24 citations · 127 across the 25 of their papers we have counts for
26 papers
MolChord: Structure-Sequence Alignment for Protein-Guided Drug Design
Wei Zhang, Zekun Guo, Yingce Xia +4
Structure-based drug design (SBDD), which maps target proteins to candidate molecular ligands, is a fundamental task in drug discovery. Effectively aligning protein structural repr…
SFM-Protein: Integrative Co-evolutionary Pre-training for Advanced Protein Sequence Representation
Liang He, Peiran Jin, Yaosen Min +7
Proteins, essential to biological systems, perform functions intricately linked to their three-dimensional structures. Understanding the relationship between protein structures and…
Exploiting Pre-trained Models for Drug Target Affinity Prediction with Nearest Neighbors
Qizhi Pei, Lijun Wu, Zhenyu He +4
Drug-Target binding Affinity (DTA) prediction is essential for drug discovery. Despite the application of deep learning methods to DTA prediction, the achieved accuracy remain subo…
BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning
Qizhi Pei, Lijun Wu, Kaiyuan Gao +6
Recent research trends in computational biology have increasingly focused on integrating text and bio-entity modeling, especially in the context of molecules and proteins. However,…
An Analysis and Mitigation of the Reversal Curse
Ang Lv, Kaiyi Zhang, Shufang Xie +4
Recent research observed a noteworthy phenomenon in large language models (LLMs), referred to as the ``reversal curse.'' The reversal curse is that when dealing with two entities,…
DeepSpeed4Science Initiative: Enabling Large-Scale Scientific Discovery through Sophisticated AI System Technologies
Shuaiwen Leon Song, Bonnie Kruft, Minjia Zhang +89
In the upcoming decade, deep learning may revolutionize the natural sciences, enhancing our capacity to model and predict natural occurrences. This could herald a new era of scient…
FABind: Fast and Accurate Protein-Ligand Binding
Qizhi Pei, Kaiyuan Gao, Lijun Wu +7
Modeling the interaction between proteins and ligands and accurately predicting their binding structures is a critical yet challenging task in drug discovery. Recent advancements i…
Retrosynthesis Prediction with Local Template Retrieval
Shufang Xie, Rui Yan, Junliang Guo +3
Retrosynthesis, which predicts the reactants of a given target molecule, is an essential task for drug discovery. In recent years, the machine learing based retrosynthesis methods…
MolXPT: Wrapping Molecules with Text for Generative Pre-training
Zequn Liu, Wei Zhang, Yingce Xia +5
Generative pre-trained Transformer (GPT) has demonstrates its great success in natural language processing and related techniques have been adapted into molecular modeling. Conside…
What are the Desired Characteristics of Calibration Sets? Identifying Correlates on Long Form Scientific Summarization
Griffin Adams, Bichlien H Nguyen, Jake Smith +7
Summarization models often generate text that is poorly calibrated to quality metrics because they are trained to maximize the likelihood of a single reference (MLE). To address th…
ResiDual: Transformer with Dual Residual Connections
Shufang Xie, Huishuai Zhang, Junliang Guo +6
Transformer networks have become the preferred architecture for many tasks due to their state-of-the-art performance. However, the optimal way to implement residual connections in…
De Novo Molecular Generation via Connection-aware Motif Mining
Zijie Geng, Shufang Xie, Yingce Xia +6
De novo molecular generation is an essential task for science discovery. Recently, fragment-based deep generative models have attracted much research attention due to their flexibi…
Retrosynthetic Planning with Dual Value Networks
Guoqing Liu, Di Xue, Shufang Xie +7
Retrosynthesis, which aims to find a route to synthesize a target molecule from commercially available starting materials, is a critical task in drug discovery and materials design…
Incorporating Pre-training Paradigm for Antibody Sequence-Structure Co-design
Kaiyuan Gao, Lijun Wu, Jinhua Zhu +8
Antibodies are versatile proteins that can bind to pathogens and provide effective protection for human body. Recently, deep learning-based computational antibody design has attrac…
Tailoring Molecules for Protein Pockets: a Transformer-based Generative Solution for Structured-based Drug Design
Kehan Wu, Yingce Xia, Yang Fan +7
Structure-based drug design is drawing growing attentions in computer-aided drug discovery. Compared with the virtual screening approach where a pre-defined library of compounds ar…
Unified 2D and 3D Pre-Training of Molecular Representations
Jinhua Zhu, Yingce Xia, Lijun Wu +5
Molecular representation learning has attracted much attention recently. A molecule can be viewed as a 2D graph with nodes/atoms connected by edges/bonds, and can also be represent…
Building Multilingual Machine Translation Systems That Serve Arbitrary X-Y Translations
Akiko Eriguchi, Shufang Xie, Tao Qin +1
Multilingual Neural Machine Translation (MNMT) enables one system to translate sentences from multiple source languages to multiple target languages, greatly reducing deployment co…
RetroGraph: Retrosynthetic Planning with Graph Search
Shufang Xie, Rui Yan, Peng Han +5
Retrosynthetic planning, which aims to find a reaction pathway to synthesize a target molecule, plays an important role in chemistry and drug discovery. This task is usually modele…
SSM-DTA: Breaking the Barriers of Data Scarcity in Drug-Target Affinity Prediction
Qizhi Pei, Lijun Wu, Jinhua Zhu +6
Accurate prediction of Drug-Target Affinity (DTA) is of vital importance in early-stage drug discovery, facilitating the identification of drugs that can effectively interact with…
Direct Molecular Conformation Generation
Jinhua Zhu, Yingce Xia, Chang Liu +9
Molecular conformation generation aims to generate three-dimensional coordinates of all the atoms in a molecule and is an important task in bioinformatics and pharmacology. Previou…
Discovering Drug-Target Interaction Knowledge from Biomedical Literature
Yutai Hou, Yingce Xia, Lijun Wu +6
The Interaction between Drugs and Targets (DTI) in human body plays a crucial role in biomedical science and applications. As millions of papers come out every year in the biomedic…
UniDrop: A Simple yet Effective Technique to Improve Transformer without Extra Cost
Zhen Wu, Lijun Wu, Qi Meng +5
Transformer architecture achieves great success in abundant natural language processing tasks. The over-parameterization of the Transformer model has motivated plenty of works to a…
IOT: Instance-wise Layer Reordering for Transformer Structures
Jinhua Zhu, Lijun Wu, Yingce Xia +5
With sequentially stacked self-attention, (optional) encoder-decoder attention, and feed-forward layers, Transformer achieves big success in natural language processing (NLP), and…
Multi-branch Attentive Transformer
Yang Fan, Shufang Xie, Yingce Xia +4
While the multi-branch architecture is one of the key ingredients to the success of computer vision tasks, it has not been well investigated in natural language processing, especia…