPARBench over the best-performing baseline. Together, SPAR and SPARBench provide a scalable, interpretable, and high-performing foundation for advancing research in scholarly retrieval. Code and data will be available at: https://github.com/xiaofengShi/SPAR

Large language models have high compute, latency, and memory requirements. While specialized accelerators such as GPUs and TPUs typically run these workloads, CPUs are more widely available and consume less energy. Accelerating LLMs with CPUs enables broader AI access at a lower cost and power consumption. This acceleration potential for CPUs is especially relevant during the memory-bound decoding stage of LLM inference, which processes one token at a time and is becoming increasingly utilized with reasoning models. We utilize Advanced Matrix Extensions (AMX) support on the latest Intel CPUs together with unstructured sparsity to achieve a 1.42 times reduction in end-to-end latency compared to the current PyTorch implementation by applying our technique in linear layers. We provide a set of open-source customized sparse kernels that can speed up any PyTorch model by automatically replacing all linear layers with our custom sparse implementation. Furthermore, we demonstrate for the first time the use of unstructured sparsity in the attention computation achieving a 1.14 times speedup over the current systems without compromising accuracy. Code: https://github.com/IntelLabs/Hardware-Aware-Automated-Machine-Learning/tree/main/SparAMX

Large language models (LLMs) have grown in their usage to provide support for question answering across numerous disciplines. The models on their own have already shown promise for answering basic questions, however fail quickly where expert domain knowledge is required or the question is nuanced. Scientific research often involves searching for relevant literature, distilling pertinent information from that literature and analysing how the findings support or contradict one another. The information is often encapsulated in the full text body of research articles, rather than just in the abstracts. Statements within these articles frequently require the wider article context to be fully understood. We have built an LLM-based system that performs such search and distillation of information encapsulated in scientific literature, and we evaluate our keyword based search and information distillation system against a set of biology related questions from previously released literature benchmarks. We demonstrate sparse retrieval methods exhibit results close to state of the art without the need for dense retrieval, with its associated infrastructure and complexity overhead. We also show how to increase the coverage of relevant documents for literature review generation.

Sparse attention offers a promising strategy to extend long-context capabilities in Transformer LLMs, yet its viability, its efficiency-accuracy trade-offs, and systematic scaling studies remain unexplored. To address this gap, we perform a careful comparison of training-free sparse attention methods at varying model scales, sequence lengths, and sparsity levels on a diverse collection of long-sequence tasks-including novel ones that rely on natural language while remaining controllable and easy to evaluate. Based on our experiments, we report a series of key findings: 1) an isoFLOPS analysis reveals that for very long sequences, larger and highly sparse models are preferable to smaller and dense ones. 2) The level of sparsity attainable while statistically guaranteeing accuracy preservation is higher during decoding than prefilling, and correlates with model size in the former. 3) There is no clear strategy that performs best across tasks and phases, with different units of sparsification or budget adaptivity needed for different scenarios. Even moderate sparsity levels often result in significant performance degradation on at least one task, highlighting that sparse attention is not a universal solution. 4) We introduce and validate novel scaling laws specifically tailored for sparse attention, providing evidence that our findings are likely to hold true beyond our range of experiments. Through these insights, we demonstrate that sparse attention is a key tool to enhance the capabilities of Transformer LLMs for processing longer sequences, but requires careful evaluation of trade-offs for performance-sensitive applications.

Robustness to adversarial attack is typically evaluated with adversarial accuracy. This metric quantifies the number of points for which, given a threat model, successful adversarial perturbations cannot be found. While essential, this metric does not capture all aspects of robustness and in particular leaves out the question of how many perturbations can be found for each point. In this work we introduce an alternative approach, adversarial sparsity, which quantifies how difficult it is to find a successful perturbation given both an input point and a constraint on the direction of the perturbation. This constraint may be angular (L2 perturbations), or based on the number of pixels (Linf perturbations). We show that sparsity provides valuable insight on neural networks in multiple ways. analyzing the sparsity of existing robust models illustrates important differences between them that accuracy analysis does not, and suggests approaches for improving their robustness. When applying broken defenses effective against weak attacks but not strong ones, sparsity can discriminate between the totally ineffective and the partially effective defenses. Finally, with sparsity we can measure increases in robustness that do not affect accuracy: we show for example that data augmentation can by itself increase adversarial robustness, without using adversarial training.

Motivation: The activity of the adaptive immune system is governed by T-cells and their specific T-cell receptors (TCR), which selectively recognize foreign antigens. Recent advances in experimental techniques have enabled sequencing of TCRs and their antigenic targets (epitopes), allowing to research the missing link between TCR sequence and epitope binding specificity. Scarcity of data and a large sequence space make this task challenging, and to date only models limited to a small set of epitopes have achieved good performance. Here, we establish a k-nearest-neighbor (K-NN) classifier as a strong baseline and then propose TITAN (Tcr epITope bimodal Attention Networks), a bimodal neural network that explicitly encodes both TCR sequences and epitopes to enable the independent study of generalization capabilities to unseen TCRs and/or epitopes. Results: By encoding epitopes at the atomic level with SMILES sequences, we leverage transfer learning and data augmentation to enrich the input data space and boost performance. TITAN achieves high performance in the prediction of specificity of unseen TCRs (ROC-AUC 0.87 in 10-fold CV) and surpasses the results of the current state-of-the-art (ImRex) by a large margin. Notably, our Levenshtein-distance-based K-NN classifier also exhibits competitive performance on unseen TCRs. While the generalization to unseen epitopes remains challenging, we report two major breakthroughs. First, by dissecting the attention heatmaps, we demonstrate that the sparsity of available epitope data favors an implicit treatment of epitopes as classes. This may be a general problem that limits unseen epitope performance for sufficiently complex models. Second, we show that TITAN nevertheless exhibits significantly improved performance on unseen epitopes and is capable of focusing attention on chemically meaningful molecular structures.

Random pruning is arguably the most naive way to attain sparsity in neural networks, but has been deemed uncompetitive by either post-training pruning or sparse training. In this paper, we focus on sparse training and highlight a perhaps counter-intuitive finding, that random pruning at initialization can be quite powerful for the sparse training of modern neural networks. Without any delicate pruning criteria or carefully pursued sparsity structures, we empirically demonstrate that sparsely training a randomly pruned network from scratch can match the performance of its dense equivalent. There are two key factors that contribute to this revival: (i) the network sizes matter: as the original dense networks grow wider and deeper, the performance of training a randomly pruned sparse network will quickly grow to matching that of its dense equivalent, even at high sparsity ratios; (ii) appropriate layer-wise sparsity ratios can be pre-chosen for sparse training, which shows to be another important performance booster. Simple as it looks, a randomly pruned subnetwork of Wide ResNet-50 can be sparsely trained to outperforming a dense Wide ResNet-50, on ImageNet. We also observed such randomly pruned networks outperform dense counterparts in other favorable aspects, such as out-of-distribution detection, uncertainty estimation, and adversarial robustness. Overall, our results strongly suggest there is larger-than-expected room for sparse training at scale, and the benefits of sparsity might be more universal beyond carefully designed pruning. Our source code can be found at https://github.com/VITA-Group/Random_Pruning.

This paper studies the curious phenomenon for machine learning models with Transformer architectures that their activation maps are sparse. By activation map we refer to the intermediate output of the multi-layer perceptrons (MLPs) after a ReLU activation function, and by sparse we mean that on average very few entries (e.g., 3.0% for T5-Base and 6.3% for ViT-B16) are nonzero for each input to MLP. Moreover, larger Transformers with more layers and wider MLP hidden dimensions are sparser as measured by the percentage of nonzero entries. Through extensive experiments we demonstrate that the emergence of sparsity is a prevalent phenomenon that occurs for both natural language processing and vision tasks, on both training and evaluation data, for Transformers of various configurations, at layers of all depth levels, as well as for other architectures including MLP-mixers and 2-layer MLPs. We show that sparsity also emerges using training datasets with random labels, or with random inputs, or with infinite amount of data, demonstrating that sparsity is not a result of a specific family of datasets. We discuss how sparsity immediately implies a way to significantly reduce the FLOP count and improve efficiency for Transformers. Moreover, we demonstrate perhaps surprisingly that enforcing an even sparser activation via Top-k thresholding with a small value of k brings a collection of desired but missing properties for Transformers, namely less sensitivity to noisy training data, more robustness to input corruptions, and better calibration for their prediction confidence.

Vision-Language Models (VLMs) excel across diverse tasks but suffer from high inference costs in time and memory. Token sparsity mitigates inefficiencies in token usage, while neuron sparsity reduces high-dimensional computations, both offering promising solutions to enhance efficiency. Recently, these two sparsity paradigms have evolved largely in parallel, fostering the prevailing assumption that they function independently. However, a fundamental yet underexplored question remains: Do they truly operate in isolation, or is there a deeper underlying interplay that has yet to be uncovered? In this paper, we conduct the first comprehensive investigation into this question. By introducing and analyzing the matching mechanism between Core Neurons and Core Tokens, we found that key neurons and tokens for inference mutually influence and reinforce each other. Building on this insight, we propose CoreMatching, a co-adaptive sparse inference framework, which leverages the synergy between token and neuron sparsity to enhance inference efficiency. Through theoretical analysis and efficiency evaluations, we demonstrate that the proposed method surpasses state-of-the-art baselines on ten image understanding tasks and three hardware devices. Notably, on the NVIDIA Titan Xp, it achieved 5x FLOPs reduction and a 10x overall speedup. Code is released at https://github.com/wangqinsi1/2025-ICML-CoreMatching/tree/main.

Text-to-speech (TTS) models have achieved remarkable naturalness in recent years, yet like most deep neural models, they have more parameters than necessary. Sparse TTS models can improve on dense models via pruning and extra retraining, or converge faster than dense models with some performance loss. Thus, we propose training TTS models using decaying sparsity, i.e. a high initial sparsity to accelerate training first, followed by a progressive rate reduction to obtain better eventual performance. This decremental approach differs from current methods of incrementing sparsity to a desired target, which costs significantly more time than dense training. We call our method SNIPER training: Single-shot Initialization Pruning Evolving-Rate training. Our experiments on FastSpeech2 show that we were able to obtain better losses in the first few training epochs with SNIPER, and that the final SNIPER-trained models outperformed constant-sparsity models and edged out dense models, with negligible difference in training time.

The energy consumption of large-scale ML models is dominated by data movement - shuffling billions of parameters across memory hierarchies and data centers. Effective sparsification to prune redundant parameters is still challenging: existing methods incur significant accuracy degradation, performance overhead, or both. We introduce (Bl)ock (a)nd (S)parse (T)ransformers (BLaST), a general, robust, and reliable sparsification method applicable to linear layers in all settings. Our method iteratively sparsifies weight matrices into a block sparsity pattern suitable for efficient sparse matrix-matrix (SpMM) multiplication. BLaST achieves up to 95% sparsity in MLP weights with negligible accuracy loss. Our fused, highly optimized Sparse MLP kernel delivers up to 16.7x speedup over dense MLPs across 9 architectures and 8 datasets, resulting in up to 1.6x inference speedup, 1.11x pretraining speedup and up to 3.12x inference memory usage reduction. BLaST enables the next generation of large-scale AI systems by reducing energy use, memory footprint, and latency.

The structure of biological neural circuits-modular, hierarchical, and sparsely interconnected-reflects an efficient trade-off between wiring cost, functional specialization, and robustness. These principles offer valuable insights for artificial neural network (ANN) design, especially as networks grow in depth and scale. Sparsity, in particular, has been widely explored for reducing memory and computation, improving speed, and enhancing generalization. Motivated by systems neuroscience findings, we explore how patterns of functional connectivity in the mouse visual cortex-specifically, ensemble-to-ensemble communication, can inform ANN design. We introduce G2GNet, a novel architecture that imposes sparse, modular connectivity across feedforward layers. Despite having significantly fewer parameters than fully connected models, G2GNet achieves superior accuracy on standard vision benchmarks. To our knowledge, this is the first architecture to incorporate biologically observed functional connectivity patterns as a structural bias in ANN design. We complement this static bias with a dynamic sparse training (DST) mechanism that prunes and regrows edges during training. We also propose a Hebbian-inspired rewiring rule based on activation correlations, drawing on principles of biological plasticity. G2GNet achieves up to 75% sparsity while improving accuracy by up to 4.3% on benchmarks, including Fashion-MNIST, CIFAR-10, and CIFAR-100, outperforming dense baselines with far fewer computations.

The transformative impact of large language models (LLMs) like LLaMA and GPT on natural language processing is countered by their prohibitive computational demands. Pruning has emerged as a pivotal compression strategy, introducing sparsity to enhance both memory and computational efficiency. Yet, traditional global pruning is impractical for LLMs due to scalability issues, while local pruning, despite its efficiency, leads to suboptimal solutions. Addressing these challenges, we propose SparseLLM, a novel framework that redefines the global pruning process into manageable, coordinated subproblems, allowing for resource-efficient optimization with global optimality. SparseLLM's approach, which conceptualizes LLMs as a chain of modular functions and leverages auxiliary variables for problem decomposition, not only facilitates a pragmatic application on LLMs but also demonstrates significant performance improvements, particularly in high-sparsity regimes where it surpasses current state-of-the-art methods.

Sparse coding, which refers to modeling a signal as sparse linear combinations of the elements of a learned dictionary, has proven to be a successful (and interpretable) approach in applications such as signal processing, computer vision, and medical imaging. While this success has spurred much work on provable guarantees for dictionary recovery when the learned dictionary is the same size as the ground-truth dictionary, work on the setting where the learned dictionary is larger (or over-realized) with respect to the ground truth is comparatively nascent. Existing theoretical results in this setting have been constrained to the case of noise-less data. We show in this work that, in the presence of noise, minimizing the standard dictionary learning objective can fail to recover the elements of the ground-truth dictionary in the over-realized regime, regardless of the magnitude of the signal in the data-generating process. Furthermore, drawing from the growing body of work on self-supervised learning, we propose a novel masking objective for which recovering the ground-truth dictionary is in fact optimal as the signal increases for a large class of data-generating processes. We corroborate our theoretical results with experiments across several parameter regimes showing that our proposed objective also enjoys better empirical performance than the standard reconstruction objective.

Historically, the pursuit of efficient inference has been one of the driving forces behind research into new deep learning architectures and building blocks. Some recent examples include: the squeeze-and-excitation module, depthwise separable convolutions in Xception, and the inverted bottleneck in MobileNet v2. Notably, in all of these cases, the resulting building blocks enabled not only higher efficiency, but also higher accuracy, and found wide adoption in the field. In this work, we further expand the arsenal of efficient building blocks for neural network architectures; but instead of combining standard primitives (such as convolution), we advocate for the replacement of these dense primitives with their sparse counterparts. While the idea of using sparsity to decrease the parameter count is not new, the conventional wisdom is that this reduction in theoretical FLOPs does not translate into real-world efficiency gains. We aim to correct this misconception by introducing a family of efficient sparse kernels for ARM and WebAssembly, which we open-source for the benefit of the community as part of the XNNPACK library. Equipped with our efficient implementation of sparse primitives, we show that sparse versions of MobileNet v1, MobileNet v2 and EfficientNet architectures substantially outperform strong dense baselines on the efficiency-accuracy curve. On Snapdragon 835 our sparse networks outperform their dense equivalents by 1.3-2.4times -- equivalent to approximately one entire generation of MobileNet-family improvement. We hope that our findings will facilitate wider adoption of sparsity as a tool for creating efficient and accurate deep learning architectures.

Model compression has emerged as a mainstream solution to reduce memory usage and computational overhead. This paper presents Group Quantization and Sparse Acceleration (GQSA), a novel compression technique tailored for LLMs. Traditional methods typically focus exclusively on either quantization or sparsification, but relying on a single strategy often results in significant performance loss at high compression rates. In contrast, GQSA integrates quantization and sparsification in a tightly coupled manner, leveraging GPU-friendly structured group sparsity and quantization for efficient acceleration. Building upon system-algorithm co-design principles, we propose a two-stage sparse optimization strategy that ensures the performance superiority of the compressed model. On the engine side, we introduce a "task-centric" parallel strategy, which, to the best of our knowledge, is the first application in the domain of sparse computing. Compared to the traditional 2:4 sparse method, the GQSA offers a more flexible and adjustable sparsity rate, as well as a higher weight compression rate, and is efficiently compatible with weight-only quantization methods. Experimental results demonstrate that, under the GQSA W4S50% compression setting, the model's accuracy surpasses that of both 2:4 pruning and W2 quantization. Furthermore, at the inference level, GQSA outperforms W2 by 1.26times and 2:4 pruning by 2.35times in terms of speed.

The sheer size of modern neural networks makes model serving a serious computational challenge. A popular class of compression techniques overcomes this challenge by pruning or sparsifying the weights of pretrained networks. While useful, these techniques often face serious tradeoffs between computational requirements and compression quality. In this work, we propose a novel optimization-based pruning framework that considers the combined effect of pruning (and updating) multiple weights subject to a sparsity constraint. Our approach, CHITA, extends the classical Optimal Brain Surgeon framework and results in significant improvements in speed, memory, and performance over existing optimization-based approaches for network pruning. CHITA's main workhorse performs combinatorial optimization updates on a memory-friendly representation of local quadratic approximation(s) of the loss function. On a standard benchmark of pretrained models and datasets, CHITA leads to significantly better sparsity-accuracy tradeoffs than competing methods. For example, for MLPNet with only 2% of the weights retained, our approach improves the accuracy by 63% relative to the state of the art. Furthermore, when used in conjunction with fine-tuning SGD steps, our method achieves significant accuracy gains over the state-of-the-art approaches.

While large language models (LLMs) have achieved remarkable performance across a wide range of tasks, their massive scale incurs prohibitive computational and memory costs for pre-training from scratch. Recent studies have investigated the use of low-rank parameterization as a means of reducing model size and training cost. In this context, sparsity is often employed as a complementary technique to recover important information lost in low-rank compression by capturing salient features in the residual space. However, existing approaches typically combine low-rank and sparse components in a simplistic or ad hoc manner, often resulting in undesirable performance degradation compared to full-rank training. In this paper, we propose LOw-rank and Sparse pre-Training (LOST) for LLMs, a novel method that ingeniously integrates low-rank and sparse structures to enable effective training of LLMs from scratch under strict efficiency constraints. LOST applies singular value decomposition to weight matrices, preserving the dominant low-rank components, while allocating the remaining singular values to construct channel-wise sparse components to complement the expressiveness of low-rank training. We evaluate LOST on LLM pretraining ranging from 60M to 7B parameters. Our experiments show that LOST achieves competitive or superior performance compared to full-rank models, while significantly reducing both memory and compute overhead. Moreover, Code is available at https://github.com/JiaxiLi1/LOST-Low-rank-and-Sparse-Training-for-Large-Language-Models{LOST Repo}

The explosion of large-scale data in fields such as finance, e-commerce, and social media has outstripped the processing capabilities of single-machine systems, driving the need for distributed statistical inference methods. Traditional approaches to distributed inference often struggle with achieving true sparsity in high-dimensional datasets and involve high computational costs. We propose a novel, two-stage, distributed best subset selection algorithm to address these issues. Our approach starts by efficiently estimating the active set while adhering to the ell_0 norm-constrained surrogate likelihood function, effectively reducing dimensionality and isolating key variables. A refined estimation within the active set follows, ensuring sparse estimates and matching the minimax ell_2 error bound. We introduce a new splicing technique for adaptive parameter selection to tackle subproblems under ell_0 constraints and a Generalized Information Criterion (GIC). Our theoretical and numerical studies show that the proposed algorithm correctly finds the true sparsity pattern, has the oracle property, and greatly lowers communication costs. This is a big step forward in distributed sparse estimation.

The lottery ticket hypothesis has sparked the rapid development of pruning algorithms that aim to reduce the computational costs associated with deep learning during training and model deployment. Currently, such algorithms are primarily evaluated on imaging data, for which we lack ground truth information and thus the understanding of how sparse lottery tickets could be. To fill this gap, we develop a framework that allows us to plant and hide winning tickets with desirable properties in randomly initialized neural networks. To analyze the ability of state-of-the-art pruning to identify tickets of extreme sparsity, we design and hide such tickets solving four challenging tasks. In extensive experiments, we observe similar trends as in imaging studies, indicating that our framework can provide transferable insights into realistic problems. Additionally, we can now see beyond such relative trends and highlight limitations of current pruning methods. Based on our results, we conclude that the current limitations in ticket sparsity are likely of algorithmic rather than fundamental nature. We anticipate that comparisons to planted tickets will facilitate future developments of efficient pruning algorithms.

Sparse training is emerging as a promising avenue for reducing the computational cost of training neural networks. Several recent studies have proposed pruning methods using learnable thresholds to efficiently explore the non-uniform distribution of sparsity inherent within the models. In this paper, we propose Gradient Annealing (GA), where gradients of masked weights are scaled down in a non-linear manner. GA provides an elegant trade-off between sparsity and accuracy without the need for additional sparsity-inducing regularization. We integrated GA with the latest learnable pruning methods to create an automated sparse training algorithm called AutoSparse, which achieves better accuracy and/or training/inference FLOPS reduction than existing learnable pruning methods for sparse ResNet50 and MobileNetV1 on ImageNet-1K: AutoSparse achieves (2x, 7x) reduction in (training,inference) FLOPS for ResNet50 on ImageNet at 80% sparsity. Finally, AutoSparse outperforms sparse-to-sparse SotA method MEST (uniform sparsity) for 80% sparse ResNet50 with similar accuracy, where MEST uses 12% more training FLOPS and 50% more inference FLOPS.

Sparse Autoencoders (SAEs) are a promising approach for extracting neural network representations by learning a sparse and overcomplete decomposition of the network's internal activations. However, SAEs are traditionally trained considering only activation values and not the effect those activations have on downstream computations. This limits the information available to learn features, and biases the autoencoder towards neglecting features which are represented with small activation values but strongly influence model outputs. To address this, we introduce Gradient SAEs (g-SAEs), which modify the k-sparse autoencoder architecture by augmenting the TopK activation function to rely on the gradients of the input activation when selecting the k elements. For a given sparsity level, g-SAEs produce reconstructions that are more faithful to original network performance when propagated through the network. Additionally, we find evidence that g-SAEs learn latents that are on average more effective at steering models in arbitrary contexts. By considering the downstream effects of activations, our approach leverages the dual nature of neural network features as both representations, retrospectively, and actions, prospectively. While previous methods have approached the problem of feature discovery primarily focused on the former aspect, g-SAEs represent a step towards accounting for the latter as well.

Understanding the internal representations of large language models (LLMs) remains a central challenge for interpretability research. Sparse autoencoders (SAEs) offer a promising solution by decomposing activations into interpretable features, but existing approaches rely on fixed sparsity constraints that fail to account for input complexity. We propose Adaptive Top K Sparse Autoencoders (AdaptiveK), a novel framework that dynamically adjusts sparsity levels based on the semantic complexity of each input. Leveraging linear probes, we demonstrate that context complexity is linearly encoded in LLM representations, and we use this signal to guide feature allocation during training. Experiments across three language models (Pythia-70M, Pythia-160M, and Gemma-2-2B) demonstrate that this complexity-driven adaptation significantly outperforms fixed-sparsity approaches on reconstruction fidelity, explained variance, and cosine similarity metrics while eliminating the computational burden of extensive hyperparameter tuning.

The high power consumption and latency-sensitive deployments of large language models (LLMs) have motivated techniques like quantization and sparsity. Contextual sparsity, where the sparsity pattern is input-dependent, is crucial in LLMs because the permanent removal of attention heads or neurons from LLMs can significantly degrade accuracy. Prior work has attempted to model contextual sparsity using neural networks trained to predict activation magnitudes, which can be used to dynamically prune structures with low predicted activation magnitude. In this paper, we look beyond magnitude-based pruning criteria to assess attention head and neuron importance in LLMs. We developed a novel predictor called ShadowLLM, which can shadow the LLM behavior and enforce better sparsity patterns, resulting in over 15% improvement in end-to-end accuracy without increasing latency compared to previous methods. ShadowLLM achieves up to a 20\% speed-up over the state-of-the-art DejaVu framework. These enhancements are validated on models with up to 30 billion parameters. Our code is available at https://github.com/abdelfattah-lab/shadow_llm/{ShadowLLM}.

Exploiting activation sparsity is a promising approach to significantly accelerating the inference process of large language models (LLMs) without compromising performance. However, activation sparsity is determined by activation functions, and commonly used ones like SwiGLU and GeGLU exhibit limited sparsity. Simply replacing these functions with ReLU fails to achieve sufficient sparsity. Moreover, inadequate training data can further increase the risk of performance degradation. To address these challenges, we propose a novel dReLU function, which is designed to improve LLM activation sparsity, along with a high-quality training data mixture ratio to facilitate effective sparsification. Additionally, we leverage sparse activation patterns within the Feed-Forward Network (FFN) experts of Mixture-of-Experts (MoE) models to further boost efficiency. By applying our neuron sparsification method to the Mistral and Mixtral models, only 2.5 billion and 4.3 billion parameters are activated per inference iteration, respectively, while achieving even more powerful model performance. Evaluation results demonstrate that this sparsity achieves a 2-5x decoding speedup. Remarkably, on mobile phones, our TurboSparse-Mixtral-47B achieves an inference speed of 11 tokens per second. Our models are available at https://huggingface.co/PowerInfer

Empirical scaling laws have driven the evolution of large language models (LLMs), yet their coefficients shift whenever the model architecture or data pipeline changes. Mixture-of-Experts (MoE) models, now standard in state-of-the-art systems, introduce a new sparsity dimension that current dense-model frontiers overlook. We investigate how MoE sparsity influences two distinct capability regimes: memorization and reasoning. We train families of MoE Transformers that systematically vary total parameters, active parameters, and top-k routing while holding the compute budget fixed. For every model we record pre-training loss, downstream task loss, and task accuracy, allowing us to separate the train-test generalization gap from the loss-accuracy gap. Memorization benchmarks improve monotonically with total parameters, mirroring training loss. By contrast, reasoning performance saturates and can even regress despite continued gains in both total parameters and training loss. Altering top-k alone has little effect when active parameters are constant, and classic hyperparameters such as learning rate and initialization modulate the generalization gap in the same direction as sparsity. Neither post-training reinforcement learning (GRPO) nor extra test-time compute rescues the reasoning deficit of overly sparse models. Our model checkpoints, code and logs are open-source at https://github.com/rioyokotalab/optimal-sparsity.

Large Language Models (LLMs), while demonstrating remarkable capabilities across various applications, present significant challenges during inference due to their substantial model size, especially when deployed on edge devices. Activation sparsity offers a promising solution to reduce computation and memory movement, enabling more efficient inference, particularly for small-batch on-device applications. However, current approaches face limitations with non-ReLU activation function, which are foundational to most advanced LLMs, or require heavy continual training. Additionally, the difficulty in predicting active channels and limited achievable sparsity ratios constrain the effectiveness of activation sparsity-based methods. In this paper, we introduce R-Sparse, a training-free activation sparsity approach capable of achieving high sparsity levels in advanced LLMs. We conducted two preliminary investigations into how different components contribute to the output within a single linear layer and found two key observations: (i) the non-sparse components of the input function can be regarded as a few bias terms, and (ii) The full computation can be effectively approximated by an appropriate combination of input channels and weight singular values. Building on this, we replace the linear layers in LLMs with a rank-aware sparse inference method that leverages the sparsity of input channels and singular value components, eliminating the need for active channel prediction like the output sparsity based approaches. Experiments on Llama-2/3 and Mistral models across ten diverse tasks demonstrate that R-Sparse achieves comparable performance at 50% model-level sparsity, resulting in a significant 43% end-to-end efficient improvements with customized kernels.

To address the challenge of increasing network size, researchers have developed sparse models through network pruning. However, maintaining model accuracy while achieving significant speedups on general computing devices remains an open problem. In this paper, we present a novel mobile inference acceleration framework SparseByteNN, which leverages fine-grained kernel sparsity to achieve real-time execution as well as high accuracy. Our framework consists of two parts: (a) A fine-grained kernel sparsity schema with a sparsity granularity between structured pruning and unstructured pruning. It designs multiple sparse patterns for different operators. Combined with our proposed whole network rearrangement strategy, the schema achieves a high compression rate and high precision at the same time. (b) Inference engine co-optimized with the sparse pattern. The conventional wisdom is that this reduction in theoretical FLOPs does not translate into real-world efficiency gains. We aim to correct this misconception by introducing a family of efficient sparse kernels for ARM and WebAssembly. Equipped with our efficient implementation of sparse primitives, we show that sparse versions of MobileNet-v1 outperform strong dense baselines on the efficiency-accuracy curve. Experimental results on Qualcomm 855 show that for 30% sparse MobileNet-v1, SparseByteNN achieves 1.27x speedup over the dense version and 1.29x speedup over the state-of-the-art sparse inference engine MNN with a slight accuracy drop of 0.224%. The source code of SparseByteNN will be available at https://github.com/lswzjuer/SparseByteNN

Sparse autoencoders (SAEs) have gained a lot of attention as a promising tool to improve the interpretability of large language models (LLMs) by mapping the complex superposition of polysemantic neurons into monosemantic features and composing a sparse dictionary of words. However, traditional performance metrics like Mean Squared Error and L0 sparsity ignore the evaluation of the semantic representational power of SAEs -- whether they can acquire interpretable monosemantic features while preserving the semantic relationship of words. For instance, it is not obvious whether a learned sparse feature could distinguish different meanings in one word. In this paper, we propose a suite of evaluations for SAEs to analyze the quality of monosemantic features by focusing on polysemous words. Our findings reveal that SAEs developed to improve the MSE-L0 Pareto frontier may confuse interpretability, which does not necessarily enhance the extraction of monosemantic features. The analysis of SAEs with polysemous words can also figure out the internal mechanism of LLMs; deeper layers and the Attention module contribute to distinguishing polysemy in a word. Our semantics focused evaluation offers new insights into the polysemy and the existing SAE objective and contributes to the development of more practical SAEs.

Recent studies have shown that, relative position encoding performs well in selective state space model scanning algorithms, and the architecture that balances SSM and Attention enhances the efficiency and effectiveness of the algorithm, while the sparse activation of the mixture of experts reduces the training cost. I studied the effectiveness of using different position encodings in structured state space dual algorithms, and the more effective SSD-Attn internal and external function mixing method, and designed a more efficient cross domain mixture of experts. I found that the same matrix is very wonderful in different algorithms, which allows us to establish a new hybrid sparse architecture: Cheems. Compared with other hybrid architectures, it is more efficient and more effective in language modeling tasks.

Proteins are fundamental to biology, executing diverse functions through complex physicochemical interactions, and they hold transformative potential across medicine, materials science, and environmental applications. Protein Language Models (pLMs) aim to unlock insights from the vast space of unlabeled protein sequences by learning rich, semantic representations from primary sequences via masked language modeling. However, these models typically exhibit limited generative capacity. In this work, we introduce the Diffusion Sequence Model (DSM), a novel pLM trained with masked diffusion to enable both high-quality representation learning and generative protein design. DSM builds upon the ESM2 architecture by incorporating a masked forward diffusion process inspired by the LLaDA framework. After training, DSM is capable of generating diverse, biomimetic sequences that align with expected amino acid compositions, secondary structures, and predicted functions, even with 90\% token corruption. Furthermore, DSM's learned representations match or exceed those of similarly sized pLMs on downstream tasks. We also introduce DSM(ppi), a variant fine-tuned to generate protein binders by attending to target sequences. We demonstrate DSM(ppi)'s effectiveness on the challenging Bench-tested Binder Benchmark (BenchBB), where both DSM and DSM(ppi) produce candidates with superior predicted binding affinity compared to known binders. Our results establish masked diffusion as a powerful paradigm for unifying protein representation and generation in a single framework.

Scaling the capacity of language models has consistently proven to be a reliable approach for improving performance and unlocking new capabilities. Capacity can be primarily defined by two dimensions: the number of model parameters and the compute per example. While scaling typically involves increasing both, the precise interplay between these factors and their combined contribution to overall capacity remains not fully understood. We explore this relationship in the context of sparse Mixture-of-Experts (MoEs), which allow scaling the number of parameters without proportionally increasing the FLOPs per example. We investigate how varying the sparsity level, i.e., the fraction of inactive parameters, impacts model's performance during pretraining and downstream few-shot evaluation. We find that under different constraints (e.g., parameter size and total training compute), there is an optimal level of sparsity that improves both training efficiency and model performance. These results provide a better understanding of the impact of sparsity in scaling laws for MoEs and complement existing works in this area, offering insights for designing more efficient architectures.

Sparse autoencoders (SAEs) are a promising approach to extracting features from neural networks, enabling model interpretability as well as causal interventions on model internals. SAEs generate sparse feature representations using a sparsifying activation function that implicitly defines a set of token-feature matches. We frame the token-feature matching as a resource allocation problem constrained by a total sparsity upper bound. For example, TopK SAEs solve this allocation problem with the additional constraint that each token matches with at most k features. In TopK SAEs, the k active features per token constraint is the same across tokens, despite some tokens being more difficult to reconstruct than others. To address this limitation, we propose two novel SAE variants, Feature Choice SAEs and Mutual Choice SAEs, which each allow for a variable number of active features per token. Feature Choice SAEs solve the sparsity allocation problem under the additional constraint that each feature matches with at most m tokens. Mutual Choice SAEs solve the unrestricted allocation problem where the total sparsity budget can be allocated freely between tokens and features. Additionally, we introduce a new auxiliary loss function, aux_zipf_loss, which generalises the aux_k_loss to mitigate dead and underutilised features. Our methods result in SAEs with fewer dead features and improved reconstruction loss at equivalent sparsity levels as a result of the inherent adaptive computation. More accurate and scalable feature extraction methods provide a path towards better understanding and more precise control of foundation models.

Large language models (LLMs) with hundreds of billions of parameters have sparked a new wave of exciting AI applications. However, they are computationally expensive at inference time. Sparsity is a natural approach to reduce this cost, but existing methods either require costly retraining, have to forgo LLM's in-context learning ability, or do not yield wall-clock time speedup on modern hardware. We hypothesize that contextual sparsity, which are small, input-dependent sets of attention heads and MLP parameters that yield approximately the same output as the dense model for a given input, can address these issues. We show that contextual sparsity exists, that it can be accurately predicted, and that we can exploit it to speed up LLM inference in wall-clock time without compromising LLM's quality or in-context learning ability. Based on these insights, we propose DejaVu, a system that uses a low-cost algorithm to predict contextual sparsity on the fly given inputs to each layer, along with an asynchronous and hardware-aware implementation that speeds up LLM inference. We validate that DejaVu can reduce the inference latency of OPT-175B by over 2X compared to the state-of-the-art FasterTransformer, and over 6X compared to the widely used Hugging Face implementation, without compromising model quality. The code is available at https://github.com/FMInference/DejaVu.

Sparse computation offers a compelling solution for the inference of Large Language Models (LLMs) in low-resource scenarios by dynamically skipping the computation of inactive neurons. While traditional approaches focus on ReLU-based LLMs, leveraging zeros in activation values, we broaden the scope of sparse LLMs beyond zero activation values. We introduce a general method that defines neuron activation through neuron output magnitudes and a tailored magnitude threshold, demonstrating that non-ReLU LLMs also exhibit sparse activation. To find the most efficient activation function for sparse computation, we propose a systematic framework to examine the sparsity of LLMs from three aspects: the trade-off between sparsity and performance, the predictivity of sparsity, and the hardware affinity. We conduct thorough experiments on LLMs utilizing different activation functions, including ReLU, SwiGLU, ReGLU, and ReLU^2. The results indicate that models employing ReLU^2 excel across all three evaluation aspects, highlighting its potential as an efficient activation function for sparse LLMs. We will release the code to facilitate future research.

Speculative decoding (SD) accelerates Large Language Model (LLM) generation by using an efficient draft model to propose the next few tokens, which are verified by the LLM in a single forward call, reducing latency while preserving its outputs. We focus on retrieval-based SD where the draft model retrieves the next tokens from a non-parametric datastore. Sparse retrieval (REST), which operates on the surface form of strings, is currently the dominant paradigm due to its simplicity and scalability. However, its effectiveness is limited due to the usage of short contexts and exact string matching. Instead, we introduce Dense Retrieval for Speculative Decoding (DReSD), a novel framework that uses approximate nearest neighbour search with contextualised token embeddings to retrieve the most semantically relevant token sequences for SD. Extensive experiments show that DReSD achieves (on average) 87% higher acceptance rates, 65% longer accepted tokens and 19% faster generation speeds compared to sparse retrieval (REST).

Transformer-based language models have found many diverse applications requiring them to process sequences of increasing length. For these applications, the causal self-attention -- which is the only component scaling quadratically w.r.t. the sequence length -- becomes a central concern. While many works have proposed schemes to sparsify the attention patterns and reduce the computational overhead of self-attention, those are often limited by implementations concerns and end up imposing a simple and static structure over the attention matrix. Conversely, implementing more dynamic sparse attentions often results in runtimes significantly slower than computing the full attention using the Flash implementation from Dao et al. (2022). We extend FlashAttention to accommodate a large class of attention sparsity patterns that, in particular, encompass key/query dropping and hashing-based attention. This leads to implementations with no computational complexity overhead and a multi-fold runtime speedup on top of FlashAttention. Even with relatively low degrees of sparsity, our method improves visibly upon FlashAttention as the sequence length increases. Without sacrificing perplexity, we increase the training speed of a transformer language model by 2.0times and 3.3times for sequences of respectively 8k and 16k tokens.

Attention is the cornerstone of modern Large Language Models (LLMs). Yet its quadratic complexity limits the efficiency and scalability of LLMs, especially for those with a long-context window. A promising approach addressing this limitation is to leverage the sparsity in attention. However, existing sparsity-based solutions predominantly rely on predefined patterns or heuristics to approximate sparsity. This practice falls short to fully capture the dynamic nature of attention sparsity in language-based tasks. This paper argues that attention sparsity should be learned rather than predefined. To this end, we design SeerAttention, a new Attention mechanism that augments the conventional attention with a learnable gate that adaptively selects significant blocks in an attention map and deems the rest blocks sparse. Such block-level sparsity effectively balances accuracy and speedup. To enable efficient learning of the gating network, we develop a customized FlashAttention implementation that extracts the block-level ground truth of attention map with minimum overhead. SeerAttention not only applies to post-training, but also excels in long-context fine-tuning. Our results show that at post-training stages, SeerAttention significantly outperforms state-of-the-art static or heuristic-based sparse attention methods, while also being more versatile and flexible to adapt to varying context lengths and sparsity ratios. When applied to long-context fine-tuning with YaRN, SeerAttention can achieve a remarkable 90% sparsity ratio at a 32k context length with minimal perplexity loss, offering a 5.67x speedup over FlashAttention-2.

We present an efficient algorithm for simultaneously training sparse generalized linear models across many related problems, which may arise from bootstrapping, cross-validation and nonparametric permutation testing. Our approach leverages the redundancies across problems to obtain significant computational improvements relative to solving the problems sequentially by a conventional algorithm. We demonstrate our fast simultaneous training of generalized linear models (FaSTGLZ) algorithm on a number of real-world datasets, and we run otherwise computationally intensive bootstrapping and permutation test analyses that are typically necessary for obtaining statistically rigorous classification results and meaningful interpretation. Code is freely available at http://liinc.bme.columbia.edu/fastglz.

The transformer architecture has driven breakthroughs in recent years on tasks which require modeling pairwise relationships between sequential elements, as is the case in natural language understanding. However, long seqeuences pose a problem due to the quadratic complexity of the attention operation. Previous research has aimed to lower the complexity by sparsifying or linearly approximating the attention matrix. Yet, these approaches cannot straightforwardly distill knowledge from a teacher's attention matrix and often require complete retraining from scratch. Furthermore, previous sparse and linear approaches lose interpretability if they cannot produce full attention matrices. To address these challenges, we propose SEA: Sparse linear attention with an Estimated Attention mask. SEA estimates the attention matrix with linear complexity via kernel-based linear attention, then subsequently creates a sparse attention matrix with a top-k selection to perform a sparse attention operation. For language modeling tasks (Wikitext2), previous linear and sparse attention methods show roughly two-fold worse perplexity scores over the quadratic OPT-1.3B baseline, while SEA achieves better perplexity than OPT-1.3B, using roughly half the memory of OPT-1.3B, providing interpretable attention matrix. We believe that our work will have a large practical impact, as it opens the possibility of running large transformers on resource-limited devices with less memory.

We provide a new efficient version of the backpropagation algorithm, specialized to the case where the weights of the neural network being trained are sparse. Our algorithm is general, as it applies to arbitrary (unstructured) sparsity and common layer types (e.g., convolutional or linear). We provide a fast vectorized implementation on commodity CPUs, and show that it can yield speedups in end-to-end runtime experiments, both in transfer learning using already-sparsified networks, and in training sparse networks from scratch. Thus, our results provide the first support for sparse training on commodity hardware.

Sparse autoencoders (SAEs) have lately been used to uncover interpretable latent features in large language models. Here, we explore their potential for decomposing latent representations in complex and high-dimensional biological data, where the underlying variables are often unknown. On simulated data we show that generative hidden variables can be captured in learned representations in the form of superpositions. The degree to which they are learned depends on the completeness of the representations. Superpositions, however, are not identifiable if these generative variables are unknown. SAEs can to some extent recover these variables, yielding interpretable features. Applied to single-cell multi-omics data, we show that an SAE can uncover key biological processes such as carbon dioxide transport and ion homeostasis, which are crucial for red blood cell differentiation and immune function. Our findings highlight how SAEs can be used in advancing interpretability in biological and other scientific domains.

The semantic matching capabilities of neural information retrieval can ameliorate synonymy and polysemy problems of symbolic approaches. However, neural models' dense representations are more suitable for re-ranking, due to their inefficiency. Sparse representations, either in symbolic or latent form, are more efficient with an inverted index. Taking the merits of the sparse and dense representations, we propose an ultra-high dimensional (UHD) representation scheme equipped with directly controllable sparsity. UHD's large capacity and minimal noise and interference among the dimensions allow for binarized representations, which are highly efficient for storage and search. Also proposed is a bucketing method, where the embeddings from multiple layers of BERT are selected/merged to represent diverse linguistic aspects. We test our models with MS MARCO and TREC CAR, showing that our models outperforms other sparse models

Foundational Vision Transformers (ViTs) have limited effectiveness in tasks requiring fine-grained spatial understanding, due to their fixed pre-training resolution and inherently coarse patch-level representations. These challenges are especially pronounced in dense prediction scenarios, such as open-vocabulary segmentation with ViT-based vision-language models, where high-resolution inputs are essential for accurate pixel-level reasoning. Existing approaches typically process large-resolution images using a sliding-window strategy at the pre-training resolution. While this improves accuracy through finer strides, it comes at a significant computational cost. We introduce SPAR: Single-Pass Any-Resolution ViT, a resolution-agnostic dense feature extractor designed for efficient high-resolution inference. We distill the spatial reasoning capabilities of a finely-strided, sliding-window teacher into a single-pass student using a feature regression loss, without requiring architectural changes or pixel-level supervision. Applied to open-vocabulary segmentation, SPAR improves single-pass baselines by up to 10.5 mIoU and even surpasses the teacher, demonstrating effectiveness in efficient, high-resolution reasoning. Code: https://github.com/naomikombol/SPAR

Recently, inspired by the concept of sparsity, Mixture-of-Experts (MoE) models have gained increasing popularity for scaling model size while keeping the number of activated parameters constant. In this study, we thoroughly investigate the sparsity of the dense LLaMA model by constructing MoE for both the attention (i.e., Attention MoE) and MLP (i.e., MLP MoE) modules in the transformer blocks. Specifically, we investigate different expert construction methods and granularities under the same activation conditions to analyze the impact of sparsifying the model. Additionally, to comprehensively evaluate the model's capabilities across various domains (e.g., conversation, code, math) after sparsification, we apply sparsity to the instructed large language models (LLMs) and construct instructed MoE models. To counteract the performance degradation resulting from increased sparsity, we design a two-stage post-training strategy to enhance model performance. Experiments on the LLaMA3 model demonstrate the potential effectiveness of this approach for future developments of instructed MoE models. The source codes and models are available at: https://github.com/OpenSparseLLMs/LLaMA-MoE-v2.

Large Language Models (LLMs) have demonstrated considerable proficiency in general natural language processing (NLP) tasks. Instruction tuning, a successful paradigm, enhances the ability of LLMs to follow natural language instructions and exhibit robust generalization across a wide range of tasks. However, these models often encounter performance limitations across multiple tasks due to constrained model capacity. Expanding this capacity during the instruction tuning phase poses significant challenges. To address this issue, we introduce a novel approach, Parameter-Efficient Sparsity Crafting (PESC), which transitions dense models to sparse models using a Mixture of Experts (MoE) architecture. PESC integrates adapters into the MoE layers of sparse models, differentiating experts without altering the individual weights within these layers. This method significantly reduces computational costs and GPU memory requirements, facilitating model capacity expansion through a minimal increase in parameters via the inserted adapters. Our empirical evaluation demonstrates the effectiveness of the PESC method. Using PESC during instruction tuning, our sparse models, dubbed Camelidae outperform all other opensource sparse models and exhibit superior general capabilities compared to GPT3.5.

Understanding and mitigating the potential risks associated with foundation models (FMs) hinges on developing effective interpretability methods. Sparse Autoencoders (SAEs) have emerged as a promising tool for disentangling FM representations, but they struggle to capture rare, yet crucial concepts in the data. We introduce Specialized Sparse Autoencoders (SSAEs), designed to illuminate these elusive dark matter features by focusing on specific subdomains. We present a practical recipe for training SSAEs, demonstrating the efficacy of dense retrieval for data selection and the benefits of Tilted Empirical Risk Minimization as a training objective to improve concept recall. Our evaluation of SSAEs on standard metrics, such as downstream perplexity and L_0 sparsity, show that they effectively capture subdomain tail concepts, exceeding the capabilities of general-purpose SAEs. We showcase the practical utility of SSAEs in a case study on the Bias in Bios dataset, where SSAEs achieve a 12.5\% increase in worst-group classification accuracy when applied to remove spurious gender information. SSAEs provide a powerful new lens for peering into the inner workings of FMs in subdomains.