Search Results for author: Xiner Li

Found 11 papers, 7 papers with code

Geometry Informed Tokenization of Molecules for Language Model Generation

no code implementations19 Aug 2024 Xiner Li, Limei Wang, Youzhi Luo, Carl Edwards, Shurui Gui, Yuchao Lin, Heng Ji, Shuiwang Ji

We consider molecule generation in 3D space using language models (LMs), which requires discrete tokenization of 3D molecular geometries.

Language Modelling

Fragment and Geometry Aware Tokenization of Molecules for Structure-Based Drug Design Using Language Models

no code implementations19 Aug 2024 Cong Fu, Xiner Li, Blake Olson, Heng Ji, Shuiwang Ji

Benefiting from employing LMs with fragment-based generation and effective protein context encoding, our model achieves the best performance on binding vina score and chemical properties such as QED and Lipinski, which shows our model's efficacy in generating drug-like ligands with higher binding affinity against target proteins.

Eliminating Position Bias of Language Models: A Mechanistic Approach

1 code implementation1 Jul 2024 Ziqi Wang, HANLIN ZHANG, Xiner Li, Kuan-Hao Huang, Chi Han, Shuiwang Ji, Sham M. Kakade, Hao Peng, Heng Ji

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.

Math object-detection +4

Active Test-Time Adaptation: Theoretical Analyses and An Algorithm

1 code implementation7 Apr 2024 Shurui Gui, Xiner Li, Shuiwang Ji

Extensive experimental results confirm consistency with our theoretical analyses and show that the proposed ATTA method yields substantial performance improvements over TTA methods while maintaining efficiency and shares similar effectiveness to the more demanding active domain adaptation (ADA) methods.

Active Learning Learning Theory +1

Graph Structure and Feature Extrapolation for Out-of-Distribution Generalization

no code implementations13 Jun 2023 Xiner Li, Shurui Gui, Youzhi Luo, Shuiwang Ji

Out-of-distribution (OOD) generalization deals with the prevalent learning scenario where test distribution shifts from training distribution.

Data Augmentation Out-of-Distribution Generalization

Joint Learning of Label and Environment Causal Independence for Graph Out-of-Distribution Generalization

2 code implementations NeurIPS 2023 Shurui Gui, Meng Liu, Xiner Li, Youzhi Luo, Shuiwang Ji

In this work, we propose to simultaneously incorporate label and environment causal independence (LECI) to fully make use of label and environment information, thereby addressing the challenges faced by prior methods on identifying causal and invariant subgraphs.

Out-of-Distribution Generalization

GOOD: A Graph Out-of-Distribution Benchmark

1 code implementation16 Jun 2022 Shurui Gui, Xiner Li, Limei Wang, Shuiwang Ji

Our GOOD benchmark is a growing project and expects to expand in both quantity and variety of resources as the area develops.

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