11 accepted papers
Virtual screening (VS) aims to identify bioactive compounds from vast chemical libraries, but remains difficult in low-label regimes where only a few actives are known. Existing methods largely rely on general-purpose molecular fingerprints and overlook class-discriminative substructures critical to…
The advent of generative AI now enables large-scale $\textit{de novo}$ design of molecules, but identifying viable drug candidates among them remains an open problem. Existing drug-likeness prediction methods often rely on ambiguous negative sets or purely structural features, limiting their ability…
Accurately predicting protein-ligand binding affinity is a critical challenge in drug discovery, crucial for understanding drug efficacy. While existing models typically rely on atom-level interactions, they often fail to capture the complex, higher-order interactions, resulting in noise and computa…
Dual-target molecule generation, which focuses on discovering compounds capable of interacting with two target proteins, has garnered significant attention due to its potential for improving therapeutic efficiency, safety and resistance mitigation. Existing approaches face two critical challenges. F…
Deciphering molecular meaning in chemistry and biomedicine depends on context — a capability that large language models (LLMs) can enhance by aligning molecular structures with language. However, existing molecule-text models ignore complementary information in different molecular views and rely on
Although there has been a growing interest among industries in integrating generative LLMs into their services, limited experience and scarcity of resources act as a barrier in launching and servicing large-scale LLM-based services. In this paper, we share our experiences in developing and operating…
The generation of energetically optimal 3D molecular conformers is crucial in cheminformatics and drug discovery. While deep generative models have been utilized for direct generation in Euclidean space, this approach encounters challenges, including the complexity of navigating a vast search space.…
Out-of-distribution (OOD) generalization in the graph domain is challenging due to complex distribution shifts and a lack of environmental contexts. Recent methods attempt to enhance graph OOD generalization by generating flat environments. However such flat environments come with inherent limitatio…
Most prior safety research of large language models (LLMs) has focused on enhancing the alignment of LLMs to better suit the safety requirements of their use cases. However, internalizing such safeguard features into larger models brought challenges of higher training cost and unintended degradation…
Leveraging knowledge from electronic health records (EHRs) to predict a patient’s condition is essential to the effective delivery of appropriate care. Clinical notes of patient EHRs contain valuable information from healthcare professionals, but have been underused due to their difficult contents a…
Recently, graph neural networks (GNNs) have been widely used for document classification. However, most existing methods are based on static word co-occurrence graphs without sentence-level information, which poses three challenges:(1) word ambiguity, (2) word synonymity, and (3) dynamic contextual…