Xien Liu

Yuxuan Zhou, Xien Liu, Kaiyin Zhou et al.

The table-based fact verification task has recently gained widespread attention and yet remains to be a very challenging problem. It inherently requires informative reasoning over natural language together with different numerical and logical reasoning on tables (e.g., count, superlative, comparative). Considering that, we exploit mixture-of-experts and present in this paper a new method: Self-adaptive Mixture-of-Experts Network (SaMoE). Specifically, we have developed a mixture-of-experts neural network to recognize and execute different types of reasoning -- the network is composed of multiple experts, each handling a specific part of the semantics for reasoning, whereas a management module is applied to decide the contribution of each expert network to the verification result. A self-adaptive method is developed to teach the management module combining results of different experts more efficiently without external knowledge. The experimental results illustrate that our framework achieves 85.1% accuracy on the benchmark dataset TabFact, comparable with the previous state-of-the-art models. We hope our framework can serve as a new baseline for table-based verification. Our code is available at https://github.com/THUMLP/SaMoE.

Yuxuan Zhou, Ziyu Jin, Meiwei Li et al.

The NLI4CT task aims to entail hypotheses based on Clinical Trial Reports (CTRs) and retrieve the corresponding evidence supporting the justification. This task poses a significant challenge, as verifying hypotheses in the NLI4CT task requires the integration of multiple pieces of evidence from one or two CTR(s) and the application of diverse levels of reasoning, including textual and numerical. To address these problems, we present a multi-granularity system for CTR-based textual entailment and evidence retrieval in this paper. Specifically, we construct a Multi-granularity Inference Network (MGNet) that exploits sentence-level and token-level encoding to handle both textual entailment and evidence retrieval tasks. Moreover, we enhance the numerical inference capability of the system by leveraging a T5-based model, SciFive, which is pre-trained on the medical corpus. Model ensembling and a joint inference method are further utilized in the system to increase the stability and consistency of inference. The system achieves f1-scores of 0.856 and 0.853 on textual entailment and evidence retrieval tasks, resulting in the best performance on both subtasks. The experimental results corroborate the effectiveness of our proposed method. Our code is publicly available at https://github.com/THUMLP/NLI4CT.

Yuxuan Zhou, Yubin Wang, Bin Wang et al.

Large language models (LLMs) have shown great promise in the medical domain, achieving strong performance on several benchmarks. However, they continue to underperform in real-world medical scenarios, which often demand stronger context-awareness, i.e., the ability to recognize missing or critical details (e.g., user identity, medical history, risk factors) and provide safe, helpful, and contextually appropriate responses. To address this issue, we propose Multifaceted Self-Refinement (MuSeR), a data-driven approach that enhances LLMs' context-awareness along three key facets (decision-making, communication, and safety) through self-evaluation and refinement. Specifically, we first design a attribute-conditioned query generator that simulates diverse real-world user contexts by varying attributes such as role, geographic region, intent, and degree of information ambiguity. An LLM then responds to these queries, self-evaluates its answers along three key facets, and refines its responses to better align with the requirements of each facet. Finally, the queries and refined responses are used for supervised fine-tuning to reinforce the model's context-awareness ability. Evaluation results on the latest HealthBench dataset demonstrate that our method significantly improves LLM performance across multiple aspects, with particularly notable gains in the context-awareness axis. Furthermore, by incorporating knowledge distillation with the proposed method, the performance of a smaller backbone LLM (e.g., Qwen3-32B) surpasses its teacher model, achieving a new SOTA across all open-source LLMs on HealthBench (63.8%) and its hard subset (43.1%). Code and dataset will be released at https://muser-llm.github.io.

Shaohui Liu, Xien Liu, Ji Wu · tsinghua

The purpose of write-missing diagnosis detection is to find diseases that have been clearly diagnosed from medical records but are missed in the discharge diagnosis. Unlike the definition of missed diagnosis, the write-missing diagnosis is clearly manifested in the medical record without further reasoning. The write-missing diagnosis is a common problem, often caused by physician negligence. The write-missing diagnosis will result in an incomplete diagnosis of medical records. While under DRG grouping, the write-missing diagnoses will miss important additional diagnoses (CC, MCC), thus affecting the correct rate of DRG enrollment. Under the circumstance that countries generally start to adopt DRG enrollment and payment, the problem of write-missing diagnosis is a common and serious problem. The current manual-based method is expensive due to the complex content of the full medical record. We think this problem is suitable to be solved as natural language processing. But to the best of our knowledge, no researchers have conducted research on this problem based on natural language processing methods. We propose a framework for solving the problem of write-missing diagnosis, which mainly includes three modules: disease recall module, disease context logic judgment module, and disease relationship comparison module. Through this framework, we verify that the problem of write-missing diagnosis can be solved well, and the results are interpretable. At the same time, we propose advanced solutions for the disease context logic judgment module and disease relationship comparison module, which have obvious advantages compared with the mainstream methods of the same type of problems. Finally, we verified the value of our proposed framework under DRG medical insurance payment in a tertiary hospital.

Yuxuan Zhou, Xien Liu, Chen Ning et al.

Mastering medical knowledge is crucial for medical-specific LLMs. However, despite the existence of medical benchmarks like MedQA, a unified framework that fully leverages existing knowledge bases to evaluate LLMs' mastery of medical knowledge is still lacking. In the study, we propose a novel framework PretexEval that dynamically generates reliable and diverse test samples to evaluate LLMs for any given medical knowledge base. We notice that test samples produced directly from knowledge bases by templates or LLMs may introduce factual errors and also lack diversity. To address these issues, we introduce a novel schema into our proposed evaluation framework that employs predicate equivalence transformations to produce a series of variants for any given medical knowledge point. Finally, these produced predicate variants are converted into textual language, resulting in a series of reliable and diverse test samples to evaluate whether LLMs fully master the given medical factual knowledge point. Here, we use our proposed framework to systematically investigate the mastery of medical factual knowledge of 12 well-known LLMs, based on two knowledge bases that are crucial for clinical diagnosis and treatment. The evaluation results illustrate that current LLMs still exhibit significant deficiencies in fully mastering medical knowledge, despite achieving considerable success on some famous public benchmarks. These new findings provide valuable insights for developing medical-specific LLMs, highlighting that current LLMs urgently need to strengthen their comprehensive and in-depth mastery of medical knowledge before being applied to real-world medical scenarios.

Wenqian Cui, Xiangling Fu, Shaohui Liu et al.

Disease name normalization is an important task in the medical domain. It classifies disease names written in various formats into standardized names, serving as a fundamental component in smart healthcare systems for various disease-related functions. Nevertheless, the most significant obstacle to existing disease name normalization systems is the severe shortage of training data. Consequently, we present a novel data augmentation approach that includes a series of data augmentation techniques and some supporting modules to help mitigate the problem. Our proposed methods rely on the Structural Invariance property of disease names and the Hierarchy property of the disease classification system. The goal is to equip the models with extensive understanding of the disease names and the hierarchical structure of the disease name classification system. Through extensive experimentation, we illustrate that our proposed approach exhibits significant performance improvements across various baseline models and training objectives, particularly in scenarios with limited training data.

Chenwei Yan, Xiangling Fu, Yuxuan Xiong et al.

Large language models (LLMs) have demonstrated impressive performance across various domains. However, for clinical diagnosis, higher expectations are required for LLM's reliability and sensitivity: thinking like physicians and remaining sensitive to key medical information that affects diagnostic reasoning, as subtle variations can lead to different diagnosis results. Yet, existing works focus mainly on investigating the sensitivity of LLMs to irrelevant context and overlook the importance of key information. In this paper, we investigate the sensitivity of LLMs, i.e. GPT-3.5, GPT-4, Gemini, Claude3 and LLaMA2-7b, to key medical information by introducing different perturbation strategies. The evaluation results highlight the limitations of current LLMs in remaining sensitive to key medical information for diagnostic decision-making. The evolution of LLMs must focus on improving their reliability, enhancing their ability to be sensitive to key information, and effectively utilizing this information. These improvements will enhance human trust in LLMs and facilitate their practical application in real-world scenarios. Our code and dataset are available at https://github.com/chenwei23333/DiagnosisQA.

Baichuan Zhou, Ying Hu, Xi Weng et al.

We present the TinyLLaVA framework that provides a unified perspective in designing and analyzing the small-scale Large Multimodal Models (LMMs). We empirically study the effects of different vision encoders, connection modules, language models, training data and training recipes. Our extensive experiments showed that better quality of data combined with better training recipes, smaller LMMs can consistently achieve on-par performances compared to bigger LMMs. Under our framework, we train a family of small-scale LMMs. Our best model, TinyLLaVA-3.1B, achieves better overall performance against existing 7B models such as LLaVA-1.5 and Qwen-VL. We hope our findings can serve as baselines for future research in terms of data scaling, training setups and model selections. Our model weights and codes will be made public.

Yuxuan Zhou, Xien Liu, Chen Ning et al.

Large language models (LLMs) have excelled across domains, also delivering notable performance on the medical evaluation benchmarks, such as MedQA. However, there still exists a significant gap between the reported performance and the practical effectiveness in real-world medical scenarios. In this paper, we aim to explore the causes of this gap by employing a multifaceted examination schema to systematically probe the actual mastery of medical knowledge by current LLMs. Specifically, we develop a novel evaluation framework MultifacetEval to examine the degree and coverage of LLMs in encoding and mastering medical knowledge at multiple facets (comparison, rectification, discrimination, and verification) concurrently. Based on the MultifacetEval framework, we construct two multifaceted evaluation datasets: MultiDiseK (by producing questions from a clinical disease knowledge base) and MultiMedQA (by rephrasing each question from a medical benchmark MedQA into multifaceted questions). The experimental results on these multifaceted datasets demonstrate that the extent of current LLMs in mastering medical knowledge is far below their performance on existing medical benchmarks, suggesting that they lack depth, precision, and comprehensiveness in mastering medical knowledge. Consequently, current LLMs are not yet ready for application in real-world medical tasks. The codes and datasets are available at https://github.com/THUMLP/MultifacetEval.

Yuxuan Zhou, Xien Liu, Chenwei Yan et al.

Large language models (LLMs) have demonstrated remarkable performance on various medical benchmarks, but their capabilities across different cognitive levels remain underexplored. Inspired by Bloom's Taxonomy, we propose a multi-cognitive-level evaluation framework for assessing LLMs in the medical domain in this study. The framework integrates existing medical datasets and introduces tasks targeting three cognitive levels: preliminary knowledge grasp, comprehensive knowledge application, and scenario-based problem solving. Using this framework, we systematically evaluate state-of-the-art general and medical LLMs from six prominent families: Llama, Qwen, Gemma, Phi, GPT, and DeepSeek. Our findings reveal a significant performance decline as cognitive complexity increases across evaluated models, with model size playing a more critical role in performance at higher cognitive levels. Our study highlights the need to enhance LLMs' medical capabilities at higher cognitive levels and provides insights for developing LLMs suited to real-world medical applications.

Xinxin You, Xien Liu, Xue Yang et al.

The task of automatically coding the International Classification of Diseases (ICD) in the medical field has been well-established and has received much attention. Automatic coding of the ICD in the medical field has been successful in English but faces challenges when dealing with Chinese electronic medical records (EMRs). The first issue lies in the difficulty of extracting disease code-related information from Chinese EMRs, primarily due to the concise writing style and specific internal structure of the EMRs. The second problem is that previous methods have failed to leverage the disease-based multi-axial knowledge and lack of association with the corresponding clinical evidence. This paper introduces a novel framework called MKE-Coder: Multi-axial Knowledge with Evidence verification in ICD coding for Chinese EMRs. Initially, we identify candidate codes for the diagnosis and categorize each of them into knowledge under four coding axes.Subsequently, we retrieve corresponding clinical evidence from the comprehensive content of EMRs and filter credible evidence through a scoring model. Finally, to ensure the validity of the candidate code, we propose an inference module based on the masked language modeling strategy. This module verifies that all the axis knowledge associated with the candidate code is supported by evidence and provides recommendations accordingly. To evaluate the performance of our framework, we conduct experiments using a large-scale Chinese EMR dataset collected from various hospitals. The experimental results demonstrate that MKE-Coder exhibits significant superiority in the task of automatic ICD coding based on Chinese EMRs. In the practical evaluation of our method within simulated real coding scenarios, it has been demonstrated that our approach significantly aids coders in enhancing both their coding accuracy and speed.

Xinxin You, Xien Liu, Qixin Sun et al.

Recent methodologies utilizing synthetic datasets have aimed to address inconsistent hallucinations in large language models (LLMs); however,these approaches are primarily tailored to specific tasks, limiting their generalizability. Inspired by the strong performance of code-trained models in logic-intensive domains, we propose a novel framework that leverages event-based text to generate corresponding code and employs cyclic training to transfer the logical consistency of code to natural language effectively. Our method significantly reduces inconsistent hallucinations across three leading LLMs and two categories of natural language tasks while maintaining overall performance. This framework effectively alleviates hallucinations without necessitating adaptation to downstream tasks, demonstrating generality and providing new perspectives to tackle the challenge of inconsistent hallucinations.

Wenqian Cui, Xiangling Fu, Shaohui Liu et al.

Disease name normalization is an important task in the medical domain. It classifies disease names written in various formats into standardized names, serving as a fundamental component in smart healthcare systems for various disease-related functions. Nevertheless, the most significant obstacle to existing disease name normalization systems is the severe shortage of training data. Consequently, we present a novel data augmentation approach that includes a series of data augmentation techniques and some supporting modules to help mitigate the problem. Through extensive experimentation, we illustrate that our proposed approach exhibits significant performance improvements across various baseline models and training objectives, particularly in scenarios with limited training data

Xien Liu, Song Wang, Xiao Zhang et al.

Text classification is one of the most important and fundamental tasks in natural language processing. Performance of this task mainly dependents on text representation learning. Currently, most existing learning frameworks mainly focus on encoding local contextual information between words. These methods always neglect to exploit global clues, such as label information, for encoding text information. In this study, we propose a label-guided learning framework LguidedLearn for text representation and classification. Our method is novel but simple that we only insert a label-guided encoding layer into the commonly used text representation learning schemas. That label-guided layer performs label-based attentive encoding to map the universal text embedding (encoded by a contextual information learner) into different label spaces, resulting in label-wise embeddings. In our proposed framework, the label-guided layer can be easily and directly applied with a contextual encoding method to perform jointly learning. Text information is encoded based on both the local contextual information and the global label clues. Therefore, the obtained text embeddings are more robust and discriminative for text classification. Extensive experiments are conducted on benchmark datasets to illustrate the effectiveness of our proposed method.

Xien Liu, Xinxin You, Xiao Zhang et al.

Compared to sequential learning models, graph-based neural networks exhibit some excellent properties, such as ability capturing global information. In this paper, we investigate graph-based neural networks for text classification problem. A new framework TensorGCN (tensor graph convolutional networks), is presented for this task. A text graph tensor is firstly constructed to describe semantic, syntactic, and sequential contextual information. Then, two kinds of propagation learning perform on the text graph tensor. The first is intra-graph propagation used for aggregating information from neighborhood nodes in a single graph. The second is inter-graph propagation used for harmonizing heterogeneous information between graphs. Extensive experiments are conducted on benchmark datasets, and the results illustrate the effectiveness of our proposed framework. Our proposed TensorGCN presents an effective way to harmonize and integrate heterogeneous information from different kinds of graphs.

Yu Hao, Xien Liu, Ji Wu et al.

Despite the great success of word embedding, sentence embedding remains a not-well-solved problem. In this paper, we present a supervised learning framework to exploit sentence embedding for the medical question answering task. The learning framework consists of two main parts: 1) a sentence embedding producing module, and 2) a scoring module. The former is developed with contextual self-attention and multi-scale techniques to encode a sentence into an embedding tensor. This module is shortly called Contextual self-Attention Multi-scale Sentence Embedding (CAMSE). The latter employs two scoring strategies: Semantic Matching Scoring (SMS) and Semantic Association Scoring (SAS). SMS measures similarity while SAS captures association between sentence pairs: a medical question concatenated with a candidate choice, and a piece of corresponding supportive evidence. The proposed framework is examined by two Medical Question Answering(MedicalQA) datasets which are collected from real-world applications: medical exam and clinical diagnosis based on electronic medical records (EMR). The comparison results show that our proposed framework achieved significant improvements compared to competitive baseline approaches. Additionally, a series of controlled experiments are also conducted to illustrate that the multi-scale strategy and the contextual self-attention layer play important roles for producing effective sentence embedding, and the two kinds of scoring strategies are highly complementary to each other for question answering problems.

Xiao Zhang, Ji Wu, Zhiyang He et al.

Reading and understanding text is one important component in computer aided diagnosis in clinical medicine, also being a major research problem in the field of NLP. In this work, we introduce a question-answering task called MedQA to study answering questions in clinical medicine using knowledge in a large-scale document collection. The aim of MedQA is to answer real-world questions with large-scale reading comprehension. We propose our solution SeaReader--a modular end-to-end reading comprehension model based on LSTM networks and dual-path attention architecture. The novel dual-path attention models information flow from two perspectives and has the ability to simultaneously read individual documents and integrate information across multiple documents. In experiments our SeaReader achieved a large increase in accuracy on MedQA over competing models. Additionally, we develop a series of novel techniques to demonstrate the interpretation of the question answering process in SeaReader.