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Applications · Health / Medicine

Ihab Bendidi, Yassir El Mesbahi, Alisandra Denton, Karush Suri, Kian Kenyon-Dean, Auguste Genovesio, Emmanuel Noutahi

Understanding cellular responses to stimuli is crucial for biological discovery and drug development. Transcriptomics provides interpretable, gene-level insights, while microscopy imaging offers rich predictive features but is harder to interpret. Weakly paired datasets, where samples share biological states, enable multimodal learning but are scarce, limiting their utility for training and multimodal inference. We propose a framework to enhance transcriptomics by distilling knowledge from microscopy images. Using weakly paired data, our method aligns and binds modalities, enriching gene expression representations with morphological information. To address data scarcity, we introduce (1) *Semi-Clipped*, an adaptation of CLIP for cross-modal distillation using pretrained foundation models, achieving state-of-the-art results, and (2) *PEA* (**P**erturbation **E**mbedding **A**ugmentation), a novel augmentation technique that enhances transcriptomics data while preserving inherent biological information. These strategies improve the predictive power and retain the interpretability of transcriptomics, enabling rich unimodal representations for complex biological tasks.

General Machine Learning · Clustering

Jicong Fan

Measuring the distance or similarity between graphs is the foundation of many graph analysis tasks, such as graph classification and clustering, but remains a challenge on large datasets. In this work, we treat the adjacency matrices of two graphs as two kernel matrices given by some unknown indefinite kernel function performed on two discrete distributions and define the distance between the two distributions as a measure, called MMFD, of the dissimilarity between two graphs. We show that MMFD is a pseudo-metric. Although the initial definition of MMFD seems complex, we show that it has a closed-form solution with extremely simple computation. To further improve the efficiency of large-scale clustering, we propose an MMFD-KM with linear space and time complexity with respect to the number of graphs. We also provide a generalization of MMFD, called MFD, which is more effective in exploiting the information of factors of adjacency matrices. The experiments on simulated graphs intuitively show that our methods are effective in comparing graphs. The experiments on real-world datasets demonstrate that, compared to the competitors, our methods have much better clustering performance in terms of three evaluation metrics and time cost.

General Machine Learning · Supervised Learning

Chengyuan Li, Liangxiao Jiang, Wenjun Zhang, Liangjun Yu, Huan Zhang

Due to its simplicity, effectiveness and robustness, naive Bayes (NB) has continued to be one of the top 10 data mining algorithms. To improve its performance, a large number of improved algorithms have been proposed in the last few decades. However, in addition to Gaussian naive Bayes (GNB), there is little work on numerical attributes. At the same time, none of them takes into account the correlations among instances. To fill this gap, we propose a novel algorithm called instance correlation graph-based naive Bayes (ICGNB). Specifically, it first uses original attributes to construct an instance correlation graph (ICG) to represent the correlations among instances. Then, it employs a variational graph auto-encoder (VGAE) to generate new attributes from the constructed ICG and uses them to augment original attributes.Finally, it weights each augmented attribute to alleviate the attribute redundancy and builds GNB on the weighted attributes. The experimental results on tens of datasets show that ICGNB significantly outperforms its deserved competitors.Our codes and datasets are available at https://github.com/jiangliangxiao/ICGNB.

Reinforcement Learning

Mikel Malagón, Josu Ceberio, Jose A Lozano

Advances in large models, reinforcement learning, and open-endedness have accelerated progress toward autonomous agents that can learn and interact in the real world. To achieve this, flexible tools are needed to create rich, yet computationally efficient, environments. While scalable 2D environments fail to address key real-world challenges like 3D navigation and spatial reasoning, more complex 3D environments are computationally expensive and lack features like customizability and multi-agent support. This paper introduces Craftium, a highly customizable and easy-to-use platform for building rich 3D single- and multi-agent environments. We showcase environments of different complexity and nature: from single- and multi-agent tasks to vast worlds with many creatures and biomes, and customizable procedural task generators. Benchmarking shows that Craftium significantly reduces the computational cost of alternatives of similar richness, achieving +2K steps per second more than Minecraft-based frameworks.

General Machine Learning · Evaluation

Wayne Chi, Valerie Chen, Anastasios Angelopoulos, Wei-Lin Chiang, Aditya Mittal, Naman Jain, Tianjun Zhang, Ion Stoica, Chris Donahue, Ameet Talwalkar

Evaluating in-the-wild coding capabilities of large language models (LLMs) is a challenging endeavor with no existing solution. We introduce Copilot Arena, a platform to collect user preferences through native integration into a developer's working environment. Copilot Arena comprises a novel interface for comparing pairs of model outputs, a sampling strategy to reduce experienced latency, and a prompting scheme to enable code completion functionality. Copilot Arena has served over 4.5 million suggestions from 10 models and collected over 11k pairwise judgements. Our results highlight the importance of model evaluations in integrated settings. We find that model rankings from Copilot Arena differ from those of existing evaluations, which we attribute to the unique distribution of data and tasks contained in Copilot Arena. We also identify novel insights into human preferences on code such as an observed consistency in user preference across programming languages yet significant variation in preference due to task category. We open-source Copilot Arena and release data to enable human-centric evaluations and improve understanding of coding assistants.

Probabilistic Methods · Gaussian Processes

Tim Steinert, David Ginsbourger, August Lykke-Møller, Ove Christiansen, Henry Moss

We study the incorporation of equivariances into vector-valued GPs and more general classes of random field models. While kernels guaranteeing equivariances have been investigated previously, their evaluation is often computationally prohibitive due to required integrations over the involved groups. In this work, we provide a kernel characterization of stochastic equivariance for centred second-order vector-valued random fields and we construct integration-free equivariant kernels based on the notion of fundamental regions of group actions. We establish data-efficient and computationally lightweight GP models for velocity fields and molecular electric dipole moments and demonstrate that proposed integration-free kernels may also be leveraged to extract equivariant components from data.

Social Aspects · Accountability, Transparency, and Interpretability

Thibaud Gloaguen, Nikola Jovanović, Robin Staab, Martin Vechev

LLM watermarks stand out as a promising way to attribute ownership of LLM-generated text. One threat to watermark credibility comes from spoofing attacks, where an unauthorized third party forges the watermark, enabling it to falsely attribute arbitrary texts to a particular LLM. Despite recent work demonstrating that state-of-the-art schemes are, in fact, vulnerable to spoofing, no prior work has focused on post-hoc methods to discover spoofing attempts. In this work, we for the first time propose a reliable statistical method to distinguish spoofed from genuinely watermarked text, suggesting that current spoofing attacks are less effective than previously thought. In particular, we show that regardless of their underlying approach, all current learning-based spoofing methods consistently leave observable artifacts in spoofed texts, indicative of watermark forgery. We build upon these findings to propose rigorous statistical tests that reliably reveal the presence of such artifacts and thus demonstrate that a watermark has been spoofed. Our experimental evaluation shows high test power across all learning-based spoofing methods, providing insights into their fundamental limitations and suggesting a way to mitigate this threat.

Deep Learning · Large Language Models

Bohan Lyu, Yadi Cao, Duncan Watson-Parris, Leon Bergen, Taylor Berg-Kirkpatrick, Rose Yu

Large Language Models (LLMs) demonstrate promising capabilities in solving scientific problems but often suffer from the issue of hallucination. While integrating LLMs with tools can mitigate this issue, models fine-tuned on tool usage become overreliant on them and incur unnecessary costs. Inspired by how human experts assess problem complexity before selecting solutions, we propose a novel two-component fine-tuning method, *Adapting while Learning* (AWL). In the first component *World Knowledge Learning* (WKL), LLMs internalize scientific knowledge by learning from tool-generated solutions. In the second component *Tool Usage Adaptation* (TUA), we categorize problems as easy or hard based on the model's accuracy, and train it to maintain direct reasoning for easy problems while switching to tools for hard ones. We validate our method on 6 scientific benchmark datasets across climate science, epidemiology, physics, and other domains. Compared to the original instruct model (8B), models post-trained with AWL achieve 29.11\% higher answer accuracy and 12.72\% better tool usage accuracy, even surpassing state-of-the-art models including GPT-4o and Claude-3.5 on 4 custom-created datasets. Our code is open-source at \url{https://github.com/Rose-STL-Lab/Adapting-While-Learning}.

Etienne Gauthier, Francis Bach, Michael Jordan

As platforms increasingly rely on learning algorithms, collectives may form and seek ways to influence these platforms to align with their own interests. This can be achieved by coordinated submission of altered data. To evaluate the potential impact of such behavior, it is essential to understand the computations that collectives must perform to impact platforms in this way. In particular, collectives need to make a priori assessments of the effect of the collective before taking action, as they may face potential risks when modifying their data. Moreover they need to develop implementable coordination algorithms based on quantities that can be inferred from observed data. We develop a framework that provides a theoretical and algorithmic treatment of these issues and present experimental results in a product evaluation domain.

Optimization · Large Scale, Parallel and Distributed

Shiwei Li, Xiandi Luo, Haozhao Wang, Xing Tang, Shijie Xu, weihongluo, Yuhua Li, xiuqiang He, Ruixuan Li

To improve the training efficiency of federated learning (FL), previous research has employed low-rank decomposition techniques to reduce communication overhead. In this paper, we seek to enhance the performance of these low-rank decomposition methods. Specifically, we focus on three key issues related to decomposition in FL: what to decompose, how to decompose, and how to aggregate. Subsequently, we introduce three novel techniques: Model Update Decomposition (MUD), Block-wise Kronecker Decomposition (BKD), and Aggregation-Aware Decomposition (AAD), each targeting a specific issue. These techniques are complementary and can be applied simultaneously to achieve optimal performance. Additionally, we provide a rigorous theoretical analysis to ensure the convergence of the proposed MUD. Extensive experimental results show that our approach achieves faster convergence and superior accuracy compared to relevant baseline methods. The code is available at https://github.com/Leopold1423/fedmud-icml25.

General Machine Learning · Causality

Xichen Guo, Feng Xie, Yan Zeng, Hao Zhang, zhi geng

We consider the problem of selecting instrumental variables from observational data, a fundamental challenge in causal inference. Existing methods mostly focus on additive linear, constant effects models, limiting their applicability in complex real-world scenarios.In this paper, we tackle a more general and challenging setting: the additive non-linear, constant effects model. We first propose a novel testable condition, termed the Cross Auxiliary-based independent Test (CAT) condition, for selecting the valid IV set. We show that this condition is both necessary and sufficient for identifying valid instrumental variable sets within such a model under milder assumptions. Building on this condition, we develop a practical algorithm for selecting the set of valid instrumental variables. Extensive experiments on both synthetic and two real-world datasets demonstrate the effectiveness and robustness of our proposed approach, highlighting its potential for broader applications in causal analysis.

General Machine Learning · Unsupervised and Semi-supervised Learning

Sagar Shrestha, Xiao Fu

Diversified distribution matching (DDM) finds a unified translation function mapping a diverse collection of conditional source distributions to their target counterparts. DDM was proposed to resolve content misalignment issues in unpaired domain translation, achieving translation identifiability. However, DDM has only been implemented using GANs due to its constraints on the translation function. GANs are often unstable to train and do not provide the transport trajectory information---yet such trajectories are useful in applications such as single-cell evolution analysis and robot route planning. This work introduces *diversified flow matching* (DFM), an ODE-based framework for DDM. Adapting flow matching (FM) to enforce a unified translation function as in DDM is challenging, as FM learns the translation function's velocity rather than the translation function itself. A custom bilevel optimization-based training loss, a nonlinear interpolant, and a structural reformulation are proposed to address these challenges, offering a tangible implementation. To our knowledge, DFM is the first ODE-based approach guaranteeing translation identifiability. Experiments on synthetic and real-world datasets validate the proposed method.

Theory · Deep Learning

Noa Rubin, Kirsten Fischer, Javed Lindner, Inbar Seroussi, Zohar Ringel, Michael Krämer, Moritz Helias

Feature learning in neural networks is crucial for their expressive power and inductive biases, motivating various theoretical approaches. Some approaches describe network behavior after training through a change in kernel scale from initialization, resulting in a generalization power comparable to a Gaussian process. Conversely, in other approaches training results in the adaptation of the kernel to the data, involving directional changes to the kernel. The relationship and respective strengths of these two views have so far remained unresolved. This work presents a theoretical framework of multi-scale adaptive feature learning bridging these two views. Using methods from statistical mechanics, we derive analytical expressions for network output statistics which are valid across scaling regimes and in the continuum between them. A systematic expansion of the network's probability distribution reveals that mean-field scaling requires only a saddle-point approximation, while standard scaling necessitates additional correction terms. Remarkably, we find across regimes that kernel adaptation can be reduced to an effective kernel rescaling when predicting the mean network output in the special case of a linear network. However, for linear and non-linear networks, the multi-scale adaptive approach captures directional feature learning effects, providing richer insights than what could be recovered from a rescaling of the kernel alone.

Deep Learning · Large Language Models

Ping Yu, Weizhe Yuan, Olga Golovneva, Tianhao Wu, Sainbayar Sukhbaatar, JASON WESTON, Jing Xu

Training data quality is one of the most important drivers of final model quality. In this work, we introduce a method for evaluating data integrity based on the assumption that low-quality input prompts result in high variance and low quality responses. This is achieved by measuring the rejected response quality and the reward gap between the chosen and rejected preference pair. Our method, Rejecting Instruction Preferences (RIP) can be used to filter prompts from existing training sets, or to make high quality synthetic datasets, yielding large performance gains across various benchmarks compared to unfiltered data. Using Llama 3.1-8B-Instruct, RIP improves AlpacaEval2 LC Win Rate by 9.4%, Arena-Hard by 8.7%, and WildBench by 9.9%. Using Llama 3.3-70B-Instruct, RIP improves Arena-Hard from 67.5 to 82.9, from 18th place to 6th overall in the leaderboard.

General Machine Learning

Gabriel Thompson, Kai Yue, Chau-Wai Wong, Huaiyu (David) Dai

Decentralized federated learning (DFL) is a collaborative machine learning framework for training a model across participants without a central server or raw data exchange. DFL faces challenges due to statistical heterogeneity, as participants often possess data of different distributions reflecting local environments and user behaviors. Recent work has shown that the neural tangent kernel (NTK) approach, when applied to federated learning in a centralized framework, can lead to improved performance. We propose an approach leveraging the NTK to train client models in the decentralized setting, while introducing a synergy between NTK-based evolution and model averaging. This synergy exploits inter-client model deviation and improves both accuracy and convergence in heterogeneous settings. Empirical results demonstrate that our approach consistently achieves higher accuracy than baselines in highly heterogeneous settings, where other approaches often underperform. Additionally, it reaches target performance in 4.6 times fewer communication rounds. We validate our approach across multiple datasets, network topologies, and heterogeneity settings to ensure robustness and generalization. Source code for NTK-DFL is available at https://github.com/Gabe-Thomp/ntk-dfl}{https://github.com/Gabe-Thomp/ntk-dfl

Social Aspects · Accountability, Transparency, and Interpretability

An Vo, Mohammad Reza Taesiri, Daeyoung Kim, Anh Nguyen

Large language models (LLMs) often exhibit strong biases, e.g, against women or in favor of the number 7. We investigate whether LLMs would be able to output less biased answers when allowed to observe their prior answers to the same question in a multi-turn conversation. To understand which types of questions invite more biased answers, we test LLMs on our proposed set of questions that span 9 topics and belong to three types: (1) Subjective; (2) Random; and (3) Objective. Interestingly, LLMs are able to "de-bias" themselves in a multi-turn conversation in response to questions that seek a Random, unbiased answer. Furthermore, we propose B-score, a novel metric that is effective in detecting biases in Subjective, Random, Easy, and Hard questions. On MMLU, HLE, and CSQA, leveraging B-score substantially improves the verification accuracy of LLM answers (i.e, accepting LLM correct answers and rejecting incorrect ones) compared to using verbalized confidence scores or the frequency of single-turn answers alone. Code and data are available at: b-score.github.io.

Social Aspects · Accountability, Transparency, and Interpretability

Xinhao Zheng, Huiqi Deng, Quanshi Zhang

This paper focuses on the fundamental challenge of partitioning input variables in attribution methods for Explainable AI, particularly in Shapley value-based approaches. Previous methods always compute attributions given a predefined partition but lack theoretical guidance on how to form meaningful variable partitions. We identify that attribution conflicts arise when the attribution of a coalition differs from the sum of its individual variables' attributions. To address this, we analyze the numerical effects of AND-OR interactions in AI models and extend the Shapley value to a new attribution metric for variable coalitions. Our theoretical findings reveal that specific interactions cause attribution conflicts, and we propose three metrics to evaluate coalition faithfulness. Experiments on synthetic data, NLP, image classification, and the game of Go validate our approach, demonstrating consistency with human intuition and practical applicability.

Applications · Robotics

Dantong Niu, Yuvan Sharma, Haoru Xue, Giscard Biamby, Junyi Zhang, Ziteng Ji, Trevor Darrell, Roi Herzig

Foundation models pre-trained on massive unlabeled datasets have revolutionized natural language and computer vision, exhibiting remarkable generalization capabilities, thus highlighting the importance of pre-training. Yet, efforts in robotics have struggled to achieve similar success, limited by either the need for costly robotic annotations or the lack of representations that effectively model the physical world. In this paper, we introduce ARM4R, an **A**uto-regressive **R**obotic **M**odel that leverages low-level **4**D **R**epresentations learned from human video data to yield a better pre-trained robotic model. Specifically, we focus on utilizing 3D point tracking representations from videos derived by lifting 2D representations into 3D space via monocular depth estimation across time. These 4D representations maintain a shared geometric structure between the points and robot state representations up to a linear transformation, enabling efficient transfer learning from human video data to low-level robotic control. Our experiments show that ARM4R can transfer efficiently from human video data to robotics and consistently improves performance on tasks across various robot environments and configurations.

Deep Learning · Large Language Models

Song Bian, Minghao Yan, Shivaram Venkataraman

Scaling laws are powerful tools to predict the performance of large language models. However, current scaling laws fall short of accounting for inference costs. In this work, we first show that model architecture affects inference latency, where models of the same size can have up to $3.5\times$ difference in latency. To tackle this challenge, we modify the Chinchilla scaling laws to co-optimize the model parameter count, the number of training tokens, and the model architecture. Due to the reason that models of similar training loss exhibit gaps in downstream evaluation, we also propose a novel method to train inference-efficient models based on the revised scaling laws. We perform extensive empirical studies to fit and evaluate our inference-aware scaling laws. We vary model parameters from 80M to 1B, training tokens from 1.6B to 30B, and model shapes, training 63 models. Guided by our inference-efficient scaling law and model selection method, we release the Morph-1B model, which improves inference latency by $1.8\times$ while maintaining accuracy on downstream tasks compared to open-source models, pushing the Pareto frontier of accuracy-latency tradeoff.Notably, our experiments reveal that wider and shallower models can yield efficiency gains while preserving accuracy.

Deep Learning · Large Language Models

Quan Wei, Chung-Yiu Yau, Hoi To Wai, Yang Zhao, Dongyeop Kang, Youngsuk Park, Mingyi Hong

Supervised fine-tuning is a standard method for adapting pre-trained large language models (LLMs) to downstream tasks. Quantization has been recently studied as a post-training technique for efficient LLM deployment. To obtain quantized fine-tuned LLMs, conventional pipelines would first fine-tune the pre-trained models, followed by post-training quantization. This often yields suboptimal performance as it fails to leverage the synergy between fine-tuning and quantization. To effectively realize low-bit quantization of weights, activations and KV caches in LLMs, we propose an algorithm named Rotated Straight-Through-Estimator (RoSTE), which combines quantization-aware supervised fine-tuning (QA-SFT) with an adaptive rotation strategy that identifies an effective rotation configuration to reduce activation outliers. We provide theoretical insights on RoSTE by analyzing its prediction error when applied to an overparameterized least square quantized training problem. Our findings reveal that the prediction error is directly proportional to the quantization error of the converged weights, which can be effectively managed through an optimized rotation configuration. Experiments on Pythia, Qwen and Llama models of different sizes demonstrate the effectiveness of RoSTE. Compared to existing post-SFT quantization baselines, our method consistently achieves superior performances across various tasks and different LLM architectures. Our code is available at https://github.com/OptimAI-Lab/RoSTE.