Unified generation of sequence and structure for scientific data (e.g., materials, molecules, proteins) is a critical task. Existing approaches primarily rely on either autoregressive sequence models or diffusion models, each offering distinct advantages and facing notable limitations. Autoregressive models, such as GPT, Llama, and Phi-4, have demonstrated remarkable success in natural language generation and have been extended to multimodal tasks (e.g., image, video, and audio) using advanced encoders like VQ-VAE to represent complex modalities as discrete sequences. However, their direct application to scientific domains is challenging due to the high precision requirements and the diverse nature of scientific data. On the other hand, diffusion models excel at generating high-dimensional scientific data, such as protein, molecule, and material structures, with remarkable accuracy. Yet, their inability to effectively model sequences limits their potential as general-purpose multimodal foundation models. To address these challenges, we propose UniGenX, a unified framework that combines autoregressive next-token prediction with conditional diffusion models. This integration leverages the strengths of autoregressive models to ease the training of conditional diffusion models, while diffusion-based generative heads enhance the precision of autoregressive predictions. We validate the effectiveness of UniGenX on material and small molecule generation tasks, achieving a significant leap in state-of-the-art performance for material crystal structure prediction and establishing new state-of-the-art results for small molecule structure prediction, de novo design, and conditional generation. Notably, UniGenX demonstrates significant improvements, especially in handling long sequences for complex structures, showcasing its efficacy as a versatile tool for scientific data generation.

We consider nonconvex optimization problem over simplex, and more generally, a product of simplices. We provide an algorithm, Langevin Multiplicative Weights Update (LMWU) for solving global optimization problems by adding a noise scaling with the non-Euclidean geometry in the simplex. Non-convex optimization has been extensively studied by machine learning community due to its application in various scenarios such as neural network approximation and finding Nash equilibrium. Despite recent progresses on provable guarantee of escaping and avoiding saddle point (convergence to local minima) and global convergence of Langevin gradient based method without constraints, the global optimization with constraints is less studied. We show that LMWU algorithm is provably convergent to interior global minima with a non-asymptotic convergence analysis. We verify the efficiency of the proposed algorithm in real data set from polynomial portfolio management, where optimization of a highly non-linear objective function plays a crucial role.

Inspired by the success of DeepSeek-R1, we explore the potential of rule-based reinforcement learning (RL) in large reasoning models. To analyze reasoning dynamics, we use synthetic logic puzzles as training data due to their controllable complexity and straightforward answer verification. We make some key technical contributions that lead to effective and stable RL training: a system prompt that emphasizes the thinking and answering process, a stringent format reward function that penalizes outputs for taking shortcuts, and a straightforward training recipe that achieves stable convergence. Our 7B model develops advanced reasoning skills-such as reflection, verification, and summarization-that are absent from the logic corpus. Remarkably, after training on just 5K logic problems, it demonstrates generalization abilities to the challenging math benchmarks AIME and AMC.

Foundation models have revolutionized natural language processing and artificial intelligence, significantly enhancing how machines comprehend and generate human languages. Inspired by the success of these foundation models, researchers have developed foundation models for individual scientific domains, including small molecules, materials, proteins, DNA, and RNA. However, these models are typically trained in isolation, lacking the ability to integrate across different scientific domains. Recognizing that entities within these domains can all be represented as sequences, which together form the "language of nature", we introduce Nature Language Model (briefly, NatureLM), a sequence-based science foundation model designed for scientific discovery. Pre-trained with data from multiple scientific domains, NatureLM offers a unified, versatile model that enables various applications including: (i) generating and optimizing small molecules, proteins, RNA, and materials using text instructions; (ii) cross-domain generation/design, such as protein-to-molecule and protein-to-RNA generation; and (iii) achieving state-of-the-art performance in tasks like SMILES-to-IUPAC translation and retrosynthesis on USPTO-50k. NatureLM offers a promising generalist approach for various scientific tasks, including drug discovery (hit generation/optimization, ADMET optimization, synthesis), novel material design, and the development of therapeutic proteins or nucleotides. We have developed NatureLM models in different sizes (1 billion, 8 billion, and 46.7 billion parameters) and observed a clear improvement in performance as the model size increases.

When machine learning (ML) algorithms are used to automate human-related decisions, human agents may gain knowledge of the decision policy and behave strategically to obtain desirable outcomes. Strategic Classification (SC) has been proposed to address the interplay between agents and decision-makers. Prior work on SC has relied on assumptions that agents are perfectly or approximately rational, responding to decision policies by maximizing their utilities. Verifying these assumptions is challenging due to the difficulty of collecting real-world agent responses. Meanwhile, the growing adoption of large language models (LLMs) makes it increasingly likely that human agents in SC settings will seek advice from these tools. We propose using strategic advice generated by LLMs to simulate human agent responses in SC. Specifically, we examine five critical SC scenarios -- hiring, loan applications, school admissions, personal income, and public assistance programs -- and simulate how human agents with diverse profiles seek advice from LLMs. We then compare the resulting agent responses with the best responses generated by existing theoretical models. Our findings reveal that: (i) LLMs and theoretical models generally lead to agent score or qualification changes in the same direction across most settings, with both achieving similar levels of fairness; (ii) state-of-the-art commercial LLMs (e.g., GPT-3.5, GPT-4) consistently provide helpful suggestions, though these suggestions typically do not result in maximal score or qualification improvements; and (iii) LLMs tend to produce more diverse agent responses, often favoring more balanced effort allocation strategies. These results suggest that theoretical models align with LLMs to some extent and that leveraging LLMs to simulate more realistic agent responses offers a promising approach to designing trustworthy ML systems.

As machine learning (ML) algorithms are used in applications that involve humans, concerns have arisen that these algorithms may be biased against certain social groups. Counterfactual fairness (CF) is a fairness notion proposed in Kusner et al. (2017) that measures the unfairness of ML predictions; it requires that the prediction perceived by an individual in the real world has the same marginal distribution as it would be in a counterfactual world, in which the individual belongs to a different group. Although CF ensures fair ML predictions, it fails to consider the downstream effects of ML predictions on individuals. Since humans are strategic and often adapt their behaviors in response to the ML system, predictions that satisfy CF may not lead to a fair future outcome for the individuals. In this paper, we introduce lookahead counterfactual fairness (LCF), a fairness notion accounting for the downstream effects of ML models which requires the individual future status to be counterfactually fair. We theoretically identify conditions under which LCF can be satisfied and propose an algorithm based on the theorems. We also extend the concept to path-dependent fairness.

We introduce BackdoorMBTI, the first backdoor learning toolkit and benchmark designed for multimodal evaluation across three representative modalities from eleven commonly used datasets. BackdoorMBTI provides a systematic backdoor learning pipeline, encompassing data processing, data poisoning, backdoor training, and evaluation. The generated poison datasets and backdoor models enable detailed evaluation of backdoor defense methods. Given the diversity of modalities, BackdoorMBTI facilitates systematic evaluation across different data types. Furthermore, BackdoorMBTI offers a standardized approach to handling practical factors in backdoor learning, such as issues related to data quality and erroneous labels. We anticipate that BackdoorMBTI will expedite future research in backdoor defense methods within a multimodal context. Code is available at https://anonymous.4open.science/r/BackdoorMBTI-D6A1/README.md.

Machine learning models deployed in open-world scenarios often encounter unfamiliar conditions and perform poorly in unanticipated situations. As AI systems advance and find application in safety-critical domains, effectively handling out-of-distribution (OOD) data is crucial to building open-world learning systems. In this work, we introduce ALOE, a novel active learning algorithm for open-world environments designed to enhance model adaptation by incorporating new OOD classes via a two-stage approach. First, diversity sampling selects a representative set of examples, followed by energy-based OOD detection to prioritize likely unknown classes for annotation. This strategy accelerates class discovery and learning, even under constrained annotation budgets. Evaluations on three long-tailed image classification benchmarks demonstrate that ALOE outperforms traditional active learning baselines, effectively expanding known categories while balancing annotation cost. Our findings reveal a crucial tradeoff between enhancing known-class performance and discovering new classes, setting the stage for future advancements in open-world machine learning.

Performative prediction (PP) is a framework that captures distribution shifts that occur during the training of machine learning models due to their deployment. As the trained model is used, its generated data could cause the model to evolve, leading to deviations from the original data distribution. The impact of such model-induced distribution shifts in the federated learning (FL) setup remains unexplored despite being increasingly likely to transpire in real-life use cases. Although Jin et al. (2024) recently extended PP to FL in a straightforward manner, the resulting model only converges to a performative stable point, which may be far from optimal. The methods in Izzo et al. (2021); Miller et al. (2021) can find a performative optimal point in centralized settings, but they require the performative risk to be convex and the training data to be noiseless, assumptions often violated in realistic FL systems. This paper overcomes all of these shortcomings and proposes Performative robust optimal Federated Learning (ProFL), an algorithm that finds performative optimal points in FL from noisy and contaminated data. We present the convergence analysis under the Polyak-Lojasiewicz condition, which applies to non-convex objectives. Extensive experiments on multiple datasets validate our proposed algorithms' efficiency.

Classifying nodes in a graph is a common problem. The ideal classifier must adapt to any imbalances in the class distribution. It must also use information in the clustering structure of real-world graphs. Existing Graph Neural Networks (GNNs) have not addressed both problems together. We propose the Enhanced Cluster-aware Graph Network (ECGN), a novel method that addresses these issues by integrating cluster-specific training with synthetic node generation. Unlike traditional GNNs that apply the same node update process for all nodes, ECGN learns different aggregations for different clusters. We also use the clusters to generate new minority-class nodes in a way that helps clarify the inter-class decision boundary. By combining cluster-aware embeddings with a global integration step, ECGN enhances the quality of the resulting node embeddings. Our method works with any underlying GNN and any cluster generation technique. Experimental results show that ECGN consistently outperforms its closest competitors by up to 11% on some widely studied benchmark datasets.