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Deep Learning · Large Language Models

Li Shen, Anke Tang, Yong Luo, Tao Sun, Han Hu, Xiaochun Cao

Pruning is a widely used technique for compressing large neural networks that eliminates weights that have minimal impact on the model's performance. Current pruning methods, exemplified by magnitude pruning, assign an importance score to each weight based on its magnitude and remove weights with scores below a certain threshold. Nonetheless, these methods often create a gap between the original dense and the pruned sparse model, potentially impairing performance. Especially when the sparsity ratio is high, the gap becomes more pronounced. To mitigate this issue, we introduce a method to bridge the gap left by pruning by utilizing a low-rank approximation of the difference between the dense and sparse matrices. Our method entails the iterative refinement of the sparse weight matrix augmented by a low-rank adjustment. This technique captures and retains the essential information often lost during pruning, thereby improving the performance of the pruned model. Furthermore, we offer a comprehensive theoretical analysis of our approach, emphasizing its convergence properties and establishing a solid basis for its efficacy. Experimental results on LLaMa models validate its effectiveness on large language models across various pruning techniques and sparsity levels. Our method shows significant improvements: at 50\% sparsity, it reduces perplexity by 53.9\% compared to conventional magnitude pruning on LLaMa-7B. Furthermore, to achieve a specific performance target, our approach enables an 8.6\% reduction in model parameters while maintaining a sparsity ratio of about 50\%.

General Machine Learning · Scalable Algorithms

Fabio Feser, Marina Evangelou

The sparse-group lasso performs both variable and group selection, simultaneously using the strengths of the lasso and group lasso. It has found widespread use in genetics, a field that regularly involves the analysis of high-dimensional data, due to its sparse-group penalty, which allows it to utilize grouping information. However, the sparse-group lasso can be computationally expensive, due to the added shrinkage complexity, and its additional hyperparameter that needs tuning. This paper presents a novel feature reduction method, Dual Feature Reduction (DFR), that uses strong screening rules for the sparse-group lasso and the adaptive sparse-group lasso to reduce their input space before optimization, without affecting solution optimality. DFR applies two layers of screening through the application of dual norms and subdifferentials. Through synthetic and real data studies, it is shown that DFR drastically reduces the computational cost under many different scenarios.

Deep Learning · Large Language Models

Jiazheng Li, Lu Yu, Qing Cui, Zhiqiang Zhang, JUN ZHOU, Yanfang Ye, Chuxu Zhang

High-quality data plays a critical role in the pretraining and fine-tuning of large language models (LLMs), even determining their performance ceiling to some degree. Consequently, numerous data selection methods have been proposed to identify subsets of data that can effectively and efficiently enhance model performance. However, most of these methods focus on general data selection and tend to overlook the specific nuances of domain-related data. In this paper, we introduce MASS, a Mathematical data Selection framework using the Skill graph for pretraining LLMs in the mathematical reasoning domain. By taking into account the unique characteristics of mathematics and reasoning, we construct a skill graph that captures the mathematical skills and their interrelations from a reference dataset. This skill graph guides us in assigning quality scores to the target dataset, enabling us to select the top-ranked subset which is further used to pretrain LLMs. Experimental results demonstrate the efficiency and effectiveness of MASS across different model sizes (1B and 7B) and pretraining datasets (web data and synthetic data). Specifically, in terms of efficiency, models trained on subsets selected by MASS can achieve similar performance to models trained on the original datasets, with a significant reduction in the number of trained tokens - ranging from 50\% to 70\% fewer tokens. In terms of effectiveness, when trained on the same amount of tokens, models trained on the data selected by MASS outperform those trained on the original datasets by 3.3\% to 5.9\%. These results underscore the potential of MASS to improve both the efficiency and effectiveness of pretraining LLMs.

Applications · Chemistry, Physics, and Earth Sciences

Henrik Schopmans, Pascal Friederich

Efficient sampling of unnormalized probability densities such as theBoltzmann distribution of molecular systems is a longstanding challenge.Next to conventional approaches like molecular dynamics or Markov chainMonte Carlo, variational approaches, such as training normalizing flows withthe reverse Kullback-Leibler divergence, have been introduced. However, suchmethods are prone to mode collapse and often do not learn to sample the fullconfigurational space. Here, we present temperature-annealed Boltzmanngenerators (TA-BG) to address this challenge. First, we demonstrate thattraining a normalizing flow with the reverse Kullback-Leibler divergence athigh temperatures is possible without mode collapse. Furthermore, weintroduce a reweighting-based training objective to anneal the distribution to lower target temperatures.We apply this methodology to three molecular systems of increasing complexity and, compared to the baseline, achieve better results in almost all metrics while requiring up to three times fewer target energy evaluations. For the largest system, our approach is the only method that accurately resolves the metastable states of the system.

Applications · Computer Vision

Junhang Li, Yu Guo, Xian, Shengfeng He

Images are often obstructed by various obstacles due to capture limitations, hindering the observation of objects of interest. Most existing methods address occlusions from specific elements like fences or raindrops, but are constrained by the wide range of real-world obstructions, making comprehensive data collection impractical. To overcome these challenges, we propose Instruct2See, a novel zero-shot framework capable of handling both seen and unseen obstacles. The core idea of our approach is to unify obstruction removal by treating it as a soft-hard mask restoration problem, where any obstruction can be represented using multi-modal prompts, such as visual semantics and textual instructions, processed through a cross-attention unit to enhance contextual understanding and improve mode control. Additionally, a tunable mask adapter allows for dynamic soft masking, enabling real-time adjustment of inaccurate masks. Extensive experiments on both in-distribution and out-of-distribution obstacles show that Instruct2See consistently achieves strong performance and generalization in obstruction removal, regardless of whether the obstacles were present during the training phase. Code and dataset are available at https://jhscut.github.io/Instruct2See.

Deep Learning · Generative Models and Autoencoders

Pengsheng Guo, Alex Schwing

We study Variational Rectified Flow Matching, a framework that enhances classic rectified flow matching by modeling multi-modal velocity vector-fields. At inference time, classic rectified flow matching 'moves' samples from a source distribution to the target distribution by solving an ordinary differential equation via integration along a velocity vector-field. At training time, the velocity vector-field is learnt by linearly interpolating between coupled samples one drawn from the source and one drawn from the target distribution randomly. This leads to ''ground-truth'' velocity vector-fields that point in different directions at the same location, i.e., the velocity vector-fields are multi-modal/ambiguous. However, since training uses a standard mean-squared-error loss, the learnt velocity vector-field averages ''ground-truth'' directions and isn't multi-modal. In contrast, variational rectified flow matching learns and samples from multi-modal flow directions. We show on synthetic data, MNIST, CIFAR-10, and ImageNet that variational rectified flow matching leads to compelling results.

General Machine Learning · Causality

Yong Wu, Yanwei Fu, Shouyan Wang, Xinwei Sun

Bivariate causal discovery is challenging when unmeasured confounders exist. To adjust for the bias, previous methods employed the proxy variable (*i.e.*, negative control outcome (NCO)) to test the treatment-outcome relationship through integral equations -- and assumed that violation of this equation indicates the causal relationship. Upon this, they could establish asymptotic properties for causal hypothesis testing. However, these methods either relied on parametric assumptions or required discretizing continuous variables, which may lead to information loss. Moreover, it is unclear when this underlying integral-related assumption holds, making it difficult to justify the utility in practice. To address these problems, we first consider the scenario where only NCO is available. We propose a novel non-parametric procedure, which enjoys asymptotic properties and preserves more information. Moreover, we find that when NCO affects the outcome, the above integral-related assumption may not hold, rendering the causal relation unidentifiable. Informed by this, we further consider the scenario when the negative control exposure (NCE) is also available. In this scenario, we construct another integral restriction aided by this proxy, which can discover causation when NCO affects the outcome. We demonstrate these findings and the effectiveness of our proposals through comprehensive numerical studies.

Deep Learning · Robustness

Sihui Dai, Christian Cianfarani, Vikash Sehwag, Prateek Mittal, Arjun Bhagoji

Robust training methods typically defend against specific attack types, such as $\ell_p$ attacks with fixed budgets, and rarely account for the fact that defenders may encounter new attacks over time. A natural solution is to adapt the defended model to new adversaries as they arise via fine-tuning, a method which we call continual robust training (CRT). However, when implemented naively, fine-tuning on new attacks degrades robustness on previous attacks. This raises the question: \textit{how can we improve the initial training and fine-tuning of the model to simultaneously achieve robustness against previous and new attacks?} We present theoretical results which show that the gap in a model's robustness against different attacks is bounded by how far each attack perturbs a sample in the model's logit space, suggesting that regularizing with respect to this logit space distance can help maintain robustness against previous attacks.Extensive experiments on 3 datasets (CIFAR-10, CIFAR-100, and ImageNette) and over 100 attack combinations demonstrate that the proposed regularization improves robust accuracy with little overhead in training time. Our findings and open-source code lay the groundwork for the deployment of models robust to evolving attacks.

Applications · Neuroscience, Cognitive Science

Yu Zhu, Chunfeng Song, Wanli Ouyang, Shan Yu, Tiejun Huang

Individual brains exhibit striking structural and physiological heterogeneity, yet neural circuits can generate remarkably consistent functional properties across individuals, an apparent paradox in neuroscience. While recent studies have observed preserved neural representations in motor cortex through manual alignment across subjects, the zero-shot validation of such preservation and its generalization to more cortices remain unexplored. Here we present PNBA (Probabilistic Neural-Behavioral Representation Alignment), a new framework that leverages probabilistic modeling to address hierarchical variability across trials, sessions, and subjects, with generative constraints preventing representation degeneration. By establishing reliable cross-modal representational alignment, PNBA reveals robust preserved neural representations in monkey primary motor cortex (M1) and dorsal premotor cortex (PMd) through zero-shot validation. We further establish similar representational preservation in mouse primary visual cortex (V1), reflecting a general neural basis. These findings resolve the paradox of neural heterogeneity by establishing zero-shot preserved neural representations across cortices and species, enriching neural coding insights and enabling zero-shot behavior decoding.

Deep Learning · Large Language Models

Yaoxiang Wang, Haoling Li, Xin Zhang, Jie Wu, Xiao Liu, Wenxiang Hu, Zhongxin Guo, Yangyu Huang, Ying Xin, Yujiu Yang 等

Existing methods for code generation use code snippets as seed data, restricting the complexity and diversity of the synthesized data. In this paper, we introduce a novel feature tree-based synthesis framework, which revolves around hierarchical code features derived from high-level abstractions of code. The feature tree is constructed from raw data and refined iteratively to increase the quantity and diversity of the extracted features, which captures and recognizes more complex patterns and relationships within the code. By adjusting the depth and breadth of the sampled subtrees, our framework provides precise control over the complexity of the generated code, enabling functionalities that range from function-level operations to multi-file scenarios. We fine-tuned widely-used base models to obtain EpiCoder series, achieving state-of-the-art performance on multiple benchmarks at both the function and file levels. In particular, empirical evidence indicates that our approach shows significant potential in the synthesizing of repository-level code data. Our code and data are publicly available.

Deep Learning · Theory

Davide Sartor, Alberto Sinigaglia, Gian Antonio Susto

Imposing input-output constraints in multi-layer perceptrons (MLPs) plays a pivotal role in many real world applications. Monotonicity in particular is a common requirement in applications that need transparent and robust machine learning models. Conventional techniques for imposing monotonicity in MLPs by construction involve the use of non-negative weight constraints and bounded activation functions, which poses well known optimization challenges. In this work, we generalize previous theoretical results, showing that MLPs with non-negative weight constraint and activations that saturate on alternating sides are universal approximators for monotonic functions. Additionally, we show an equivalence between saturation side in the activations and sign of the weight constraint. This connection allows us to prove that MLPs with convex monotone activations and non-positive constrained weights also qualify as universal approximators, in contrast to their non-negative constrained counterparts. This results provide theoretical grounding to the empirical effectiveness observed in previous works, while leading to possible architectural simplification. Moreover, to further alleviate the optimization difficulties, we propose an alternative formulation that allows the network to adjust its activations according to the sign of the weights. This eliminates the requirement for weight reparameterization, easing initialization and improving training stability. Experimental evaluation reinforce the validity of the theoretical results, showing that our novel approach compares favorably to traditional monotonic architectures.

Theory · Probabilistic Methods

Haifeng Wen, Hong XING, Osvaldo Simeone

Post-hoc calibration of pre-trained models is critical for ensuring reliable inference, especially in safety-critical domains such as healthcare. Conformal Prediction (CP) offers a robust post-hoc calibration framework, providing distribution-free statistical coverage guarantees for prediction sets by leveraging held-out datasets. In this work, we address a decentralized setting where each device has limited calibration data and can communicate only with its neighbors over an arbitrary graph topology. We propose two message-passing-based approaches for achieving reliable inference via CP: quantile-based distributed conformal prediction (Q-DCP) and histogram-based distributed conformal prediction (H-DCP). Q-DCP employs distributed quantile regression enhanced with tailored smoothing and regularization terms to accelerate convergence, while H-DCP uses a consensus-based histogram estimation approach. Through extensive experiments, we investigate the trade-offs between hyperparameter tuning requirements, communication overhead, coverage guarantees, and prediction set sizes across different network topologies. The code of our work is released on: https://github.com/HaifengWen/Distributed-Conformal-Prediction.

Theory

Subhodh Kotekal

Given independent and identically distributed data from a compactly supported, $\alpha$-Hölder density $f$, we study estimation of the Fisher information of the Gaussian-smoothed density $f*\varphi_t$, where $\varphi_t$ is the density of $N(0, t)$. We derive the minimax rate including the sharp dependence on $t$ and show some simple, plug-in type estimators are optimal for $t > 0$, even though extra debiasing steps are widely employed in the literature to achieve the sharp rate in the unsmoothed ($t = 0$) case. Due to our result's sharp characterization of the scaling in $t$, plug-in estimators of the mutual information and entropy are shown to achieve the parametric rate by way of the I-MMSE and de Bruijn's identities.

Deep Learning · Foundation Models

Antonia Wüst, Tim Woydt, Lukas Helff, Inga Ibs, Wolfgang Stammer, Devendra Dhami, Constantin Rothkopf, Kristian Kersting

Recently, newly developed Vision-Language Models (VLMs), such as OpenAI's o1, have emerged, seemingly demonstrating advanced reasoning capabilities across text and image modalities. However, the depth of these advances in language-guided perception and abstract reasoning remains underexplored, and it is unclear whether these models can truly live up to their ambitious promises. To assess the progress and identify shortcomings, we enter the wonderland of Bongard problems, a set of classic visual reasoning puzzles that require human-like abilities of pattern recognition and abstract reasoning. With our extensive evaluation setup, we show that while VLMs occasionally succeed in identifying discriminative concepts and solving some of the problems, they frequently falter. Surprisingly, even elementary concepts that may seem trivial to humans, such as simple spirals, pose significant challenges. Moreover, when explicitly asked to recognize ground truth concepts, they continue to falter, suggesting not only a lack of understanding of these elementary visual concepts but also an inability to generalize to unseen concepts. We compare the results of VLMs to human performance and observe that a significant gap remains between human visual reasoning capabilities and machine cognition.

Deep Learning

Haotian Ni, Yake Wei, Hang Liu, Gong Chen, Chong Peng, Hao Lin, Di Hu

Multimodal learning faces challenges in effectively fusing information from diverse modalities, especially when modality quality varies across samples. Dynamic fusion strategies, such as attention mechanism in Transformers, aim to address such challenge by adaptively emphasizing modalities based on the characteristics of input data. However, through amounts of carefully designed experiments, we surprisingly observed that the dynamic adaptability of widely-used self-attention models diminishes. Model tends to prefer one modality regardless of data characteristics. This bias triggers a self-reinforcing cycle that progressively overemphasizes the favored modality, widening the distribution gap in attention keys across modalities and deactivating attention mechanism's dynamic properties. To revive adaptability, we propose a simple yet effective method Rolling Query (RollingQ), which balances attention allocation by rotating the query to break the self-reinforcing cycle and mitigate the key distribution gap. Extensive experiments on various multimodal scenarios validate the effectiveness of RollingQ and the restoration of cooperation dynamics is pivotal for enhancing the broader capabilities of widely deployed multimodal Transformers. The source code is available at https://github.com/GeWu-Lab/RollingQ_ICML2025.

General Machine Learning · Transfer, Multitask and Meta-learning

Ron Tsibulsky, Daniel Nevo, Uri Shalit

Despite the impressive advancements in modern machine learning, achieving robustness in Domain Generalization (DG) tasks remains a significant challenge. In DG, models are expected to perform well on samples from unseen test distributions (also called domains), by learning from multiple related training distributions. Most existing approaches to this problem rely on single-valued predictions, which inherently limit their robustness. We argue that set-valued predictors could be leveraged to enhance robustness across unseen domains, while also taking into account that these sets should be as small as possible. We introduce a theoretical framework defining successful set prediction in the DG setting, focusing on meeting a predefined performance criterion across as many domains as possible, and provide theoretical insights into the conditions under which such domain generalization is achievable. We further propose a practical optimization method compatible with modern learning architectures, that balances robust performance on unseen domains with small prediction set sizes. We evaluate our approach on several real-world datasets from the WILDS benchmark, demonstrating its potential as a promising direction for robust domain generalization.

Applications · Language, Speech and Dialog

Dongchao Yang, Songxiang Liu, Haohan Guo, Jiankun Zhao, Yuanyuan Wang, Helin Wang, Zeqian Ju, Xubo Liu, Xueyuan Chen, Xu Tan 等

Recent advancements in audio language models have underscored the pivotal role of audio tokenization, which converts audio signals into discrete tokens, thereby facilitating the application of language model architectures to the audio domain. In this study, we introduce ALMTokenizer, a novel low-bitrate and semantically rich audio codec tokenizer for audio language models. Prior methods, such as Encodec, typically encode individual audio frames into discrete tokens without considering the use of context information across frames. Unlike these methods, we introduce a novel query-based compression strategy to capture holistic information with a set of learnable query tokens by explicitly modeling the context information across frames. This design not only enables the codec model to capture more semantic information but also encodes the audio signal with fewer token sequences. Additionally, to enhance the semantic information in audio codec models, we introduce the following: (1) A masked autoencoder (MAE) loss, (2) Vector quantization based on semantic priors, and (3) An autoregressive (AR) prediction loss. As a result, ALMTokenizer achieves competitive reconstruction performance relative to state-of-the-art approaches while operating at a lower bitrate. Within the same audio language model framework, ALMTokenizer outperforms previous tokenizers in audio understanding and generation tasks.\footnote{http://dongchaoyang.top/ALMTokenizer/}

Deep Learning · Graph Neural Networks

Yongjian Zhong, Liao Zhu, Hieu Vu, Bijaya Adhikari

Subgraph neural networks have recently gained prominence for various subgraph-level predictive tasks. However, existing methods either \emph{1)} apply simple standard pooling over graph convolutional networks, failing to capture essential subgraph properties, or \emph{2)} rely on rigid subgraph definitions, leading to suboptimal performance. Moreover, these approaches fail to model long-range dependencies both between and within subgraphs—a critical limitation, as many real-world networks contain subgraphs of varying sizes and connectivity patterns. In this paper, we propose a novel implicit subgraph neural network, the first of its kind, designed to capture dependencies across subgraphs. Our approach also integrates label-aware subgraph-level information. We formulate implicit subgraph learning as a bilevel optimization problem and develop a provably convergent algorithm that requires fewer gradient estimations than standard bilevel optimization methods. We evaluate our approach on real-world networks against state-of-the-art baselines, demonstrating its effectiveness and superiority.

Deep Learning · Graph Neural Networks

Daeho Um, Sunoh Kim, Jiwoong Park, Jongin Lim, Seong Jin Ahn, Seulki Park

In this paper, we address learning tasks on graphs with missing features, enhancing the applicability of graph neural networks to real-world graph-structured data. We identify a critical limitation of existing imputation methods based on feature propagation: they produce channels with nearly identical values within each channel, and these low-variance channels contribute very little to performance in graph learning tasks. To overcome this issue, we introduce synthetic features that target the root cause of low-variance channel production, thereby increasing variance in these channels. By preventing propagation-based imputation methods from generating meaningless feature values shared across all nodes, our synthetic feature propagation scheme mitigates significant performance degradation, even under extreme missing rates. Extensive experiments demonstrate the effectiveness of our approach across various graph learning tasks with missing features, ranging from low to extremely high missing rates. Additionally, we provide both empirical evidence and theoretical proof to validate the low-variance problem. The source code is available at https://github.com/daehoum1/fisf.

Deep Learning · Robustness

Simon Geisler, Tom Wollschläger, M. Hesham Abdalla, Vincent Cohen-Addad, Johannes Gasteiger, Stephan Günnemann

To circumvent the alignment of large language models (LLMs), current optimization-based adversarial attacks usually craft adversarial prompts by maximizing the likelihood of a so-called affirmative response. An affirmative response is a manually designed start of a harmful answer to an inappropriate request. While it is often easy to craft prompts that yield a substantial likelihood for the affirmative response, the attacked model frequently does not complete the response in a harmful manner. Moreover, the affirmative objective is usually not adapted to model-specific preferences and essentially ignores the fact that LLMs output a distribution over responses. If low attack success under such an objective is taken as a measure of robustness, the true robustness might be grossly overestimated. To alleviate these flaws, we propose an adaptive and semantic optimization problem over the population of responses. We derive a generally applicable objective via the REINFORCE policy-gradient formalism and demonstrate its efficacy with the state-of-the-art jailbreak algorithms Greedy Coordinate Gradient (GCG) and Projected Gradient Descent (PGD). For example, our objective doubles the attack success rate (ASR) on Llama3 and increases the ASR from 2\% to 50\% with circuit breaker defense.