25 accepted papers
Chain-of-Thought (CoT) reasoning has significantly improved the performance of Large Language Models (LLMs) but comes with substantial computational costs due to excessive token consumption. Existing approaches to reduce inference latency, such as explicit length penalties, often degrade reasoning q…
Experience learning has achieved promising results in enhancing LLM agent planning and reasoning by integrating past interactions as reusable knowledge. However, existing methods remain confined to explicit text space---retrieving experiences via semantic similarity and concatenating them into the c…
Many scientific problems require inferring unobserved mechanistic latent states from indirect observations. While classical approaches, including expectation-maximization, do not scale to combinatorially large spaces, deep learning approaches such as variational autoencoders typically form artificia…
The role of reasoning in Audio Large Language Models remains widely underexplored, as introducing a reasoning process often degrades rather than improves performance during inference, a phenomenon we term test-time inverse scaling, where longer reasoning chains yield progressively worse results. We…
Predicting protein mutation effects is fundamental to protein engineering and disease variant interpretation, yet experimental mutation data remain accurate but extremely sparse. Large-scale computational augmentation offers scalability, but introduces heterogeneous and poorly calibrated supervision…
Large Language Models (LLMs) can be seen as compressed knowledge bases, but it remains unclear what knowledge they truly contain and how far their knowledge boundaries extend. Existing benchmarks are mostly static and provide limited support for systematic knowledge probing. In this paper, we propos…
We present protein autoregressive modeling (PAR), the first multi-scale autoregressive framework for protein backbone generation via coarse-to-fine next-scale prediction. Using the hierarchical nature of proteins, PAR generates structures that mimic sculpting a statue, forming a coarse topology and …
Foundation models for medical image segmentation struggle under out-of-distribution (OOD) shifts, often producing fragmented false positives on OOD tumors. We introduce **R^2-Seg**, a **training-free** framework for robust OOD tumor segmentation that operates via a two-stage **Reason-and-Reject** pr
Retrieval-Augmented Generation (RAG) systems remain brittle under realistic retrieval noise, even when the required evidence appears in the top-$K$ results. A key reason is that retrievers and rerankers optimize solely for relevance, often selecting either trivial, answer-revealing passages or evide…
Accurate molecular representations are critical for drug discovery, and a central challenge lies in capturing the chemical environment of molecular fragments, as key interactions, such as H-bond and π stacking—occur only under specific local conditions. Most existing approaches represent molecules a…
Despite their ability to understand chemical knowledge, large language models (LLMs) remain limited in their capacity to propose novel molecules with desired functions (e.g., drug-like properties). In addition, the molecules that LLMs propose can often be challenging to make, and are almost never co…
Balancing exploration and exploitation during reinforcement learning fine-tuning of generative models presents a critical challenge, as existing approaches rely on fixed divergence regularization that creates an inherent dilemma: strong regularization preserves model capabilities but limits reward o…
Peptides, short chains of amino acids, interact with target proteins, making them a unique class of protein-based therapeutics for treating human diseases. Recently, deep generative models have shown great promise in peptide generation. However, several challenges remain in designing effective pepti…
Recent advancements in reinforcement learning (RL) have achieved great success in fine-tuning diffusion-based generative models. However, fine-tuning continuous flow-based generative models to align with arbitrary user-defined reward functions remains challenging, particularly due to issues such as…
Consistency models are a class of generative models that enable few-step generation for diffusion and flow matching models. While consistency models have achieved promising results on Euclidean domains like images, their applications to Riemannian manifolds remain challenging due to the curved geome…
Controlled generation with pre-trained Diffusion and Flow Matching models has vast applications. One strategy for guiding ODE-based generative models is through optimizing a target loss $R(x_1)$ while staying close to the prior distribution. Along this line, some recent work showed the effectiveness…
Contrastive learning has proven to be highly efficient and adaptable in shaping representation spaces across diverse modalities by pulling similar samples together and pushing dissimilar ones apart. However, two key limitations persist: (1) Without explicit regulation of the embedding distribution,…
As scientific research proliferates, researchers face the daunting task of navigating and reading vast amounts of literature. Existing solutions, such as document QA, fail to provide personalized and up-to-date information efficiently. We present Arxiv Copilot, a self-evolving, efficient LLM system…
We introduce Statistical Flow Matching (SFM), a novel and mathematically rigorous flow-matching framework on the manifold of parameterized probability measures inspired by the results from information geometry. We demonstrate the effectiveness of our method on the discrete generation problem by inst…
Hierarchical text classification (HTC) is a significant but challenging task in natural language processing (NLP) due to its complex taxonomic label hierarchy. Recently, there have been a number of approaches that applied prompt learning to HTC problems, demonstrating impressive efficacy. The majori…
Geometric graph neural networks (GNNs) have emerged as powerful tools for modeling molecular geometry. However, they encounter limitations in effectively capturing long-range interactions in large molecular systems. To address this challenge, we introduce **Neural P$^3$M**, a versatile enhancer of g…
Learning of preference models from human feedback has been central to recent advances in artificial intelligence. Motivated by the cost of obtaining high-quality human annotations, we study efficient human preference elicitation for learning preference models. The key idea in our work is to generali…
Multi-objective optimization is a class of optimization problems with multiple conflicting objectives. We study offline optimization of multi-objective policies from data collected by a previously deployed policy. We propose a pessimistic estimator for policy values that can be easily plugged into e…
This paper studies some under-explored connections between personalized recommendation and marketing systems. Obviously, these two systems are different, in two main ways. Firstly, personalized item-recommendation (ItemRec) is user-centric, whereas marketing recommends the best user-state segments (…
We introduce the maximum $n$-times coverage problem that selects $k$ overlays to maximize the summed coverage of weighted elements, where each element must be covered at least $n$ times. We also define the min-cost $n$-times coverage problem where the objective is to select the minimum set of overla…