16 accepted papers
RNA molecules underlie regulation, catalysis, and therapeutics in biological systems, yet de novo RNA design remains difficult with the tight and highly non-linear sequence–structure coupling. The RNA sequence–structure co-design problem generates nucleotide sequences and 3D conformations jointly,…
We aim to improve the reasoning capabilities of language models via reinforcement learning with verifiable rewards (RLVR). Recent RLVR post-trained models like DeepSeek-R1 have demonstrated reasoning abilities on mathematical and coding tasks. However, prior studies suggest that using RLVR alone to…
In scientific reasoning tasks, the veracity of the reasoning process is as critical as the final outcome. While Process Reward Models (PRMs) offer a solution to the coarse-grained supervision problems inherent in Outcome Reward Models (ORMs), their deployment is hindered by the prohibitive cost of o…
We address the problem of fine-tuning diffusion models for reward-guided generation in biomolecular design. While diffusion models have proven highly effective in modeling complex, high-dimensional data distributions, real-world applications often demand more than high-fidelity generation, requiring…
Diffusion models excel at capturing the natural design spaces of images, molecules, DNA, RNA, and protein sequences. However, rather than merely generating designs that are natural, we often aim to optimize downstream reward functions while preserving the naturalness of these design spaces. Existing…
We consider learning underlying laws of dynamical systems governed by ordinary differential equations (ODE). A key challenge is how to discover intrinsic dynamics across multiple environments while circumventing environment-specific mechanisms. Unlike prior work, we tackle more complex environments…
Position bias has proven to be a prevalent issue of modern language models (LMs), where the models prioritize content based on its position within the given context. This bias often leads to unexpected model failures and hurts performance, robustness, and reliability across various applications. A s…
Structure-based drug design (SBDD) is crucial for developing specific and effective therapeutics against protein targets but remains challenging due to complex protein-ligand interactions and vast chemical space. Although language models (LMs) have excelled in natural language processing, their appl…
We consider molecule generation in 3D space using language models (LMs), which requires discrete tokenization of 3D molecular geometries. Although tokenization of molecular graphs exists, that for 3D geometries is largely unexplored. Here, we attempt to bridge this gap by proposing a novel method wh…
To fully leverage the capabilities of diffusion models, we are often interested in optimizing downstream reward functions during inference. While numerous algorithms for reward-guided generation have been recently proposed due to their significance, current approaches predominantly focus on single-s…
Test-time adaptation (TTA) addresses distribution shifts for streaming test data in unsupervised settings. Currently, most TTA methods can only deal with minor shifts and rely heavily on heuristic and empirical studies. To advance TTA under domain shifts, we propose the novel problem setting of a…
Out-of-distribution (OOD) generalization deals with the prevalent learning scenario where test distribution shifts from training distribution. With rising application demands and inherent complexity, graph OOD problems call for specialized solutions. While data-centric methods exhibit performance en…
We consider the problem of crystal materials generation using language models (LMs). A key step is to convert 3D crystal structures into 1D sequences to be processed by LMs. Prior studies used the crystallographic information framework (CIF) file stream, which fails to ensure SE(3) and periodic inva…
Large language models (LLMs) have gained considerable attention for their excellent natural language processing capabilities. Nonetheless, these LLMs present many challenges, particularly in the realm of trustworthiness. This paper introduces TrustLLM, a comprehensive study of trustworthiness in LLM…
We tackle the problem of graph out-of-distribution (OOD) generalization. Existing graph OOD algorithms either rely on restricted assumptions or fail to exploit environment information in training data. In this work, we propose to simultaneously incorporate label and environment causal independence (…
Out-of-distribution (OOD) learning deals with scenarios in which training and test data follow different distributions. Although general OOD problems have been intensively studied in machine learning, graph OOD is only an emerging area of research. Currently, there lacks a systematic benchmark tailo…