115 citations · 414 across the 28 of their papers we have counts for
28 papers
scMamba: A Scalable Foundation Model for Single-Cell Multi-Omics Integration Beyond Highly Variable Feature Selection
Zhen Yuan, Shaoqing Jiao, Yihang Xiao +1
The advent of single-cell multi-omics technologies has enabled the simultaneous profiling of diverse omics layers within individual cells. Integrating such multimodal data provides…
Routing to the Expert: Efficient Reward-guided Ensemble of Large Language Models
Keming Lu, Hongyi Yuan, Runji Lin +4
The complementary potential of Large Language Models (LLM) assumes off-the-shelf LLMs have heterogeneous expertise in a wide range of domains and tasks so that an ensemble of LLMs…
Speculative Contrastive Decoding
Hongyi Yuan, Keming Lu, Fei Huang +2
Large language models~(LLMs) exhibit exceptional performance in language tasks, yet their auto-regressive inference is limited due to high computational requirements and is sub-opt…
OccuQuest: Mitigating Occupational Bias for Inclusive Large Language Models
Mingfeng Xue, Dayiheng Liu, Kexin Yang +5
The emergence of large language models (LLMs) has revolutionized natural language processing tasks. However, existing instruction-tuning datasets suffer from occupational bias: the…
MuggleMath: Assessing the Impact of Query and Response Augmentation on Math Reasoning
Chengpeng Li, Zheng Yuan, Hongyi Yuan +6
In math reasoning with large language models (LLMs), fine-tuning data augmentation by query evolution and diverse reasoning paths is empirically verified effective, profoundly narr…
How Abilities in Large Language Models are Affected by Supervised Fine-tuning Data Composition
Guanting Dong, Hongyi Yuan, Keming Lu +7
Large language models (LLMs) with enormous pre-training tokens and parameters emerge diverse abilities, including math reasoning, code generation, and instruction following. These…
Qwen Technical Report
Jinze Bai, Shuai Bai, Yunfei Chu +45
Large language models (LLMs) have revolutionized the field of artificial intelligence, enabling natural language processing tasks that were previously thought to be exclusive to hu…
Scaling Relationship on Learning Mathematical Reasoning with Large Language Models
Zheng Yuan, Hongyi Yuan, Chengpeng Li +5
Mathematical reasoning is a challenging task for large language models (LLMs), while the scaling relationship of it with respect to LLM capacity is under-explored. In this paper, w…
#InsTag: Instruction Tagging for Analyzing Supervised Fine-tuning of Large Language Models
Keming Lu, Hongyi Yuan, Zheng Yuan +5
Foundation language models obtain the instruction-following ability through supervised fine-tuning (SFT). Diversity and complexity are considered critical factors of a successful S…
Hierarchical Pretraining for Biomedical Term Embeddings
Bryan Cai, Sihang Zeng, Yucong Lin +3
Electronic health records (EHR) contain narrative notes that provide extensive details on the medical condition and management of patients. Natural language processing (NLP) of cli…
DiffDTM: A conditional structure-free framework for bioactive molecules generation targeted for dual proteins
Lei Huang, Zheng Yuan, Huihui Yan +9
Advances in deep generative models shed light on de novo molecule generation with desired properties. However, molecule generation targeted for dual protein targets still faces for…
RRHF: Rank Responses to Align Language Models with Human Feedback without tears
Zheng Yuan, Hongyi Yuan, Chuanqi Tan +3
Reinforcement Learning from Human Feedback (RLHF) facilitates the alignment of large language models with human preferences, significantly enhancing the quality of interactions bet…
How well do Large Language Models perform in Arithmetic tasks?
Zheng Yuan, Hongyi Yuan, Chuanqi Tan +2
Large language models have emerged abilities including chain-of-thought to answer math word problems step by step. Solving math word problems not only requires abilities to disasse…
Exploring Partial Knowledge Base Inference in Biomedical Entity Linking
Hongyi Yuan, Keming Lu, Zheng Yuan
Biomedical entity linking (EL) consists of named entity recognition (NER) and named entity disambiguation (NED). EL models are trained on corpora labeled by a predefined KB. Howeve…
RAMM: Retrieval-augmented Biomedical Visual Question Answering with Multi-modal Pre-training
Zheng Yuan, Qiao Jin, Chuanqi Tan +4
Vision-and-language multi-modal pretraining and fine-tuning have shown great success in visual question answering (VQA). Compared to general domain VQA, the performance of biomedic…
Molecular Geometry-aware Transformer for accurate 3D Atomic System modeling
Zheng Yuan, Yaoyun Zhang, Chuanqi Tan +3
Molecular dynamic simulations are important in computational physics, chemistry, material, and biology. Machine learning-based methods have shown strong abilities in predicting mol…
SeqDiffuSeq: Text Diffusion with Encoder-Decoder Transformers
Hongyi Yuan, Zheng Yuan, Chuanqi Tan +2
Diffusion model, a new generative modelling paradigm, has achieved great success in image, audio, and video generation. However, considering the discrete categorical nature of text…
HyPe: Better Pre-trained Language Model Fine-tuning with Hidden Representation Perturbation
Hongyi Yuan, Zheng Yuan, Chuanqi Tan +2
Language models with the Transformers structure have shown great performance in natural language processing. However, there still poses problems when fine-tuning pre-trained langua…
Generative Biomedical Entity Linking via Knowledge Base-Guided Pre-training and Synonyms-Aware Fine-tuning
Hongyi Yuan, Zheng Yuan, Sheng Yu
Entities lie in the heart of biomedical natural language understanding, and the biomedical entity linking (EL) task remains challenging due to the fine-grained and diversiform conc…
BIOS: An Algorithmically Generated Biomedical Knowledge Graph
Sheng Yu, Zheng Yuan, Jun Xia +11
Biomedical knowledge graphs (BioMedKGs) are essential infrastructures for biomedical and healthcare big data and artificial intelligence (AI), facilitating natural language process…
BioBART: Pretraining and Evaluation of A Biomedical Generative Language Model
Hongyi Yuan, Zheng Yuan, Ruyi Gan +3
Pretrained language models have served as important backbones for natural language processing. Recently, in-domain pretraining has been shown to benefit various domain-specific dow…
Automatic Biomedical Term Clustering by Learning Fine-grained Term Representations
Sihang Zeng, Zheng Yuan, Sheng Yu
Term clustering is important in biomedical knowledge graph construction. Using similarities between terms embedding is helpful for term clustering. State-of-the-art term embeddings…
Code Synonyms Do Matter: Multiple Synonyms Matching Network for Automatic ICD Coding
Zheng Yuan, Chuanqi Tan, Songfang Huang
Automatic ICD coding is defined as assigning disease codes to electronic medical records (EMRs). Existing methods usually apply label attention with code representations to match r…
Fusing Heterogeneous Factors with Triaffine Mechanism for Nested Named Entity Recognition
Zheng Yuan, Chuanqi Tan, Songfang Huang +1
Nested entities are observed in many domains due to their compositionality, which cannot be easily recognized by the widely-used sequence labeling framework. A natural solution is…