9 accepted papers
A significant portion of disease-relevant proteins remain undruggable due to shallow, flexible, or otherwise ill-defined binding pockets that hinder conventional molecule screening. Fragment-based drug discovery (FBDD) offers a promising alternative, as small, low-complexity fragments can flexibly e…
Structure-guided molecular generation is pivotal in early-stage drug discovery, enabling the design of compounds tailored to specific protein targets. However, despite recent advances in 3D generative modeling, particularly in improving docking scores, these methods often produce rare and intrinsica…
Large language models (LLMs) often exhibit Context Faithfulness Hallucinations, where outputs deviate from retrieved information due to incomplete context integration. Our analysis reveals a strong correlation between token-level uncertainty and hallucinations. We hypothesize that attention mechanis…
Small molecules are vital to modern medicine, and accurately predicting their bioactivity against protein targets is crucial for therapeutic discovery and development. However, current machine learning models often rely on spurious features, leading to biased outcomes. Notably, a simple pocket-only…
Recent advances in structure-based drug design (SBDD) have produced surprising results, with models often generating molecules that achieve better Vina docking scores than actual ligands. However, these results are frequently overly optimistic due to the limitations of docking score accuracy and the…
Multi-hop reasoning with reinforcement learning has proven effective in discovering inference paths in incomplete knowledge graphs. However, a major challenge remains: spurious paths (incorrect reasoning paths that accidentally lead to correct answers) often arise due to reward mechanisms that prior
Curriculum learning is a training paradigm where machine learning models are trained in a meaningful order, inspired by the way humans learn curricula. Due to its capability to improve model generalization and convergence, curriculum learning has gained considerable attention and has been widely app…
In the field of Structure-based Drug Design (SBDD), deep learning-based generative models have achieved outstanding performance in terms of docking score. However, further study shows that the existing molecular generative methods and docking scores both have lacked consideration in terms of specifi…
Recently, a noticeable trend has emerged in developing pre-trained foundation models in the domains of CV and NLP. However, for molecular pre-training, there lacks a universal model capable of effectively applying to various categories of molecular tasks, since existing prevalent pre-training method…