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Social Aspects · Accountability, Transparency and Interpretability

Mateusz Pach, Shyamgopal Karthik, Quentin Bouniot, Serge Belongie, Zeynep Akata

Sparse Autoencoders (SAEs) have recently gained attention as a means to improve the interpretability and steerability of Large Language Models (LLMs), both of which are essential for AI safety. In this work, we extend the application of SAEs to Vision-Language Models (VLMs), such as CLIP, and introduce a comprehensive framework for evaluating monosemanticity at the neuron-level in visual representations. To ensure that our evaluation aligns with human perception, we propose a benchmark derived from a large-scale user study. Our experimental results reveal that SAEs trained on VLMs significantly enhance the monosemanticity of individual neurons, with sparsity and wide latents being the most influential factors. Further, we demonstrate that applying SAE interventions on CLIP's vision encoder directly steers multimodal LLM outputs (e.g., LLaVA), without any modifications to the underlying language model. These findings emphasize the practicality and efficacy of SAEs as an unsupervised tool for enhancing both interpretability and control of VLMs. Code and benchmark data are available at https://github.com/ExplainableML/sae-for-vlm.

Reinforcement Learning · Deep RL

Qinsi Wang, Jinghan Ke, Hancheng Ye, Yueqian Lin, Yuzhe Fu, Jianyi Zhang, Kurt Keutzer, Chenfeng Xu, Yiran Chen

Current Reinforcement Fine-tuning (RFT) paradigms for Large Language Models (LLMs) suffer from sample inefficiency due to the redundant exposure of identical queries under uniform data sampling. While previous work has explored curriculum learning via heuristic difficulty metrics, these strategies exhibit limitations by neglecting the intrinsic learning signals generated by the model itself, thus leading to suboptimal training regimes. In this paper, we identify a model-inherent signal termed *angle concentration* that effectively reflects an LLM's capacity to learn from specific data. We theoretically and empirically demonstrate a correlation between the angular distribution of token hidden state vectors and the resulting gradient, revealing a learning preference for data exhibiting higher angle concentration. Inspired by this finding, we propose GAIN-RL, a Gradient-driven Angle-Informed Navigated RL framework. By leveraging the model's intrinsic angle concentration signal, GAIN-RL dynamically selects training data in each epoch, ensuring consistently impactful gradient updates and thus significantly enhancing overall training efficiency. Empirical evaluations show that GAIN-RL (GRPO) achieves over a 2.5$\times$ acceleration in training efficiency across diverse mathematical and coding tasks and varying model scales. Furthermore, GAIN-RL (GRPO)'s efficient sampling yields data-efficient training, achieving better performance with half the original data compared to vanilla GRPO with full training data.

Applications · Chemistry and Drug Discovery

Yanchen Luo, ZHIYUAN LIU, Yi Zhao, Sihang Li, Hengxing Cai, Kenji Kawaguchi, Tat-Seng Chua, Yang Zhang, Xiang Wang

3D molecule generation is crucial for drug discovery and material science, requiring models to process complex multi-modalities, including atom types, chemical bonds, and 3D coordinates. A key challenge is integrating these modalities of different shapes while maintaining SE(3) equivariance for 3D coordinates. To achieve this, existing approaches typically maintain separate latent spaces for invariant and equivariant modalities, reducing efficiency in both training and sampling. In this work, we propose **U**nified Variational **A**uto-**E**ncoder for **3D** Molecular Latent Diffusion Modeling (**UAE-3D**), a multi-modal VAE that compresses 3D molecules into latent sequences from a unified latent space, while maintaining near-zero reconstruction error. This unified latent space eliminates the complexities of handling multi-modality and equivariance when performing latent diffusion modeling. We demonstrate this by employing the Diffusion Transformer--a general-purpose diffusion model without any molecular inductive bias--for latent generation. Extensive experiments on GEOM-Drugs and QM9 datasets demonstrate that our method significantly establishes new benchmarks in both *de novo* and conditional 3D molecule generation, achieving leading efficiency and quality. On GEOM-Drugs, it reduces FCD by 72.6% over the previous best result, while achieving over 70% relative average improvements in geometric fidelity. Our code is released at [https://github.com/lyc0930/UAE-3D/](https://github.com/lyc0930/UAE-3D/).

Deep Learning · Algorithms

Yunshui Li, Yiyuan Ma, Shen Yan, Chaoyi Zhang, Jing Liu, Jianqiao Lu, Ziwen Xu, Mengzhao Chen, Minrui Wang, Shiyi Zhan 等

Model merging has emerged as a promising technique for enhancing large language models, though its application in large-scale pre-training remains relatively unexplored. In this paper, we present a comprehensive investigation of model merging techniques during the pre-training process. Through extensive experiments with both dense and Mixture-of-Experts (MoE) architectures ranging from millions to over 100 billion parameters, we demonstrate that merging checkpoints trained with constant learning rates not only achieves significant performance improvements but also enables accurate prediction of annealing behavior. These improvements lead to both more efficient model development and significantly lower training costs. Our detailed ablation studies on merging strategies and hyperparameters provide new insights into the underlying mechanisms while uncovering novel applications. Through comprehensive experimental analysis, we offer the open-source community practical pre-training guidelines for effective model merging.

Computer Vision · Everything Else

Namhoon Kim, Sara Fridovich-Keil

Implicit Neural Representations (INRs) have recently shown impressive results, but their fundamental capacity, implicit biases, and scaling behavior remain poorly understood. We investigate the performance of diverse INRs across a suite of 2D and 3D real and synthetic signals with varying effective bandwidth, as well as both overfitting and generalization tasks including tomography, super-resolution, and denoising. By stratifying performance according to model size as well as signal type and bandwidth, our results shed light on how different INR and grid representations allocate their capacity. We find that, for most tasks and signals, a simple regularized grid with interpolation trains faster and to higher quality than any INR with the same number of parameters. We also find limited settings–namely fitting binary signals such as shape contours–where INRs outperform grids, to guide future development and use of INRs towards the most advantageous applications.

Deep Learning · Generative Models and Autoencoders

Chong You, Kan Wu, Zhipeng Jia, Lin Chen, Srinadh Bhojanapalli, Jiaxian Guo, Utku Evci, Jan Wassenberg, Praneeth Netrapalli, Jeremiah Willcock 等

The discovery of the *lazy neuron phenomenon* (Li et al., 2022), where fewer than 10% of the feedforward networks (FFN) parameters in trained Transformers are activated per token, has spurred significant interests in *activation sparsity* for enhancing large model efficiency. While notable progress has been made in translating such sparsity to wall-time benefits across CPUs, GPUs, and TPUs, modern Transformers have moved away from the ReLU activation function crucial to this phenomenon. Existing efforts on re-introducing activation sparsity, e.g., by reverting to ReLU or applying top-k masking, often degrade model quality, increase parameter count, or complicate training. Sparse attention, the application of sparse activation to the attention mechanism, often face similar challenges. This paper introduces the Spark Transformer, a novel architecture that achieves high activation sparsity in both FFN and the attention mechanism while maintaining model quality, parameter count, and standard training procedures. Our method realizes sparsity via top-$k$ masking for explicit control over sparsity level. Crucially, we introduce *statistical top-k*, a hardware-accelerator-friendly, linear-time approximate algorithm that avoids costly sorting and mitigates significant training slowdown from standard top-k operators. Furthermore, Spark Transformer reallocates existing FFN parameters and attention key embeddings to form a low-cost predictor for identifying activated entries. This design not only mitigates quality loss from enforced sparsity, but also enhances wall-time benefit. Pretrained with the Gemma-2 recipe, Spark Transformer demonstrates competitive performance on standard benchmarks while exhibiting significant sparsity: only 8\% of FFN neurons are activated, and each token attends to a maximum of 256 tokens. This translates to a 2.5x reduction in FLOPs, leading to decoding wall-time speedups of up to 1.79x on CPU and 1.40xon GPU.

Social Aspects · Accountability, Transparency and Interpretability

Berk Tinaz, Zalan Fabian, Mahdi Soltanolkotabi

Diffusion models have become the go-to method for text-to-image generation, producing high-quality images from pure noise. However, the inner workings of diffusion models is still largely a mystery due to their black-box nature and complex, multi-step generation process. Mechanistic interpretability techniques, such as Sparse Autoencoders (SAEs), have been successful in understanding and steering the behavior of large language models at scale. However, the great potential of SAEs has not yet been applied toward gaining insight into the intricate generative process of diffusion models. In this work, we leverage the SAE framework to probe the inner workings of a popular text-to-image diffusion model, and uncover a variety of human-interpretable concepts in its activations. Interestingly, we find that *even before the first reverse diffusion step* is completed, the final composition of the scene can be predicted surprisingly well by looking at the spatial distribution of activated concepts. Moreover, going beyond correlational analysis, we design intervention techniques aimed at manipulating image composition and style, and demonstrate that (1) in early stages of diffusion image composition can be effectively controlled, (2) in the middle stages image composition is finalized, however stylistic interventions are effective, and (3) in the final stages only minor textural details are subject to change.

Computer Vision · Vision Models & Multimodal

Mingfei Chen, Zijun Cui, Xiulong Liu, Jinlin Xiang, Yang Zheng, Jingyuan Li, Eli Shlizerman

3D spatial reasoning in dynamic, audio-visual environments is a cornerstone of human cognition yet remains largely unexplored by existing Audio-Visual Large Language Models (AV-LLMs) and benchmarks, which predominantly focus on static or 2D scenes. We introduce SAVVY-Bench, the first benchmark for 3D spatial reasoning in dynamic scenes with synchronized spatial audio. SAVVY-Bench is comprised of thousands of carefully curated question–answer pairs probing both directional and distance relationships involving static and moving objects, and requires fine-grained temporal grounding, consistent 3D localization, and multi-modal annotation. To tackle this challenge, we propose SAVVY, a novel training-free reasoning pipeline that consists of two stages: (i) Egocentric Spatial Tracks Estimation, which leverages AV-LLMs as well as other audio-visual methods to track the trajectories of key objects related to the query using both visual and spatial audio cues, and (ii) Dynamic Global Map Construction, which aggregates multi-modal queried object trajectories and converts them into a unified global dynamic map. Using the constructed map, a final QA answer is obtained through a coordinate transformation that aligns the global map with the queried viewpoint. Empirical evaluation demonstrates that SAVVY substantially enhances performance of state-of-the-art AV-LLMs, setting a new standard and stage for approaching dynamic 3D spatial reasoning in AV-LLMs.

Applications · Physics

Jinlin Xiang, Minho Choi, Yubo Zhang, Zhihao Zhou, Arka Majumdar, Eli Shlizerman

Hybrid Optical Neural Networks (ONNs, typically consisting of an optical frontend and a digital backend) offer an energy-efficient alternative to fully digital deep networks for real-time, power-constrained systems. However, their adoption is limited by two main challenges: the accuracy gap compared to large-scale networks during training, and discrepancies between simulated and fabricated systems that further degrade accuracy. While previous work has proposed end-to-end optimizations for specific datasets (e.g., MNIST) and optical systems, these approaches typically lack generalization across tasks and hardware designs. To address these limitations, we propose a task-agnostic and hardware-agnostic pipeline that supports image classification and segmentation across diverse optical systems. To assist optical system design before training, we design the metasurface layout based on fabrication constraints. For training, we introduce Neural Tangent Knowledge Distillation (NTKD), which aligns optical models with electronic teacher networks, thereby narrowing the accuracy gap. After fabrication, NTKD also guides fine-tuning of the digital backend to compensate for implementation errors. Experiments on multiple datasets (e.g., MNIST, CIFAR, Carvana Masking) and hardware configurations show that our pipeline consistently improves ONN performance and enables practical deployment in both pre-fabrication simulations and physical implementations.

Deep Learning · Algorithms

Kechi Zhang, Ge Li, Jia Li, Huangzhao Zhang, Yihong Dong, Jia Li, Jingjing Xu, Zhi Jin

The Transformer architecture has emerged as a landmark advancement within the broad field of artificial intelligence, effectively catalyzing the advent of large language models (LLMs). However, despite its remarkable capabilities and the substantial progress it has facilitated, the Transformer architecture still has some limitations. One such intrinsic limitation is its inability to effectively recognize regular expressions or deterministic context-free grammars. Drawing inspiration from pushdown automata, which efficiently resolve deterministic context-free grammars using stacks, we equip layers with a differentiable stack and propose StackTrans to address the aforementioned issue within LLMs. Unlike previous approaches that modify the attention computation, StackTrans explicitly incorporates hidden state stacks between Transformer layers. This design maintains compatibility with existing frameworks like flash-attention. Specifically, our design features stack operations -- such as pushing and popping hidden states -- that are differentiable and can be learned in an end-to-end manner. Our comprehensive evaluation spans benchmarks for both Chomsky hierarchy and large-scale natural languages. Across these diverse tasks, StackTrans consistently outperforms standard Transformer models and other baselines. We have successfully scaled StackTrans up from 360M to 7B parameters. In particular, our from-scratch pretrained model StackTrans-360M outperforms several larger open-source LLMs with 2–3x more parameters, showcasing its superior efficiency and reasoning capability.

Deep Learning · Everything Else

Huanyu Liu, Jia Li, Hao Zhu, Kechi Zhang, Yihong Dong, Ge Li

How to design reinforcement learning (RL) tasks that effectively unleash the reasoning capability of large language models (LLMs) remains an open question. Existing RL tasks (e.g., math, programming, and constructing reasoning tasks) suffer from three key limitations: (1) Scalability. They rely heavily on human annotation or expensive LLM synthesis to generate sufficient training data. (2) Verifiability. LLMs' outputs are hard to verify automatically and reliably. (3) Controllable Difficulty. Most tasks lack fine-grained difficulty control, making it hard to train LLMs to develop reasoning ability from easy to hard. To address these limitations, we propose Saturn, a SAT-based RL framework that uses Boolean Satisfiability (SAT) problems to train and evaluate LLMs reasoning. Saturn enables scalable task construction, rule-based verification, and precise difficulty control. Saturn designs a curriculum learning pipeline that continuously improves LLMs' reasoning capability by constructing SAT tasks of increasing difficulty and training LLMs from easy to hard. To ensure stable training, we design a principled mechanism to control difficulty transitions. We introduce Saturn-2.6k, a dataset of 2,660 SAT problems with varying difficulty. It supports the evaluation of how LLM reasoning changes with problem difficulty. We apply Saturn to DeepSeek-R1-Distill-Qwen and obtain Saturn-1.5B and Saturn-7B. We achieve several notable results: (1) On SAT problems, Saturn-1.5B and Saturn-7B achieve average pass@3 improvements of +14.0 and +28.1, respectively. (2) On math and programming tasks, Saturn-1.5B and Saturn-7B improve average scores by +4.9 and +1.8 on benchmarks (e.g., AIME, LiveCodeBench). (3) Compared to the state-of-the-art (SOTA) approach in constructing RL tasks, Saturn achieves further improvements of +8.8\%. We release the source code, data, and models to support future research.

Deep Learning · Everything Else

Yihong Dong, Ge Li, Yongding Tao, Xue Jiang, Kechi Zhang, Jia Li, Jinliang Deng, Jing Su, Jun Zhang, Jingjing Xu

Despite the remarkable successes of general-purpose neural networks, such as MLPs and Transformers, we find that they exhibit notable shortcomings in modeling and reasoning about periodic phenomena, achieving only marginal performance within the training domain and failing to generalize effectively to out-of-domain (OOD) scenarios. Periodicity is ubiquitous throughout nature and science. Therefore, neural networks should be equipped with the essential ability to model and handle periodicity. In this work, we propose FAN, a novel neural network that effectively addresses periodicity modeling challenges while offering broad applicability similar to MLP with fewer parameters and FLOPs. Periodicity is naturally integrated into FAN's structure and computational processes by introducing the Fourier Principle. Unlike existing Fourier-based networks, which possess particular periodicity modeling abilities but face challenges in scaling to deeper networks and are typically designed for specific tasks, our approach overcomes this challenge to enable scaling to large-scale models and maintains the capability to be applied to more types of tasks. Through extensive experiments, we demonstrate the superiority of FAN in periodicity modeling tasks and the effectiveness and generalizability of FAN across a range of real-world tasks. Moreover, we reveal that compared to existing Fourier-based networks, FAN accommodates both periodicity modeling and general-purpose modeling well.

General Machine Learning · Everything Else

Annie Marsden, Elad Hazan

We study the problem of preconditioning in the setting of sequential prediction. From the theoretical lens of linear dynamical systems, we show that applying a convolution to the input sequence translates to applying a polynomial to the unknown transition matrix in the hidden space. With this insight, we develop a novel preconditioning method that convolves the input sequence with the coefficients of the Chebyshev or Legendre polynomials. We formally prove that this improves the regret of a wide family of prediction methods. We proceed to apply this preconditioning technique to the method of spectral filtering. This gives the first sublinear regret bound that is also hidden-dimension free (up to logarithmic factors) even when the hidden transition matrix is asymmetric. From rigorous experiments on synthetic data we show that our simple preconditioning method generalizes to both 1) settings where the data is \emph{not} from a linear dynamical system and 2) a broad range of learning algorithms, including recurrent neural networks.

Applications · Genetics, Cell Biology, etc

Jianle Sun, Chaoqi Liang, Ran Wei, Peng Zheng, LEI BAI, Wanli Ouyang, Hongliang Yan, Peng Ye

Advances in single-cell sequencing have enabled high-resolution profiling of diverse molecular modalities, while integrating unpaired multi-omics single-cell data remains challenging. Existing approaches either rely on pair information or prior correspondences, or require computing a global pairwise coupling matrix, limiting their scalability and flexibility. In this paper, we introduce a scalable and flexible generative framework called single-cell Multi-omics Regularized Disentangled Representations (scMRDR) for unpaired multi-omics integration. Specifically, we disentangle each cell’s latent representations into modality-shared and modality-specific components using a well-designed $\beta$-VAE architecture, which are augmented with isometric regularization to preserve intra-omics biological heterogeneity, adversarial objective to encourage cross-modal alignment, and masked reconstruction loss strategy to address the issue of missing features across modalities. Our method achieves excellent performance on benchmark datasets in terms of batch correction, modality alignment, and biological signal preservation. Crucially, it scales effectively to large-level datasets and supports integration of more than two omics, offering a powerful and flexible solution for large-scale multi-omics data integration and downstream biological discovery.

Optimization · Stochastic & Convex Optimization

Annie Marsden, Liam O'Carroll, Aaron Sidford, Chenyi Zhang

We consider the problem of minimizing a $d$-dimensional Lipschitz convex function using a stochastic gradient oracle. We introduce and motivate a setting where the noise of the stochastic gradient is isotropic in that it is bounded in every direction with high probability. We then develop an algorithm for this setting which improves upon prior results by a factor of $d$ in certain regimes, and as a corollary, achieves a new state-of-the-art complexity for sub-exponential noise. We give matching lower bounds (up to polylogarithmic factors) for both results. Additionally, we develop an efficient quantum isotropifier, a quantum algorithm which converts a variance-bounded quantum sampling oracle into one that outputs an unbiased estimate with isotropic error. Combining our results, we obtain improved dimension-dependent rates for quantum stochastic convex optimization.

Applications · Neuroscience, Cognitive Science

Leonie Bossemeyer, Samuel Heinrich, Grant Van Horn, Oisin Mac Aodha

Mastering fine-grained visual recognition, essential in many expert domains, can require that specialists undergo years of dedicated training. Modeling the progression of such expertize in humans remains challenging, and accurately inferring a human learner’s knowledge state is a key step toward understanding visual learning. We introduce CleverBirds, a large-scale knowledge tracing benchmark for fine-grained bird species recognition. Collected by the citizen-science platform eBird, it offers insight into how individuals acquire expertize in complex fine-grained classification. More than 40,000 participants have engaged in the quiz, answering over 17 million multiple-choice questions spanning over 10,000 bird species, with long-range learning patterns across an average of 400 questions per participant. We release this dataset to support the development and evaluation of new methods for visual knowledge tracing. We show that tracking learners' knowledge is challenging, especially across participant subgroups and question types, with different forms of contextual information offering varying degrees of predictive benefit. CleverBirds is among the largest benchmark of its kind, offering a substantially higher number of learnable concepts. With it, we hope to enable new avenues for studying the development of visual expertize over time and across individuals.

Applications · Time Series

Bosong Huang, Ming Jin, Yuxuan Liang, Johan Barthelemy, Debo Cheng, Qingsong Wen, Chenghao Liu, Shirui Pan

Explaining time series classification models is crucial, particularly in high-stakes applications such as healthcare and finance, where transparency and trust play a critical role. Although numerous time series classification methods have identified key subsequences, known as shapelets, as core features for achieving state-of-the-art performance and validating their pivotal role in classification outcomes, existing post-hoc time series explanation (PHTSE) methods primarily focus on timestep-level feature attribution. These explanation methods overlook the fundamental prior that classification outcomes are predominantly driven by key shapelets. To bridge this gap, we present ShapeX, an innovative framework that segments time series into meaningful shapelet-driven segments and employs Shapley values to assess their saliency. At the core of ShapeX lies the Shapelet Describe-and-Detect (SDD) framework, which effectively learns a diverse set of shapelets essential for classification. We further demonstrate that ShapeX produces explanations which reveal causal relationships instead of just correlations, owing to the atomicity properties of shapelets. Experimental results on both synthetic and real-world datasets demonstrate that ShapeX outperforms existing methods in identifying the most relevant subsequences, enhancing both the precision and causal fidelity of time series explanations.

General Machine Learning · Everything Else

Ben Gao, Jordan Patracone, Stephane Chretien, Olivier Alata

We introduce Conformal Online Learning of Koopman embeddings (COLoKe), a novel framework for adaptively updating Koopman-invariant representations of nonlinear dynamical systems from streaming data. Our modeling approach combines deep feature learning with multistep prediction consistency in the lifted space, where the dynamics evolve linearly. To prevent overfitting, COLoKe employs a conformal-style mechanism that shifts the focus from evaluating the conformity of new states to assessing the consistency of the current Koopman model. Updates are triggered only when the current model’s prediction error exceeds a dynamically calibrated threshold, allowing selective refinement of the Koopman operator and embedding. Empirical results on benchmark dynamical systems demonstrate the effectiveness of COLoKe in maintaining long-term predictive accuracy while significantly reducing unnecessary updates and avoiding overfitting.

Theory · Everything Else

Zheng He, Roman Pogodin, Yazhe Li, Namrata Deka, Arthur Gretton, Danica J. Sutherland

Tests of conditional independence (CI) underpin a number of important problems in machine learning and statistics, from causal discovery to evaluation of predictor fairness and out-of-distribution robustness. Shah and Peters (2020) showed that, contrary to the unconditional case, no universally finite-sample valid test can ever achieve nontrivial power. While informative, this result (based on “hiding” dependence) does not seem to explain the frequent practical failures observed with popular CI tests. We investigate the Kernel-based Conditional Independence (KCI) test – of which we show the Generalized Covariance Measure underlying many recent tests is _nearly_ a special case – and identify the major factors underlying its practical behavior. We highlight the key role of errors in the conditional mean embedding estimate for the Type I error, while pointing out the importance of selecting an appropriate conditioning kernel (not recognized in previous work) as being necessary for good test power but also tending to inflate Type I error.

Deep Learning · Generative Models and Autoencoders

Yijia Dai, Zhaolin Gao, Yahya Sattar, Sarah Dean, Jennifer Sun

Hidden Markov Models (HMMs) are fundamental tools for modeling sequential data with latent states that follow Markovian dynamics. However, they present significant challenges in model fitting and computational efficiency on real-world datasets. In this work, we demonstrate that pre-trained large language models (LLMs) can effectively model data generated by HMMs through in-context learning (ICL) — their ability to learn patterns from examples within the input context. We evaluate LLMs' performance on diverse synthetic HMMs, showing that their prediction accuracy converges to the theoretical optimum. We discover novel scaling trends influenced by HMM properties and provide theoretical conjectures for these empirical observations. Furthermore, we present practical guidelines for scientists on using ICL as a diagnostic tool for complex data. Applied to real-world animal decision-making tasks, ICL achieves competitive performance with models designed by human experts. Our results demonstrate potential for advancing understanding of LLMs' capabilities while opening new avenues for scientific discovery of biological mechanisms and hidden structures in real-world phenomena.