Search Results for author: Jinhua Zhu

Found 23 papers, 15 papers with code

mixSeq: A Simple Data Augmentation Methodfor Neural Machine Translation

no code implementations ACL (IWSLT) 2021 Xueqing Wu, Yingce Xia, Jinhua Zhu, Lijun Wu, Shufang Xie, Yang Fan, Tao Qin

Data augmentation, which refers to manipulating the inputs (e. g., adding random noise, masking specific parts) to enlarge the dataset, has been widely adopted in machine learning.

Data Augmentation Machine Translation +1

Machine Translation With Weakly Paired Bilingual Documents

no code implementations ICLR 2019 Lijun Wu, Jinhua Zhu, Di He, Fei Gao, Xu Tan, Tao Qin, Tie-Yan Liu

Neural machine translation, which achieves near human-level performance in some languages, strongly relies on the availability of large amounts of parallel sentences, which hinders its applicability to low-resource language pairs.

Sentence Translation +1

Concurrent Linguistic Error Detection (CLED) for Large Language Models

no code implementations25 Mar 2024 Jinhua Zhu, Javier Conde, Zhen Gao, Pedro Reviriego, Shanshan Liu, Fabrizio Lombardi

Since the proposed error detection mechanism only relies on the outputs of the model, then it can be used on LLMs in which there is no access to the internal nodes.

News Summarization valid

Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey

2 code implementations3 Mar 2024 Qizhi Pei, Lijun Wu, Kaiyuan Gao, Jinhua Zhu, Yue Wang, Zun Wang, Tao Qin, Rui Yan

The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology.

Property Prediction

BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning

1 code implementation27 Feb 2024 Qizhi Pei, Lijun Wu, Kaiyuan Gao, Xiaozhuan Liang, Yin Fang, Jinhua Zhu, Shufang Xie, Tao Qin, Rui Yan

However, previous efforts like BioT5 faced challenges in generalizing across diverse tasks and lacked a nuanced understanding of molecular structures, particularly in their textual representations (e. g., IUPAC).

Forward reaction prediction Molecule Captioning +3

FABind: Fast and Accurate Protein-Ligand Binding

1 code implementation NeurIPS 2023 Qizhi Pei, Kaiyuan Gao, Lijun Wu, Jinhua Zhu, Yingce Xia, Shufang Xie, Tao Qin, Kun He, Tie-Yan Liu, Rui Yan

In this work, we propose $\mathbf{FABind}$, an end-to-end model that combines pocket prediction and docking to achieve accurate and fast protein-ligand binding.

Drug Discovery Pose Estimation +1

O-GNN: Incorporating Ring Priors into Molecular Modeling

1 code implementation ICLR 2023 Jinhua Zhu, Kehan Wu, Bohan Wang, Yingce Xia, Shufang Xie, Qi Meng, Lijun Wu, Tao Qin, Wengang Zhou, Houqiang Li, Tie-Yan Liu

Despite the recent success of molecular modeling with graph neural networks (GNNs), few models explicitly take rings in compounds into consideration, consequently limiting the expressiveness of the models.

 Ranked #1 on Graph Regression on PCQM4M-LSC (Validation MAE metric)

Graph Regression Molecular Property Prediction +3

Incorporating Pre-training Paradigm for Antibody Sequence-Structure Co-design

no code implementations26 Oct 2022 Kaiyuan Gao, Lijun Wu, Jinhua Zhu, Tianbo Peng, Yingce Xia, Liang He, Shufang Xie, Tao Qin, Haiguang Liu, Kun He, Tie-Yan Liu

Specifically, we first pre-train an antibody language model based on the sequence data, then propose a one-shot way for sequence and structure generation of CDR to avoid the heavy cost and error propagation from an autoregressive manner, and finally leverage the pre-trained antibody model for the antigen-specific antibody generation model with some carefully designed modules.

Language Modelling Specificity

Unified 2D and 3D Pre-Training of Molecular Representations

1 code implementation14 Jul 2022 Jinhua Zhu, Yingce Xia, Lijun Wu, Shufang Xie, Tao Qin, Wengang Zhou, Houqiang Li, Tie-Yan Liu

The model is pre-trained on three tasks: reconstruction of masked atoms and coordinates, 3D conformation generation conditioned on 2D graph, and 2D graph generation conditioned on 3D conformation.

Graph Generation Molecular Property Prediction +3

SSM-DTA: Breaking the Barriers of Data Scarcity in Drug-Target Affinity Prediction

2 code implementations20 Jun 2022 Qizhi Pei, Lijun Wu, Jinhua Zhu, Yingce Xia, Shufang Xie, Tao Qin, Haiguang Liu, Tie-Yan Liu, Rui Yan

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 specific targets and regulate their activities.

Drug Discovery Language Modelling +2

Direct Molecular Conformation Generation

1 code implementation3 Feb 2022 Jinhua Zhu, Yingce Xia, Chang Liu, Lijun Wu, Shufang Xie, Yusong Wang, Tong Wang, Tao Qin, Wengang Zhou, Houqiang Li, Haiguang Liu, Tie-Yan Liu

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.

Molecular Docking

Discovering Drug-Target Interaction Knowledge from Biomedical Literature

no code implementations27 Sep 2021 Yutai Hou, Yingce Xia, Lijun Wu, Shufang Xie, Yang Fan, Jinhua Zhu, Wanxiang Che, Tao Qin, Tie-Yan Liu

We regard the DTI triplets as a sequence and use a Transformer-based model to directly generate them without using the detailed annotations of entities and relations.

Dual-view Molecule Pre-training

1 code implementation17 Jun 2021 Jinhua Zhu, Yingce Xia, Tao Qin, Wengang Zhou, Houqiang Li, Tie-Yan Liu

After pre-training, we can use either the Transformer branch (this one is recommended according to empirical results), the GNN branch, or both for downstream tasks.

Molecular Property Prediction Property Prediction +2

IOT: Instance-wise Layer Reordering for Transformer Structures

1 code implementation ICLR 2021 Jinhua Zhu, Lijun Wu, Yingce Xia, Shufang Xie, Tao Qin, Wengang Zhou, Houqiang Li, Tie-Yan Liu

Based on this observation, in this work, we break the assumption of the fixed layer order in the Transformer and introduce instance-wise layer reordering into the model structure.

Abstractive Text Summarization Code Generation +3

Return-Based Contrastive Representation Learning for Reinforcement Learning

no code implementations ICLR 2021 Guoqing Liu, Chuheng Zhang, Li Zhao, Tao Qin, Jinhua Zhu, Jian Li, Nenghai Yu, Tie-Yan Liu

Recently, various auxiliary tasks have been proposed to accelerate representation learning and improve sample efficiency in deep reinforcement learning (RL).

Atari Games reinforcement-learning +2

Masked Contrastive Representation Learning for Reinforcement Learning

1 code implementation15 Oct 2020 Jinhua Zhu, Yingce Xia, Lijun Wu, Jiajun Deng, Wengang Zhou, Tao Qin, Houqiang Li

During inference, the CNN encoder and the policy network are used to take actions, and the Transformer module is discarded.

Atari Games Contrastive Learning +3

Incorporating BERT into Neural Machine Translation

3 code implementations ICLR 2020 Jinhua Zhu, Yingce Xia, Lijun Wu, Di He, Tao Qin, Wengang Zhou, Houqiang Li, Tie-Yan Liu

While BERT is more commonly used as fine-tuning instead of contextual embedding for downstream language understanding tasks, in NMT, our preliminary exploration of using BERT as contextual embedding is better than using for fine-tuning.

Decoder Natural Language Understanding +6

Normalization Helps Training of Quantized LSTM

1 code implementation NeurIPS 2019 Lu Hou, Jinhua Zhu, James Kwok, Fei Gao, Tao Qin, Tie-Yan Liu

The long-short-term memory (LSTM), though powerful, is memory and computa\x02tion expensive.


Machine Translation With Weakly Paired Documents

no code implementations IJCNLP 2019 Lijun Wu, Jinhua Zhu, Di He, Fei Gao, Tao Qin, Jian-Huang Lai, Tie-Yan Liu

1) We provide a simple approach to mine implicitly bilingual sentence pairs from document pairs which can then be used as supervised training signals.

Sentence Translation +1

Soft Contextual Data Augmentation for Neural Machine Translation

1 code implementation ACL 2019 Jinhua Zhu, Fei Gao, Lijun Wu, Yingce Xia, Tao Qin, Wengang Zhou, Xue-Qi Cheng, Tie-Yan Liu

While data augmentation is an important trick to boost the accuracy of deep learning methods in computer vision tasks, its study in natural language tasks is still very limited.

Data Augmentation Language Modelling +3

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