Jiajie Peng

Zhijie Bao, Wei Chen, Shengze Xiao et al.

We propose DISC-MedLLM, a comprehensive solution that leverages Large Language Models (LLMs) to provide accurate and truthful medical response in end-to-end conversational healthcare services. To construct high-quality Supervised Fine-Tuning (SFT) datasets, we employ three strategies: utilizing medical knowledge-graphs, reconstructing real-world dialogues, and incorporating human-guided preference rephrasing. These datasets are instrumental in training DISC-MedLLM, surpassing existing medical LLMs in both single-turn and multi-turn consultation scenarios. Extensive experimental results demonstrate the effectiveness of the proposed model in bridging the gap between general language models and real-world medical consultation. Additionally, we release the constructed dataset and model weights to further contribute to research and development. Further details and resources can be found at https://github.com/FudanDISC/DISC-MedLLM

Wei Chen, Zhiwei Li, Hongyi Fang et al.

In recent years, interest has arisen in using machine learning to improve the efficiency of automatic medical consultation and enhance patient experience. In this article, we propose two frameworks to support automatic medical consultation, namely doctor-patient dialogue understanding and task-oriented interaction. We create a new large medical dialogue dataset with multi-level finegrained annotations and establish five independent tasks, including named entity recognition, dialogue act classification, symptom label inference, medical report generation and diagnosis-oriented dialogue policy. We report a set of benchmark results for each task, which shows the usability of the dataset and sets a baseline for future studies. Both code and data is available from https://github.com/lemuria-wchen/imcs21.

Wei Chen, Cheng Zhong, Jiajie Peng et al.

Diagnosis-oriented dialogue system queries the patient's health condition and makes predictions about possible diseases through continuous interaction with the patient. A few studies use reinforcement learning (RL) to learn the optimal policy from the joint action space of symptoms and diseases. However, existing RL (or Non-RL) methods cannot achieve sufficiently good prediction accuracy, still far from its upper limit. To address the problem, we propose a decoupled automatic diagnostic framework DxFormer, which divides the diagnosis process into two steps: symptom inquiry and disease diagnosis, where the transition from symptom inquiry to disease diagnosis is explicitly determined by the stopping criteria. In DxFormer, we treat each symptom as a token, and formalize the symptom inquiry and disease diagnosis to a language generation model and a sequence classification model respectively. We use the inverted version of Transformer, i.e., the decoder-encoder structure, to learn the representation of symptoms by jointly optimizing the reinforce reward and cross entropy loss. Extensive experiments on three public real-world datasets prove that our proposed model can effectively learn doctors' clinical experience and achieve the state-of-the-art results in terms of symptom recall and diagnostic accuracy.

Zhijie Bao, Fangke Chen, Licheng Bao et al.

The potential of Multimodal Large Language Models (MLLMs) in domain of medical imaging raise the demands of systematic and rigorous evaluation frameworks that are aligned with the real-world medical imaging practice. Existing practices that report single or coarse-grained metrics are lack the granularity required for specialized clinical support and fail to assess the reliability of reasoning mechanisms. To address this, we propose a paradigm shift toward multidimensional, fine-grained and in-depth evaluation. Based on a two-stage systematic construction pipeline designed for this paradigm, we instantiate it with MedRCube. We benchmark 33 MLLMs, \textit{Lingshu-32B} achieve top-tier performance. Crucially, MedRCube exposes a series of pronounced insights inaccessible under prior evaluation settings. Furthermore, we introduce a credibility evaluation subset to quantify reasoning credibility, uncover a highly significant positive association between shortcut behavior and diagnostic task performance, raising concerns for clinically trustworthy deployment. The resources of this work can be found at https://github.com/F1mc/MedRCube.

Yihang Xiao, Jinyi Liu, Yan Zheng et al.

Single-cell RNA sequencing (scRNA-seq) data analysis is crucial for biological research, as it enables the precise characterization of cellular heterogeneity. However, manual manipulation of various tools to achieve desired outcomes can be labor-intensive for researchers. To address this, we introduce CellAgent (http://cell.agent4science.cn/), an LLM-driven multi-agent framework, specifically designed for the automatic processing and execution of scRNA-seq data analysis tasks, providing high-quality results with no human intervention. Firstly, to adapt general LLMs to the biological field, CellAgent constructs LLM-driven biological expert roles - planner, executor, and evaluator - each with specific responsibilities. Then, CellAgent introduces a hierarchical decision-making mechanism to coordinate these biological experts, effectively driving the planning and step-by-step execution of complex data analysis tasks. Furthermore, we propose a self-iterative optimization mechanism, enabling CellAgent to autonomously evaluate and optimize solutions, thereby guaranteeing output quality. We evaluate CellAgent on a comprehensive benchmark dataset encompassing dozens of tissues and hundreds of distinct cell types. Evaluation results consistently show that CellAgent effectively identifies the most suitable tools and hyperparameters for single-cell analysis tasks, achieving optimal performance. This automated framework dramatically reduces the workload for science data analyses, bringing us into the "Agent for Science" era.

Zhijie Bao, Qingyun Liu, Ying Guo et al.

In China, receptionist nurses face overwhelming workloads in outpatient settings, limiting their time and attention for each patient and ultimately reducing service quality. In this paper, we present the Personalized Intelligent Outpatient Reception System (PIORS). This system integrates an LLM-based reception nurse and a collaboration between LLM and hospital information system (HIS) into real outpatient reception setting, aiming to deliver personalized, high-quality, and efficient reception services. Additionally, to enhance the performance of LLMs in real-world healthcare scenarios, we propose a medical conversational data generation framework named Service Flow aware Medical Scenario Simulation (SFMSS), aiming to adapt the LLM to the real-world environments and PIORS settings. We evaluate the effectiveness of PIORS and SFMSS through automatic and human assessments involving 15 users and 15 clinical experts. The results demonstrate that PIORS-Nurse outperforms all baselines, including the current state-of-the-art model GPT-4o, and aligns with human preferences and clinical needs. Further details and demo can be found at https://github.com/FudanDISC/PIORS

Cheng Zhong, Kangenbei Liao, Wei Chen et al.

Motivation: Disease diagnosis oriented dialogue system models the interactive consultation procedure as Markov Decision Process and reinforcement learning algorithms are used to solve the problem. Existing approaches usually employ a flat policy structure that treat all symptoms and diseases equally for action making. This strategy works well in the simple scenario when the action space is small, however, its efficiency will be challenged in the real environment. Inspired by the offline consultation process, we propose to integrate a hierarchical policy structure of two levels into the dialogue systemfor policy learning. The high-level policy consists of amastermodel that is responsible for triggering a low-levelmodel, the lowlevel policy consists of several symptom checkers and a disease classifier. The proposed policy structure is capable to deal with diagnosis problem including large number of diseases and symptoms. Results: Experimental results on three real-world datasets and a synthetic dataset demonstrate that our hierarchical framework achieves higher accuracy and symptom recall in disease diagnosis compared with existing systems. We construct a benchmark including datasets and implementation of existing algorithms to encourage follow-up researches. Availability: The code and data is available from https://github.com/FudanDISC/DISCOpen-MedBox-DialoDiagnosis Contact: 21210980124@m.fudan.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online.

Shujian Jiao, Bingxuan Li, Lei Wang et al.

Proteins are essential to life's processes, underpinning evolution and diversity. Advances in sequencing technology have revealed millions of proteins, underscoring the need for sophisticated pre-trained protein models for biological analysis and AI development. Facebook's ESM2, the most advanced protein language model to date, leverages a masked prediction task for unsupervised learning, crafting amino acid representations with notable biochemical accuracy. Yet, it lacks in delivering functional protein insights, signaling an opportunity for enhancing representation quality.Our study addresses this gap by incorporating protein family classification into ESM2's training.This approach, augmented with Community Propagation-Based Clustering Algorithm, improves global protein representations, while a contextual prediction task fine-tunes local amino acid accuracy. Significantly, our model achieved state-of-the-art results in several downstream experiments, demonstrating the power of combining global and local methodologies to substantially boost protein representation quality.

Zhen Yuan, Shaoqing Jiao, Yihang Xiao et al.

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 unprecedented insights into cellular identity, regulatory processes, and disease mechanisms. However, it remains challenging, as current methods often rely on selecting highly variable genes or peaks during preprocessing, which may inadvertently discard crucial biological information. Here, we present scMamba, a foundation model designed to integrate single-cell multi-omics data without the need for prior feature selection while preserving genomic positional information. scMamba introduces a patch-based cell tokenization strategy that treats genomics regions as words (tokens) and cells as sentences. Building upon the concept of state space duality, scMamba distills rich biological insights from high-dimensional, sparse single-cell multi-omics data. Additionally, our novel contrastive learning approach, enhanced with cosine similarity regularization, enables superior alignment across omics layers compared to traditional methods. Systematic benchmarking across multiple datasets demonstrates that scMamba significantly outperforms state-of-the-art methods in preserving biological variation, aligning omics layers, and enhancing key downstream tasks such as clustering, cell type annotation, and trajectory inference. Our findings position scMamba as a powerful tool for large-scale single-cell multi-omics integration, capable of handling large-scale atlases and advancing biological discovery.

Jingcong Liang, Junlong Wang, Xinyu Zhai et al.

We give a detailed overview of the CAIL 2023 Argument Mining Track, one of the Chinese AI and Law Challenge (CAIL) 2023 tracks. The main goal of the track is to identify and extract interacting argument pairs in trial dialogs. It mainly uses summarized judgment documents but can also refer to trial recordings. The track consists of two stages, and we introduce the tasks designed for each stage; we also extend the data from previous events into a new dataset -- CAIL2023-ArgMine -- with annotated new cases from various causes of action. We outline several submissions that achieve the best results, including their methods for different stages. While all submissions rely on language models, they have incorporated strategies that may benefit future work in this field.

Jiwen Zhang, Zhongyu Wei, Jianqing Fan et al.

Vision-and-Language Navigation (VLN) is a task where an agent navigates in an embodied indoor environment under human instructions. Previous works ignore the distribution of sample difficulty and we argue that this potentially degrade their agent performance. To tackle this issue, we propose a novel curriculum-based training paradigm for VLN tasks that can balance human prior knowledge and agent learning progress about training samples. We develop the principle of curriculum design and re-arrange the benchmark Room-to-Room (R2R) dataset to make it suitable for curriculum training. Experiments show that our method is model-agnostic and can significantly improve the performance, the generalizability, and the training efficiency of current state-of-the-art navigation agents without increasing model complexity.

Tianpei Yang, Jianye Hao, Zhaopeng Meng et al.

Transfer Learning (TL) has shown great potential to accelerate Reinforcement Learning (RL) by leveraging prior knowledge from past learned policies of relevant tasks. Existing transfer approaches either explicitly computes the similarity between tasks or select appropriate source policies to provide guided explorations for the target task. However, how to directly optimize the target policy by alternatively utilizing knowledge from appropriate source policies without explicitly measuring the similarity is currently missing. In this paper, we propose a novel Policy Transfer Framework (PTF) to accelerate RL by taking advantage of this idea. Our framework learns when and which source policy is the best to reuse for the target policy and when to terminate it by modeling multi-policy transfer as the option learning problem. PTF can be easily combined with existing deep RL approaches. Experimental results show it significantly accelerates the learning process and surpasses state-of-the-art policy transfer methods in terms of learning efficiency and final performance in both discrete and continuous action spaces.

Hansheng Xue, Jiajie Peng, Xuequn Shang

Networks are ubiquitous structure that describes complex relationships between different entities in the real world. As a critical component of prediction task over nodes in networks, learning the feature representation of nodes has become one of the most active areas recently. Network Embedding, aiming to learn non-linear and low-dimensional feature representation based on network topology, has been proved to be helpful on tasks of network analysis, especially node classification. For many real-world systems, multiple types of relations are naturally represented by multiple networks. However, existing network embedding methods mainly focus on single network embedding and neglect the information shared among different networks. In this paper, we propose a novel multiple network embedding method based on semisupervised autoencoder, named DeepMNE, which captures complex topological structures of multi-networks and takes the correlation among multi-networks into account. We evaluate DeepMNE on the task of node classification with two real-world datasets. The experimental results demonstrate the superior performance of our method over four state-of-the-art algorithms.