Hua Xu

Hanlei Zhang, Hua Xu, Xin Wang et al. · tsinghua

Multimodal intent recognition is a significant task for understanding human language in real-world multimodal scenes. Most existing intent recognition methods have limitations in leveraging the multimodal information due to the restrictions of the benchmark datasets with only text information. This paper introduces a novel dataset for multimodal intent recognition (MIntRec) to address this issue. It formulates coarse-grained and fine-grained intent taxonomies based on the data collected from the TV series Superstore. The dataset consists of 2,224 high-quality samples with text, video, and audio modalities and has multimodal annotations among twenty intent categories. Furthermore, we provide annotated bounding boxes of speakers in each video segment and achieve an automatic process for speaker annotation. MIntRec is helpful for researchers to mine relationships between different modalities to enhance the capability of intent recognition. We extract features from each modality and model cross-modal interactions by adapting three powerful multimodal fusion methods to build baselines. Extensive experiments show that employing the non-verbal modalities achieves substantial improvements compared with the text-only modality, demonstrating the effectiveness of using multimodal information for intent recognition. The gap between the best-performing methods and humans indicates the challenge and importance of this task for the community. The full dataset and codes are available for use at https://github.com/thuiar/MIntRec.

Brian Ondov, Chia-Hsuan Chang, Weipeng Zhou et al.

High-dimensional biomedical data, such as cell-by-gene matrices, are increasingly generated temporally. However, Manifold Learning algorithms, like t-SNE and UMAP, cannot incorporate time-ordering in their layouts, obfuscating the dynamics of cell types or other classes. As a solution, we present IRIS, a new Manifold Learning algorithm that structures layouts both chronologically and by manifold topology. IRIS can visualize a wide range of dynamic biomedical data, including scRNA-seq, comparative metagenomics, and literature.

Rui Yang, Qingcheng Zeng, Keen You et al.

This study introduces Ascle, a pioneering natural language processing (NLP) toolkit designed for medical text generation. Ascle is tailored for biomedical researchers and healthcare professionals with an easy-to-use, all-in-one solution that requires minimal programming expertise. For the first time, Ascle evaluates and provides interfaces for the latest pre-trained language models, encompassing four advanced and challenging generative functions: question-answering, text summarization, text simplification, and machine translation. In addition, Ascle integrates 12 essential NLP functions, along with query and search capabilities for clinical databases. The toolkit, its models, and associated data are publicly available via https://github.com/Yale-LILY/MedGen.

Huisheng Mao, Ziqi Yuan, Hua Xu et al.

M-SENA is an open-sourced platform for Multimodal Sentiment Analysis. It aims to facilitate advanced research by providing flexible toolkits, reliable benchmarks, and intuitive demonstrations. The platform features a fully modular video sentiment analysis framework consisting of data management, feature extraction, model training, and result analysis modules. In this paper, we first illustrate the overall architecture of the M-SENA platform and then introduce features of the core modules. Reliable baseline results of different modality features and MSA benchmarks are also reported. Moreover, we use model evaluation and analysis tools provided by M-SENA to present intermediate representation visualization, on-the-fly instance test, and generalization ability test results. The source code of the platform is publicly available at https://github.com/thuiar/M-SENA.

Hanlei Zhang, Hua Xu, Xin Wang et al. · tsinghua

New intent discovery is of great value to natural language processing, allowing for a better understanding of user needs and providing friendly services. However, most existing methods struggle to capture the complicated semantics of discrete text representations when limited or no prior knowledge of labeled data is available. To tackle this problem, we propose a novel clustering framework, USNID, for unsupervised and semi-supervised new intent discovery, which has three key technologies. First, it fully utilizes unsupervised or semi-supervised data to mine shallow semantic similarity relations and provide well-initialized representations for clustering. Second, it designs a centroid-guided clustering mechanism to address the issue of cluster allocation inconsistency and provide high-quality self-supervised targets for representation learning. Third, it captures high-level semantics in unsupervised or semi-supervised data to discover fine-grained intent-wise clusters by optimizing both cluster-level and instance-level objectives. We also propose an effective method for estimating the cluster number in open-world scenarios without knowing the number of new intents beforehand. USNID performs exceptionally well on several benchmark intent datasets, achieving new state-of-the-art results in unsupervised and semi-supervised new intent discovery and demonstrating robust performance with different cluster numbers.

Cathy Shyr, Yan Hu, Paul A. Harris et al.

Rare diseases (RDs) are collectively common and affect 300 million people worldwide. Accurate phenotyping is critical for informing diagnosis and treatment, but RD phenotypes are often embedded in unstructured text and time-consuming to extract manually. While natural language processing (NLP) models can perform named entity recognition (NER) to automate extraction, a major bottleneck is the development of a large, annotated corpus for model training. Recently, prompt learning emerged as an NLP paradigm that can lead to more generalizable results without any (zero-shot) or few labeled samples (few-shot). Despite growing interest in ChatGPT, a revolutionary large language model capable of following complex human prompts and generating high-quality responses, none have studied its NER performance for RDs in the zero- and few-shot settings. To this end, we engineered novel prompts aimed at extracting RD phenotypes and, to the best of our knowledge, are the first the establish a benchmark for evaluating ChatGPT's performance in these settings. We compared its performance to the traditional fine-tuning approach and conducted an in-depth error analysis. Overall, fine-tuning BioClinicalBERT resulted in higher performance (F1 of 0.689) than ChatGPT (F1 of 0.472 and 0.591 in the zero- and few-shot settings, respectively). Despite this, ChatGPT achieved similar or higher accuracy for certain entities (i.e., rare diseases and signs) in the one-shot setting (F1 of 0.776 and 0.725). This suggests that with appropriate prompt engineering, ChatGPT has the potential to match or outperform fine-tuned language models for certain entity types with just one labeled sample. While the proliferation of large language models may provide opportunities for supporting RD diagnosis and treatment, researchers and clinicians should critically evaluate model outputs and be well-informed of their limitations.

Jiaming Ji, Tianyi Qiu, Boyuan Chen et al.

AI alignment aims to make AI systems behave in line with human intentions and values. As AI systems grow more capable, so do risks from misalignment. To provide a comprehensive and up-to-date overview of the alignment field, in this survey, we delve into the core concepts, methodology, and practice of alignment. First, we identify four principles as the key objectives of AI alignment: Robustness, Interpretability, Controllability, and Ethicality (RICE). Guided by these four principles, we outline the landscape of current alignment research and decompose them into two key components: forward alignment and backward alignment. The former aims to make AI systems aligned via alignment training, while the latter aims to gain evidence about the systems' alignment and govern them appropriately to avoid exacerbating misalignment risks. On forward alignment, we discuss techniques for learning from feedback and learning under distribution shift. On backward alignment, we discuss assurance techniques and governance practices. We also release and continually update the website (www.alignmentsurvey.com) which features tutorials, collections of papers, blog posts, and other resources.

Betina Idnay, Zihan Xu, William G. Adams et al.

This study reports a comprehensive environmental scan of the generative AI (GenAI) infrastructure in the national network for clinical and translational science across 36 institutions supported by the Clinical and Translational Science Award (CTSA) Program led by the National Center for Advancing Translational Sciences (NCATS) of the National Institutes of Health (NIH) at the United States. With the rapid advancement of GenAI technologies, including large language models (LLMs), healthcare institutions face unprecedented opportunities and challenges. This research explores the current status of GenAI integration, focusing on stakeholder roles, governance structures, and ethical considerations by administering a survey among leaders of health institutions (i.e., representing academic medical centers and health systems) to assess the institutional readiness and approach towards GenAI adoption. Key findings indicate a diverse range of institutional strategies, with most organizations in the experimental phase of GenAI deployment. The study highlights significant variations in governance models, with a strong preference for centralized decision-making but notable gaps in workforce training and ethical oversight. Moreover, the results underscore the need for a more coordinated approach to GenAI governance, emphasizing collaboration among senior leaders, clinicians, information technology staff, and researchers. Our analysis also reveals concerns regarding GenAI bias, data security, and stakeholder trust, which must be addressed to ensure the ethical and effective implementation of GenAI technologies. This study offers valuable insights into the challenges and opportunities of GenAI integration in healthcare, providing a roadmap for institutions aiming to leverage GenAI for improved quality of care and operational efficiency.

Hanlei Zhang, Hua Xu, Shaojie Zhao et al. · tsinghua

Open intent detection is a significant problem in natural language understanding, which aims to identify the unseen open intent while ensuring known intent identification performance. However, current methods face two major challenges. Firstly, they struggle to learn friendly representations to detect the open intent with prior knowledge of only known intents. Secondly, there is a lack of an effective approach to obtaining specific and compact decision boundaries for known intents. To address these issues, this paper presents an original framework called DA-ADB, which successively learns distance-aware intent representations and adaptive decision boundaries for open intent detection. Specifically, we first leverage distance information to enhance the distinguishing capability of the intent representations. Then, we design a novel loss function to obtain appropriate decision boundaries by balancing both empirical and open space risks. Extensive experiments demonstrate the effectiveness of the proposed distance-aware and boundary learning strategies. Compared to state-of-the-art methods, our framework achieves substantial improvements on three benchmark datasets. Furthermore, it yields robust performance with varying proportions of labeled data and known categories.

Aidan Gilson, Xuguang Ai, Thilaka Arunachalam et al.

Despite the potential of Large Language Models (LLMs) in medicine, they may generate responses lacking supporting evidence or based on hallucinated evidence. While Retrieval Augment Generation (RAG) is popular to address this issue, few studies implemented and evaluated RAG in downstream domain-specific applications. We developed a RAG pipeline with 70,000 ophthalmology-specific documents that retrieve relevant documents to augment LLMs during inference time. In a case study on long-form consumer health questions, we systematically evaluated the responses including over 500 references of LLMs with and without RAG on 100 questions with 10 healthcare professionals. The evaluation focuses on factuality of evidence, selection and ranking of evidence, attribution of evidence, and answer accuracy and completeness. LLMs without RAG provided 252 references in total. Of which, 45.3% hallucinated, 34.1% consisted of minor errors, and 20.6% were correct. In contrast, LLMs with RAG significantly improved accuracy (54.5% being correct) and reduced error rates (18.8% with minor hallucinations and 26.7% with errors). 62.5% of the top 10 documents retrieved by RAG were selected as the top references in the LLM response, with an average ranking of 4.9. The use of RAG also improved evidence attribution (increasing from 1.85 to 2.49 on a 5-point scale, P<0.001), albeit with slight decreases in accuracy (from 3.52 to 3.23, P=0.03) and completeness (from 3.47 to 3.27, P=0.17). The results demonstrate that LLMs frequently exhibited hallucinated and erroneous evidence in the responses, raising concerns for downstream applications in the medical domain. RAG substantially reduced the proportion of such evidence but encountered challenges.

Rachael Fleurence, Jiang Bian, Xiaoyan Wang et al.

This review introduces the transformative potential of generative Artificial Intelligence (AI) and foundation models, including large language models (LLMs), for health technology assessment (HTA). We explore their applications in four critical areas, evidence synthesis, evidence generation, clinical trials and economic modeling: (1) Evidence synthesis: Generative AI has the potential to assist in automating literature reviews and meta-analyses by proposing search terms, screening abstracts, and extracting data with notable accuracy; (2) Evidence generation: These models can potentially facilitate automating the process and analyze the increasingly available large collections of real-world data (RWD), including unstructured clinical notes and imaging, enhancing the speed and quality of real-world evidence (RWE) generation; (3) Clinical trials: Generative AI can be used to optimize trial design, improve patient matching, and manage trial data more efficiently; and (4) Economic modeling: Generative AI can also aid in the development of health economic models, from conceptualization to validation, thus streamlining the overall HTA process. Despite their promise, these technologies, while rapidly improving, are still nascent and continued careful evaluation in their applications to HTA is required. To ensure their responsible use and implementation, both developers and users of research incorporating these tools, should familiarize themselves with their current limitations, including the issues related to scientific validity, risk of bias, and consider equity and ethical implications. We also surveyed the current policy landscape and provide suggestions for HTA agencies on responsibly integrating generative AI into their workflows, emphasizing the importance of human oversight and the fast-evolving nature of these tools.

Yihe Liu, Ziqi Yuan, Huisheng Mao et al.

Multimodal sentiment analysis (MSA), which supposes to improve text-based sentiment analysis with associated acoustic and visual modalities, is an emerging research area due to its potential applications in Human-Computer Interaction (HCI). However, the existing researches observe that the acoustic and visual modalities contribute much less than the textual modality, termed as text-predominant. Under such circumstances, in this work, we emphasize making non-verbal cues matter for the MSA task. Firstly, from the resource perspective, we present the CH-SIMS v2.0 dataset, an extension and enhancement of the CH-SIMS. Compared with the original dataset, the CH-SIMS v2.0 doubles its size with another 2121 refined video segments with both unimodal and multimodal annotations and collects 10161 unlabelled raw video segments with rich acoustic and visual emotion-bearing context to highlight non-verbal cues for sentiment prediction. Secondly, from the model perspective, benefiting from the unimodal annotations and the unsupervised data in the CH-SIMS v2.0, the Acoustic Visual Mixup Consistent (AV-MC) framework is proposed. The designed modality mixup module can be regarded as an augmentation, which mixes the acoustic and visual modalities from different videos. Through drawing unobserved multimodal context along with the text, the model can learn to be aware of different non-verbal contexts for sentiment prediction. Our evaluations demonstrate that both CH-SIMS v2.0 and AV-MC framework enables further research for discovering emotion-bearing acoustic and visual cues and paves the path to interpretable end-to-end HCI applications for real-world scenarios.

Kang Zhao, Hua Xu, Jiangong Yang et al.

Continual relation extraction (CRE) aims to continuously train a model on data with new relations while avoiding forgetting old ones. Some previous work has proved that storing a few typical samples of old relations and replaying them when learning new relations can effectively avoid forgetting. However, these memory-based methods tend to overfit the memory samples and perform poorly on imbalanced datasets. To solve these challenges, a consistent representation learning method is proposed, which maintains the stability of the relation embedding by adopting contrastive learning and knowledge distillation when replaying memory. Specifically, supervised contrastive learning based on a memory bank is first used to train each new task so that the model can effectively learn the relation representation. Then, contrastive replay is conducted of the samples in memory and makes the model retain the knowledge of historical relations through memory knowledge distillation to prevent the catastrophic forgetting of the old task. The proposed method can better learn consistent representations to alleviate forgetting effectively. Extensive experiments on FewRel and TACRED datasets show that our method significantly outperforms state-of-the-art baselines and yield strong robustness on the imbalanced dataset.

Yuezhang Peng, Chonghao Cai, Ziang Liu et al.

Spoken Language Understanding (SLU), which aims to extract user semantics to execute downstream tasks, is a crucial component of task-oriented dialog systems. Existing SLU datasets generally lack sufficient diversity and complexity, and there is an absence of a unified benchmark for the latest Large Language Models (LLMs) and Large Audio Language Models (LALMs). This work introduces MAC-SLU, a novel Multi-Intent Automotive Cabin Spoken Language Understanding Dataset, which increases the difficulty of the SLU task by incorporating authentic and complex multi-intent data. Based on MAC-SLU, we conducted a comprehensive benchmark of leading open-source LLMs and LALMs, covering methods like in-context learning, supervised fine-tuning (SFT), and end-to-end (E2E) and pipeline paradigms. Our experiments show that while LLMs and LALMs have the potential to complete SLU tasks through in-context learning, their performance still lags significantly behind SFT. Meanwhile, E2E LALMs demonstrate performance comparable to pipeline approaches and effectively avoid error propagation from speech recognition. Code\footnote{https://github.com/Gatsby-web/MAC\_SLU} and datasets\footnote{huggingface.co/datasets/Gatsby1984/MAC\_SLU} are released publicly.

Anran Li, Yuanyuan Chen, Wenjun Long et al.

Large language models (LLMs) have demonstrated strong performance on medical benchmarks, including question answering and diagnosis. To enable their use in clinical settings, LLMs are typically further adapted through continued pretraining or post-training using clinical data. However, most medical LLMs are trained on data from a single institution, which faces limitations in generalizability and safety in heterogeneous systems. Federated learning (FL) is a promising solution for enabling collaborative model development across healthcare institutions. Yet applying FL to LLMs in medicine remains fundamentally limited. First, conventional FL requires transmitting the full model during each communication round, which becomes impractical for multi-billion-parameter LLMs given the limited computational resources. Second, many FL algorithms implicitly assume data homogeneity, whereas real-world clinical data are highly heterogeneous across patients, diseases, and institutional practices. We introduce the model-agnostic and parameter-efficient federated learning framework for adapting LLMs to medical applications. Fed-MedLoRA transmits only low-rank adapter parameters, reducing communication and computation overhead, while Fed-MedLoRA+ further incorporates adaptive, data-aware aggregation to improve convergence under cross-site heterogeneity. We apply the framework to clinical information extraction (IE), which transforms patient narratives into structured medical entities and relations. Accuracy was assessed across five patient cohorts through comparisons with BERT models, and LLaMA-3 and DeepSeek-R1, GPT-4o models. Evaluation settings included (1) in-domain training and testing, (2) external validation on independent cohorts, and (3) a low-resource new-site adaptation scenario using real-world clinical notes from the Yale New Haven Health System.

Zehan Li, Yan Hu, Scott Lane et al.

Accurate identification and categorization of suicidal events can yield better suicide precautions, reducing operational burden, and improving care quality in high-acuity psychiatric settings. Pre-trained language models offer promise for identifying suicidality from unstructured clinical narratives. We evaluated the performance of four BERT-based models using two fine-tuning strategies (multiple single-label and single multi-label) for detecting coexisting suicidal events from 500 annotated psychiatric evaluation notes. The notes were labeled for suicidal ideation (SI), suicide attempts (SA), exposure to suicide (ES), and non-suicidal self-injury (NSSI). RoBERTa outperformed other models using multiple single-label classification strategy (acc=0.86, F1=0.78). MentalBERT (acc=0.83, F1=0.74) also exceeded BioClinicalBERT (acc=0.82, F1=0.72) which outperformed BERT (acc=0.80, F1=0.70). RoBERTa fine-tuned with single multi-label classification further improved the model performance (acc=0.88, F1=0.81). The findings highlight that the model optimization, pretraining with domain-relevant data, and the single multi-label classification strategy enhance the model performance of suicide phenotyping. Keywords: EHR-based Phenotyping; Natural Language Processing; Secondary Use of EHR Data; Suicide Classification; BERT-based Model; Psychiatry; Mental Health

Maijunxian Wang, Ruisi Wang, Juyi Lin et al.

Rapid progress in video models has largely focused on visual quality, leaving their reasoning capabilities underexplored. Video reasoning grounds intelligence in spatiotemporally consistent visual environments that go beyond what text can naturally capture, enabling intuitive reasoning over spatiotemporal structure such as continuity, interaction, and causality. However, systematically studying video reasoning and its scaling behavior is hindered by the lack of large-scale training data. To address this gap, we introduce the Very Big Video Reasoning (VBVR) Dataset, an unprecedentedly large-scale resource spanning 200 curated reasoning tasks following a principled taxonomy and over one million video clips, approximately three orders of magnitude larger than existing datasets. We further present VBVR-Bench, a verifiable evaluation framework that moves beyond model-based judging by incorporating rule-based, human-aligned scorers, enabling reproducible and interpretable diagnosis of video reasoning capabilities. Leveraging the VBVR suite, we conduct one of the first large-scale scaling studies of video reasoning and observe early signs of emergent generalization to unseen reasoning tasks. Together, VBVR lays a foundation for the next stage of research in generalizable video reasoning. The data, benchmark toolkit, and models are publicly available at https://video-reason.com/ .

Hua Xu, Julián D. Arias-Londoño, Juan I. Godino-Llorente

In critical decision support systems based on medical imaging, the reliability of AI-assisted decision-making is as relevant as predictive accuracy. Although deep learning models have demonstrated significant accuracy, they frequently suffer from miscalibration, manifested as overconfidence in erroneous predictions. To facilitate clinical acceptance, it is imperative that models quantify uncertainty in a manner that correlates with prediction correctness, allowing clinicians to identify unreliable outputs for further review. In order to address this necessity, the present paper proposes a generalizable probabilistic optimization framework grounded in Bayesian deep learning. Specifically, a novel Confidence-Uncertainty Boundary Loss (CUB-Loss) is introduced that imposes penalties on high-certainty errors and low-certainty correct predictions, explicitly enforcing alignment between prediction correctness and uncertainty estimates. Complementing this training-time optimization, a Dual Temperature Scaling (DTS) strategy is devised for post-hoc calibration, further refining the posterior distribution to improve intuitive explainability. The proposed framework is validated on three distinct medical imaging tasks: automatic screening of pneumonia, diabetic retinopathy detection, and identification of skin lesions. Empirical results demonstrate that the proposed approach achieves consistent calibration improvements across diverse modalities, maintains robust performance in data-scarce scenarios, and remains effective on severely imbalanced datasets, underscoring its potential for real clinical deployment.

Tianyu Liu, Weihao Xuan, Hao Wu et al.

Advances in AI have introduced several strong models in computational pathology to usher it into the era of multi-modal diagnosis, analysis, and interpretation. However, the current pathology-specific visual language models still lack capacities in making the diagnosis with rigorous reasoning paths as well as handling divergent tasks, and thus, challenges of building AI Copilots for real scenarios still exist. Here we introduce TeamPath, an AI system powered by reinforcement learning and router-enhanced solutions based on large-scale histopathology multimodal datasets, to work as a virtual assistant for expert-level disease diagnosis, patch-level information summarization, and cross-modality generation to integrate transcriptomic information for clinical usage. We also collaborate with pathologists from Yale School of Medicine to demonstrate that TeamPath can assist them in working more efficiently by identifying and correcting expert conclusions and reasoning paths. We also discuss the human evaluation results to support the reasoning quality from TeamPath. Overall, TeamPath can flexibly choose the best settings according to the needs, and serve as an innovative and reliable system for information communication across different modalities and experts.

Jiaming Ji, Jiayi Zhou, Hantao Lou et al.

Reinforcement learning from human feedback (RLHF) has proven effective in enhancing the instruction-following capabilities of large language models; however, it remains underexplored in the cross-modality domain. As the number of modalities increases, aligning all-modality models with human intentions -- such as instruction following -- becomes a pressing challenge. In this work, we make the first attempt to fine-tune all-modality models (i.e. input and output with any modality, also named any-to-any models) using human preference data across all modalities (including text, image, audio, and video), ensuring its behavior aligns with human intentions. This endeavor presents several challenges. First, there is no large-scale all-modality human preference data in existing open-source resources, as most datasets are limited to specific modalities, predominantly text and image. Secondly, the effectiveness of binary preferences in RLHF for post-training alignment in complex all-modality scenarios remains an unexplored area. Finally, there is a lack of a systematic framework to evaluate the capabilities of all-modality models, particularly regarding modality selection and synergy. To address these challenges, we propose the align-anything framework, which includes meticulously annotated 200k all-modality human preference data. Then, we introduce an alignment method that learns from unified language feedback, effectively capturing complex modality-specific human preferences and enhancing the model's instruction-following capabilities. Furthermore, to assess performance improvements in all-modality models after post-training alignment, we construct a challenging all-modality capability evaluation framework -- eval-anything. All data, models, and code frameworks have been open-sourced for the community. For more details, please refer to https://github.com/PKU-Alignment/align-anything.

Qianrui Zhou, Hua Xu, Hao Li et al. · tsinghua

Multimodal intent recognition aims to leverage diverse modalities such as expressions, body movements and tone of speech to comprehend user's intent, constituting a critical task for understanding human language and behavior in real-world multimodal scenarios. Nevertheless, the majority of existing methods ignore potential correlations among different modalities and own limitations in effectively learning semantic features from nonverbal modalities. In this paper, we introduce a token-level contrastive learning method with modality-aware prompting (TCL-MAP) to address the above challenges. To establish an optimal multimodal semantic environment for text modality, we develop a modality-aware prompting module (MAP), which effectively aligns and fuses features from text, video and audio modalities with similarity-based modality alignment and cross-modality attention mechanism. Based on the modality-aware prompt and ground truth labels, the proposed token-level contrastive learning framework (TCL) constructs augmented samples and employs NT-Xent loss on the label token. Specifically, TCL capitalizes on the optimal textual semantic insights derived from intent labels to guide the learning processes of other modalities in return. Extensive experiments show that our method achieves remarkable improvements compared to state-of-the-art methods. Additionally, ablation analyses demonstrate the superiority of the modality-aware prompt over the handcrafted prompt, which holds substantial significance for multimodal prompt learning. The codes are released at https://github.com/thuiar/TCL-MAP.

Kaicheng Yang, Ruxuan Zhang, Hua Xu et al.

Inter-modal interaction plays an indispensable role in multimodal sentiment analysis. Due to different modalities sequences are usually non-alignment, how to integrate relevant information of each modality to learn fusion representations has been one of the central challenges in multimodal learning. In this paper, a Self-Adjusting Fusion Representation Learning Model (SA-FRLM) is proposed to learn robust crossmodal fusion representations directly from the unaligned text and audio sequences. Different from previous works, our model not only makes full use of the interaction between different modalities but also maximizes the protection of the unimodal characteristics. Specifically, we first employ a crossmodal alignment module to project different modalities features to the same dimension. The crossmodal collaboration attention is then adopted to model the inter-modal interaction between text and audio sequences and initialize the fusion representations. After that, as the core unit of the SA-FRLM, the crossmodal adjustment transformer is proposed to protect original unimodal characteristics. It can dynamically adapt the fusion representations by using single modal streams. We evaluate our approach on the public multimodal sentiment analysis datasets CMU-MOSI and CMU-MOSEI. The experiment results show that our model has significantly improved the performance of all the metrics on the unaligned text-audio sequences.

Hanlei Zhang, Xin Wang, Hua Xu et al. · tsinghua

Multimodal intent recognition poses significant challenges, requiring the incorporation of non-verbal modalities from real-world contexts to enhance the comprehension of human intentions. Existing benchmark datasets are limited in scale and suffer from difficulties in handling out-of-scope samples that arise in multi-turn conversational interactions. We introduce MIntRec2.0, a large-scale benchmark dataset for multimodal intent recognition in multi-party conversations. It contains 1,245 dialogues with 15,040 samples, each annotated within a new intent taxonomy of 30 fine-grained classes. Besides 9,304 in-scope samples, it also includes 5,736 out-of-scope samples appearing in multi-turn contexts, which naturally occur in real-world scenarios. Furthermore, we provide comprehensive information on the speakers in each utterance, enriching its utility for multi-party conversational research. We establish a general framework supporting the organization of single-turn and multi-turn dialogue data, modality feature extraction, multimodal fusion, as well as in-scope classification and out-of-scope detection. Evaluation benchmarks are built using classic multimodal fusion methods, ChatGPT, and human evaluators. While existing methods incorporating nonverbal information yield improvements, effectively leveraging context information and detecting out-of-scope samples remains a substantial challenge. Notably, large language models exhibit a significant performance gap compared to humans, highlighting the limitations of machine learning methods in the cognitive intent understanding task. We believe that MIntRec2.0 will serve as a valuable resource, providing a pioneering foundation for research in human-machine conversational interactions, and significantly facilitating related applications. The full dataset and codes are available at https://github.com/thuiar/MIntRec2.0.

Yan Hu, Qingyu Chen, Jingcheng Du et al.

Objective: This study quantifies the capabilities of GPT-3.5 and GPT-4 for clinical named entity recognition (NER) tasks and proposes task-specific prompts to improve their performance. Materials and Methods: We evaluated these models on two clinical NER tasks: (1) to extract medical problems, treatments, and tests from clinical notes in the MTSamples corpus, following the 2010 i2b2 concept extraction shared task, and (2) identifying nervous system disorder-related adverse events from safety reports in the vaccine adverse event reporting system (VAERS). To improve the GPT models' performance, we developed a clinical task-specific prompt framework that includes (1) baseline prompts with task description and format specification, (2) annotation guideline-based prompts, (3) error analysis-based instructions, and (4) annotated samples for few-shot learning. We assessed each prompt's effectiveness and compared the models to BioClinicalBERT. Results: Using baseline prompts, GPT-3.5 and GPT-4 achieved relaxed F1 scores of 0.634, 0.804 for MTSamples, and 0.301, 0.593 for VAERS. Additional prompt components consistently improved model performance. When all four components were used, GPT-3.5 and GPT-4 achieved relaxed F1 socres of 0.794, 0.861 for MTSamples and 0.676, 0.736 for VAERS, demonstrating the effectiveness of our prompt framework. Although these results trail BioClinicalBERT (F1 of 0.901 for the MTSamples dataset and 0.802 for the VAERS), it is very promising considering few training samples are needed. Conclusion: While direct application of GPT models to clinical NER tasks falls short of optimal performance, our task-specific prompt framework, incorporating medical knowledge and training samples, significantly enhances GPT models' feasibility for potential clinical applications.

Yan Hu, Xu Zuo, Yujia Zhou et al.

Backgrounds: Information extraction (IE) is critical in clinical natural language processing (NLP). While large language models (LLMs) excel on generative tasks, their performance on extractive tasks remains debated. Methods: We investigated Named Entity Recognition (NER) and Relation Extraction (RE) using 1,588 clinical notes from four sources (UT Physicians, MTSamples, MIMIC-III, and i2b2). We developed an annotated corpus covering 4 clinical entities and 16 modifiers, and compared instruction-tuned LLaMA-2 and LLaMA-3 against BERT in terms of performance, generalizability, computational resources, and throughput to BERT. Results: LLaMA models outperformed BERT across datasets. With sufficient training data, LLaMA showed modest improvements (1% on NER, 1.5-3.7% on RE); improvements were larger with limited training data. On unseen i2b2 data, LLaMA-3-70B outperformed BERT by 7% (F1) on NER and 4% on RE. However, LLaMA models required more computing resources and ran up to 28 times slower. We implemented "Kiwi," a clinical IE package featuring both models, available at https://kiwi.clinicalnlp.org/. Conclusion: This study is among the first to develop and evaluate a comprehensive clinical IE system using open-source LLMs. Results indicate that LLaMA models outperform BERT for clinical NER and RE but with higher computational costs and lower throughputs. These findings highlight that choosing between LLMs and traditional deep learning methods for clinical IE applications should remain task-specific, taking into account both performance metrics and practical considerations such as available computing resources and the intended use case scenarios.

Huigen Ye, Hongyan Wang, Hua Xu et al.

Integer programming problems (IPs) are challenging to be solved efficiently due to the NP-hardness, especially for large-scale IPs. To solve this type of IPs, Large neighborhood search (LNS) uses an initial feasible solution and iteratively improves it by searching a large neighborhood around the current solution. However, LNS easily steps into local optima and ignores the correlation between variables to be optimized, leading to compromised performance. This paper presents a general adaptive constraint partition-based optimization framework (ACP) for large-scale IPs that can efficiently use any existing optimization solver as a subroutine. Specifically, ACP first randomly partitions the constraints into blocks, where the number of blocks is adaptively adjusted to avoid local optima. Then, ACP uses a subroutine solver to optimize the decision variables in a randomly selected block of constraints to enhance the variable correlation. ACP is compared with LNS framework with different subroutine solvers on four IPs and a real-world IP. The experimental results demonstrate that in specified wall-clock time ACP shows better performance than SCIP and Gurobi.

Zhijing Wu, Hua Xu, Jingliang Fang et al.

Continual Machine Reading Comprehension aims to incrementally learn from a continuous data stream across time without access the previous seen data, which is crucial for the development of real-world MRC systems. However, it is a great challenge to learn a new domain incrementally without catastrophically forgetting previous knowledge. In this paper, MA-MRC, a continual MRC model with uncertainty-aware fixed Memory and Adversarial domain adaptation, is proposed. In MA-MRC, a fixed size memory stores a small number of samples in previous domain data along with an uncertainty-aware updating strategy when new domain data arrives. For incremental learning, MA-MRC not only keeps a stable understanding by learning both memory and new domain data, but also makes full use of the domain adaptation relationship between them by adversarial learning strategy. The experimental results show that MA-MRC is superior to strong baselines and has a substantial incremental learning ability without catastrophically forgetting under two different continual MRC settings.

Brian Ondov, Chia-Hsuan Chang, Yujia Zhou et al.

Text embeddings have become an essential part of a variety of language applications. However, methods for interpreting, exploring and reversing embedding spaces are limited, reducing transparency and precluding potentially valuable generative use cases. In this work, we align Large Language Models to embeddings of clinical trials using the recently reported Embedding Language Model (ELM) method. We develop an open-source, domain-agnostic ELM architecture and training framework, design training tasks for clinical trials, and introduce an expert-validated synthetic dataset. We then train a series of ELMs exploring the impact of tasks and training regimes. Our final model, ctELM, can accurately describe and compare unseen clinical trials from embeddings alone and produce plausible clinical trials from novel vectors. We further show that generated trial abstracts are responsive to moving embeddings along concept vectors for age and sex of study subjects. Our public ELM implementation and experimental results will aid the alignment of Large Language Models to embedding spaces in the biomedical domain and beyond.

Lingfei Qian, Mauro Giuffre, Yan Wang et al.

Clinical decision-making increasingly relies on timely and context-aware access to patient information within Electronic Health Records (EHRs), yet most existing natural language question-answering (QA) systems are evaluated solely on benchmark datasets, limiting their practical relevance. To overcome this limitation, we introduce EHRNavigator, a multi-agent framework that harnesses AI agents to perform patient-level question answering across heterogeneous and multimodal EHR data. We assessed its performance using both public benchmark and institutional datasets under realistic hospital conditions characterized by diverse schemas, temporal reasoning demands, and multimodal evidence integration. Through quantitative evaluation and clinician-validated chart review, EHRNavigator demonstrated strong generalization, achieving 86% accuracy on real-world cases while maintaining clinically acceptable response times. Overall, these findings confirm that EHRNavigator effectively bridges the gap between benchmark evaluation and clinical deployment, offering a robust, adaptive, and efficient solution for real-world EHR question answering.

Cathy Shyr, Yan Hu, Rory J. Tinker et al.

Phenotyping is fundamental to rare disease diagnosis, but manual curation of structured phenotypes from clinical notes is labor-intensive and difficult to scale. Existing artificial intelligence approaches typically optimize individual components of phenotyping but do not operationalize the full clinical workflow of extracting features from clinical text, standardizing them to Human Phenotype Ontology (HPO) terms, and prioritizing diagnostically informative HPO terms. We developed RARE-PHENIX, an end-to-end AI framework for rare disease phenotyping that integrates large language model-based phenotype extraction, ontology-grounded standardization to HPO terms, and supervised ranking of diagnostically informative phenotypes. We trained RARE-PHENIX using data from 2,671 patients across 11 Undiagnosed Diseases Network clinical sites, and externally validated it on 16,357 real-world clinical notes from Vanderbilt University Medical Center. Using clinician-curated HPO terms as the gold standard, RARE-PHENIX consistently outperformed a state-of-the-art deep learning baseline (PhenoBERT) across ontology-based similarity and precision-recall-F1 metrics in end-to-end evaluation (i.e., ontology-based similarity of 0.70 vs. 0.58). Ablation analyses demonstrated performance improvements with the addition of each module in RARE-PHENIX (extraction, standardization, and prioritization), supporting the value of modeling the full clinical phenotyping workflow. By modeling phenotyping as a clinically aligned workflow rather than a single extraction task, RARE-PHENIX provides structured, ranked phenotypes that are more concordant with clinician curation and has the potential to support human-in-the-loop rare disease diagnosis in real-world settings.

Hanlei Zhang, Hua Xu, Fei Long et al. · tsinghua

Discovering the semantics of multimodal utterances is essential for understanding human language and enhancing human-machine interactions. Existing methods manifest limitations in leveraging nonverbal information for discerning complex semantics in unsupervised scenarios. This paper introduces a novel unsupervised multimodal clustering method (UMC), making a pioneering contribution to this field. UMC introduces a unique approach to constructing augmentation views for multimodal data, which are then used to perform pre-training to establish well-initialized representations for subsequent clustering. An innovative strategy is proposed to dynamically select high-quality samples as guidance for representation learning, gauged by the density of each sample's nearest neighbors. Besides, it is equipped to automatically determine the optimal value for the top-$K$ parameter in each cluster to refine sample selection. Finally, both high- and low-quality samples are used to learn representations conducive to effective clustering. We build baselines on benchmark multimodal intent and dialogue act datasets. UMC shows remarkable improvements of 2-6\% scores in clustering metrics over state-of-the-art methods, marking the first successful endeavor in this domain. The complete code and data are available at https://github.com/thuiar/UMC.

Varada Khanna, Nilay Bhatt, Ikgyu Shin et al.

Understanding how individuals with Parkinson's disease (PD) describe cognitive experiences in their daily lives can offer valuable insights into disease-related cognitive and emotional changes. However, extracting such information from unstructured patient narratives is challenging due to the subtle, overlapping nature of cognitive constructs. This study developed and evaluated natural language processing (NLP) models to automatically identify categories that reflect various cognitive processes from de-identified first-person narratives. Three model families, a Bio_ClinicalBERT-based span categorization model for nested entity recognition, a fine-tuned Meta-Llama-3-8B-Instruct model using QLoRA for instruction following, and GPT-4o mini evaluated under zero- and few-shot settings, were compared on their performance on extracting seven categories. Our findings indicated that model performance varied substantially across categories and model families. The fine-tuned Meta-Llama-3-8B-Instruct achieved the highest overall F1-scores (0.74 micro-average and 0.59 macro-average), particularly excelling in context-dependent categories such as thought and social interaction. Bio_ClinicalBERT exhibited high precision but low recall and performed comparable to Llama for some category types such as location and time but failed on other categories such as thought, emotion and social interaction. Compared to conventional information extraction tasks, this task presents a greater challenge due to the abstract and overlapping nature of narrative accounts of complex cognitive processes. Nonetheless, with continued refinement, these NLP systems hold promise for enabling low-burden, longitudinal monitoring of cognitive function and serving as a valuable complement to formal neuropsychological assessments in PD.

Yutong Xie, Yijun Pan, Hua Xu et al.

Artificial Intelligence has proven to be a transformative tool for advancing scientific research across a wide range of disciplines. However, a significant gap still exists between AI and scientific communities, limiting the full potential of AI methods in driving broad scientific discovery. Existing efforts in identifying and bridging this gap have often relied on qualitative examination of small samples of literature, offering a limited perspective on the broader AI4Science landscape. In this work, we present a large-scale analysis of the AI4Science literature, starting by using large language models to identify scientific problems and AI methods in publications from top science and AI venues. Leveraging this new dataset, we quantitatively highlight key disparities between AI methods and scientific problems, revealing substantial opportunities for deeper AI integration across scientific disciplines. Furthermore, we explore the potential and challenges of facilitating collaboration between AI and scientific communities through the lens of link prediction. Our findings and tools aim to promote more impactful interdisciplinary collaborations and accelerate scientific discovery through deeper and broader AI integration. Our code and dataset are available at: https://github.com/charles-pyj/Bridging-AI-and-Science.

Qianqian Xie, Qingyu Chen, Aokun Chen et al.

Recent advancements in large language models (LLMs) like ChatGPT and LLaMA show promise in medical applications, yet challenges remain in medical language comprehension. This study presents Me-LLaMA, a new medical LLM family based on open-source LLaMA models, optimized for medical text analysis and diagnosis by leveraging large-scale, domain-specific datasets. The Me-LLaMA family, including foundation models Me-LLaMA 13/70B and their chat-enhanced versions, was developed through continued pre-training and instruction tuning with 129B tokens and 214K samples from biomedical and clinical sources. Training the 70B models required over 100,000 A100 GPU hours. Me-LLaMA's performance was evaluated across six medical text analysis tasks using 12 benchmark datasets and complex clinical case diagnosis, with automatic and human evaluations. Results indicate Me-LLaMA outperforms LLaMA and other open-source medical LLMs in zero-shot and supervised settings. Task-specific tuning further boosts performance, surpassing ChatGPT on 7 of 8 datasets and GPT-4 on 5 of 8. For complex clinical cases, Me-LLaMA achieves performance comparable to ChatGPT and GPT-4. This work underscores the importance of domain-specific data in developing medical LLMs and addresses the high computational costs involved in training, highlighting a balance between pre-training and fine-tuning strategies. Me-LLaMA models are now accessible under user agreements, providing a valuable resource for advancing medical AI.

Tianyu Liu, Simeng Han, Xiao Luo et al.

Large language models (LLMs) and large multimodal models (LMMs) promise to accelerate biomedical discovery, yet their reliability remains unclear. We introduce ARIEL (AI Research Assistant for Expert-in-the-Loop Learning), an open-source evaluation and optimization framework that pairs a curated multimodal biomedical corpus with expert-vetted tasks to probe two capabilities: full-length article summarization and fine-grained figure interpretation. Using uniform protocols and blinded PhD-level evaluation, we find that state-of-the-art models generate fluent but incomplete summaries, whereas LMMs struggle with detailed visual reasoning. We later observe that prompt engineering and lightweight fine-tuning substantially improve textual coverage, and a compute-scaled inference strategy enhances visual question answering. We build an ARIEL agent that integrates textual and visual cues, and we show it can propose testable mechanistic hypotheses. ARIEL delineates current strengths and limitations of foundation models, and provides a reproducible platform for advancing trustworthy AI in biomedicine.

Hanlei Zhang, Zhuohang Li, Yeshuang Zhu et al. · tsinghua

Multimodal language analysis is a rapidly evolving field that leverages multiple modalities to enhance the understanding of high-level semantics underlying human conversational utterances. Despite its significance, little research has investigated the capability of multimodal large language models (MLLMs) to comprehend cognitive-level semantics. In this paper, we introduce MMLA, a comprehensive benchmark specifically designed to address this gap. MMLA comprises over 61K multimodal utterances drawn from both staged and real-world scenarios, covering six core dimensions of multimodal semantics: intent, emotion, dialogue act, sentiment, speaking style, and communication behavior. We evaluate eight mainstream branches of LLMs and MLLMs using three methods: zero-shot inference, supervised fine-tuning, and instruction tuning. Extensive experiments reveal that even fine-tuned models achieve only about 60%~70% accuracy, underscoring the limitations of current MLLMs in understanding complex human language. We believe that MMLA will serve as a solid foundation for exploring the potential of large language models in multimodal language analysis and provide valuable resources to advance this field. The datasets and code are open-sourced at https://github.com/thuiar/MMLA.

Zhixiao Xiong, Fangyu Zong, Huigen Ye et al.

Machine Learning (ML) optimization frameworks have gained attention for their ability to accelerate the optimization of large-scale Quadratically Constrained Quadratic Programs (QCQPs) by learning shared problem structures. However, existing ML frameworks often rely heavily on strong problem assumptions and large-scale solvers. This paper introduces NeuralQP, a general hypergraph-based framework for large-scale QCQPs. NeuralQP features two main components: Hypergraph-based Neural Prediction, which generates embeddings and predicted solutions for QCQPs without problem assumptions, and Parallel Neighborhood Optimization, which employs a McCormick relaxation-based repair strategy to identify and correct illegal variables, iteratively improving the solution with a small-scale solver. We further prove that our framework UniEGNN with our hypergraph representation is equivalent to the Interior-Point Method (IPM) for quadratic programming. Experiments on two benchmark problems and large-scale real-world instances from QPLIB demonstrate that NeuralQP outperforms state-of-the-art solvers (e.g., Gurobi and SCIP) in both solution quality and time efficiency, further validating the efficiency of ML optimization frameworks for QCQPs.

Liang Zhang, Yin Xu, Mohan Wu et al.

Quantum computing combined with machine learning (ML) is a highly promising research area, with numerous studies demonstrating that quantum machine learning (QML) is expected to solve scientific problems more effectively than classical ML. In this work, we present Quantum Long Short-Term Memory (QLSTM), a QML architecture, and demonstrate its effectiveness in drug discovery. We evaluate QLSTM on five benchmark datasets (BBBP, BACE, SIDER, BCAP37, T-47D), and observe consistent performance gains over classical LSTM, with ROC-AUC improvements ranging from 3% to over 6%. Furthermore, QLSTM exhibits improved predictive accuracy as the number of qubits increases, and faster convergence than classical LSTM under the same training conditions. Notably, QLSTM maintains strong robustness against quantum computer noise, outperforming noise-free classical LSTM in certain settings. These findings highlight the potential of QLSTM as a scalable and noise-resilient model for scientific applications, particularly as quantum hardware continues to advance in qubit capacity and fidelity.

Hyunjae Kim, Jiwoong Sohn, Aidan Gilson et al.

Large language models (LLMs) are transforming the landscape of medicine, yet two fundamental challenges persist: keeping up with rapidly evolving medical knowledge and providing verifiable, evidence-grounded reasoning. Retrieval-augmented generation (RAG) has been widely adopted to address these limitations by supplementing model outputs with retrieved evidence. However, whether RAG reliably achieves these goals remains unclear. Here, we present the most comprehensive expert evaluation of RAG in medicine to date. Eighteen medical experts contributed a total of 80,502 annotations, assessing 800 model outputs generated by GPT-4o and Llama-3.1-8B across 200 real-world patient and USMLE-style queries. We systematically decomposed the RAG pipeline into three components: (i) evidence retrieval (relevance of retrieved passages), (ii) evidence selection (accuracy of evidence usage), and (iii) response generation (factuality and completeness of outputs). Contrary to expectation, standard RAG often degraded performance: only 22% of top-16 passages were relevant, evidence selection remained weak (precision 41-43%, recall 27-49%), and factuality and completeness dropped by up to 6% and 5%, respectively, compared with non-RAG variants. Retrieval and evidence selection remain key failure points for the model, contributing to the overall performance drop. We further show that simple yet effective strategies, including evidence filtering and query reformulation, substantially mitigate these issues, improving performance on MedMCQA and MedXpertQA by up to 12% and 8.2%, respectively. These findings call for re-examining RAG's role in medicine and highlight the importance of stage-aware evaluation and deliberate system design for reliable medical LLM applications.

Fan Ma, Qier An, Peng Chen et al.

Learning transferable representations for electroencephalography (EEG) remains challenging because EEG signals are inherently multi-channel and non-stationary. Channels observed at the same time provide coupled measurements of neural activity, while the relevant temporal dynamics vary across contexts. This structure is poorly matched by architectures that apply uniform computation across time or route each channel patch independently. To this end, we propose TRACE, an autoregressive EEG pre-training framework that predicts future EEG patches from causal context while performing temporally adaptive and cross-channel coherent computation. At each temporal step, TRACE derives an expert routing decision from the causal cross-channel history and applies it jointly to all channels at that step. This preserves instantaneous cross-channel coherence while allowing different temporal regimes to activate different computation. Since routing is defined over the available channel set and causal temporal context, TRACE is compatible with heterogeneous pre-training across corpora with different channel counts, montages, sequence lengths, and recording domains. Across eight downstream EEG benchmarks, TRACE is evaluated in both settings: when downstream domains are seen only as unlabeled pre-training data and when downstream datasets are completely unseen during pre-training. It obtains the best results on several benchmarks while remaining competitive on motor imagery and clinical event classification tasks, with ablations supporting the importance of cross-channel temporal routing.

Qianrui Zhou, Hua Xu, Yifan Wang et al. · tsinghua

Understanding human intents from multimodal signals is critical for analyzing human behaviors and enhancing human-machine interactions in real-world scenarios. However, existing methods exhibit limitations in their modality-level reliance, constraining relational reasoning over fine-grained semantics for complex intent understanding. This paper proposes a novel LLM-Guided Semantic Relational Reasoning (LGSRR) method, which harnesses the expansive knowledge of large language models (LLMs) to establish semantic foundations that boost smaller models' relational reasoning performance. Specifically, an LLM-based strategy is proposed to extract fine-grained semantics as guidance for subsequent reasoning, driven by a shallow-to-deep Chain-of-Thought (CoT) that autonomously uncovers, describes, and ranks semantic cues by their importance without relying on manually defined priors. Besides, we formally model three fundamental types of semantic relations grounded in logical principles and analyze their nuanced interplay to enable more effective relational reasoning. Extensive experiments on multimodal intent and dialogue act recognition tasks demonstrate LGSRR's superiority over state-of-the-art methods, with consistent performance gains across diverse semantic understanding scenarios. The complete data and code are available at https://github.com/thuiar/LGSRR.

Zhangyi Hu, Jiemin Wu, Hua Xu et al.

Irregular Multivariate Time Series (IMTS) forecasting is challenging due to the unaligned nature of multi-channel signals and the prevalence of extensive missing data. Existing methods struggle to capture reliable temporal patterns from such data due to significant missing values. While pre-trained foundation models show potential for addressing these challenges, they are typically designed for Regularly Sampled Time Series (RTS). Motivated by the visual Mask AutoEncoder's (MAE) powerful capability for modeling sparse multi-channel information and its success in RTS forecasting, we propose VIMTS, a framework adapting Visual MAE for IMTS forecasting. To mitigate the effect of missing values, VIMTS first processes IMTS along the timeline into feature patches at equal intervals. These patches are then complemented using learned cross-channel dependencies. Then it leverages visual MAE's capability in handling sparse multichannel data for patch reconstruction, followed by a coarse-to-fine technique to generate precise predictions from focused contexts. In addition, we integrate self-supervised learning for improved IMTS modeling by adapting the visual MAE to IMTS data. Extensive experiments demonstrate VIMTS's superior performance and few-shot capability, advancing the application of visual foundation models in more general time series tasks. Our code is available at https://github.com/WHU-HZY/VIMTS.

Tianyu Liu, Yijia Xiao, Xiao Luo et al.

The applications of large language models (LLMs) are promising for biomedical and healthcare research. Despite the availability of open-source LLMs trained using a wide range of biomedical data, current research on the applications of LLMs to genomics and proteomics is still limited. To fill this gap, we propose a collection of finetuned LLMs and multimodal LLMs (MLLMs), known as Geneverse, for three novel tasks in genomic and proteomic research. The models in Geneverse are trained and evaluated based on domain-specific datasets, and we use advanced parameter-efficient finetuning techniques to achieve the model adaptation for tasks including the generation of descriptions for gene functions, protein function inference from its structure, and marker gene selection from spatial transcriptomic data. We demonstrate that adapted LLMs and MLLMs perform well for these tasks and may outperform closed-source large-scale models based on our evaluations focusing on both truthfulness and structural correctness. All of the training strategies and base models we used are freely accessible.

Qingyu Chen, Yan Hu, Xueqing Peng et al.

The rapid growth of biomedical literature poses challenges for manual knowledge curation and synthesis. Biomedical Natural Language Processing (BioNLP) automates the process. While Large Language Models (LLMs) have shown promise in general domains, their effectiveness in BioNLP tasks remains unclear due to limited benchmarks and practical guidelines. We perform a systematic evaluation of four LLMs, GPT and LLaMA representatives on 12 BioNLP benchmarks across six applications. We compare their zero-shot, few-shot, and fine-tuning performance with traditional fine-tuning of BERT or BART models. We examine inconsistencies, missing information, hallucinations, and perform cost analysis. Here we show that traditional fine-tuning outperforms zero or few shot LLMs in most tasks. However, closed-source LLMs like GPT-4 excel in reasoning-related tasks such as medical question answering. Open source LLMs still require fine-tuning to close performance gaps. We find issues like missing information and hallucinations in LLM outputs. These results offer practical insights for applying LLMs in BioNLP.

Laila Rasmy, Jie Zhu, Zhiheng Li et al.

Recently, there is great interest to investigate the application of deep learning models for the prediction of clinical events using electronic health records (EHR) data. In EHR data, a patient's history is often represented as a sequence of visits, and each visit contains multiple events. As a result, deep learning models developed for sequence modeling, like recurrent neural networks (RNNs) are common architecture for EHR-based clinical events predictive models. While a large variety of RNN models were proposed in the literature, it is unclear if complex architecture innovations will offer superior predictive performance. In order to move this field forward, a rigorous evaluation of various methods is needed. In this study, we conducted a thorough benchmark of RNN architectures in modeling EHR data. We used two prediction tasks: the risk for developing heart failure and the risk of early readmission for inpatient hospitalization. We found that simple gated RNN models, including GRUs and LSTMs, often offer competitive results when properly tuned with Bayesian Optimization, which is in line with similar to findings in the natural language processing (NLP) domain. For reproducibility, Our codebase is shared at https://github.com/ZhiGroup/pytorch_ehr.

Hanlei Zhang, Xiaoteng Li, Hua Xu et al.

TEXTOIR is the first integrated and visualized platform for text open intent recognition. It is composed of two main modules: open intent detection and open intent discovery. Each module integrates most of the state-of-the-art algorithms and benchmark intent datasets. It also contains an overall framework connecting the two modules in a pipeline scheme. In addition, this platform has visualized tools for data and model management, training, evaluation and analysis of the performance from different aspects. TEXTOIR provides useful toolkits and convenient visualized interfaces for each sub-module (Toolkit code: https://github.com/thuiar/TEXTOIR), and designs a framework to implement a complete process to both identify known intents and discover open intents (Demo code: https://github.com/thuiar/TEXTOIR-DEMO).

Wenmeng Yu, Hua Xu, Ziqi Yuan et al.

Representation Learning is a significant and challenging task in multimodal learning. Effective modality representations should contain two parts of characteristics: the consistency and the difference. Due to the unified multimodal annotation, existing methods are restricted in capturing differentiated information. However, additional uni-modal annotations are high time- and labor-cost. In this paper, we design a label generation module based on the self-supervised learning strategy to acquire independent unimodal supervisions. Then, joint training the multi-modal and uni-modal tasks to learn the consistency and difference, respectively. Moreover, during the training stage, we design a weight-adjustment strategy to balance the learning progress among different subtasks. That is to guide the subtasks to focus on samples with a larger difference between modality supervisions. Last, we conduct extensive experiments on three public multimodal baseline datasets. The experimental results validate the reliability and stability of auto-generated unimodal supervisions. On MOSI and MOSEI datasets, our method surpasses the current state-of-the-art methods. On the SIMS dataset, our method achieves comparable performance than human-annotated unimodal labels. The full codes are available at https://github.com/thuiar/Self-MM.

Hanlei Zhang, Hua Xu, Ting-En Lin

Open intent classification is a challenging task in dialogue systems. On the one hand, it should ensure the quality of known intent identification. On the other hand, it needs to detect the open (unknown) intent without prior knowledge. Current models are limited in finding the appropriate decision boundary to balance the performances of both known intents and the open intent. In this paper, we propose a post-processing method to learn the adaptive decision boundary (ADB) for open intent classification. We first utilize the labeled known intent samples to pre-train the model. Then, we automatically learn the adaptive spherical decision boundary for each known class with the aid of well-trained features. Specifically, we propose a new loss function to balance both the empirical risk and the open space risk. Our method does not need open intent samples and is free from modifying the model architecture. Moreover, our approach is surprisingly insensitive with less labeled data and fewer known intents. Extensive experiments on three benchmark datasets show that our method yields significant improvements compared with the state-of-the-art methods. The codes are released at https://github.com/thuiar/Adaptive-Decision-Boundary.

Hanlei Zhang, Hua Xu, Ting-En Lin et al.

Discovering new intents is a crucial task in dialogue systems. Most existing methods are limited in transferring the prior knowledge from known intents to new intents. They also have difficulties in providing high-quality supervised signals to learn clustering-friendly features for grouping unlabeled intents. In this work, we propose an effective method, Deep Aligned Clustering, to discover new intents with the aid of the limited known intent data. Firstly, we leverage a few labeled known intent samples as prior knowledge to pre-train the model. Then, we perform k-means to produce cluster assignments as pseudo-labels. Moreover, we propose an alignment strategy to tackle the label inconsistency problem during clustering assignments. Finally, we learn the intent representations under the supervision of the aligned pseudo-labels. With an unknown number of new intents, we predict the number of intent categories by eliminating low-confidence intent-wise clusters. Extensive experiments on two benchmark datasets show that our method is more robust and achieves substantial improvements over the state-of-the-art methods. The codes are released at https://github.com/thuiar/DeepAligned-Clustering.

Tianyu Liu, Wangjie Zheng, Rui Yang et al.

Accurate and timely diagnosis is essential for effective treatment, particularly in the context of rare diseases. However, current diagnostic workflows often lead to prolonged assessment times and low accuracy. To address these limitations, we introduce Hygieia, a multi-modal AI agent system designed to support precision disease diagnosis by integrating diverse data sources, including phenotypic features, genetic profiles, and clinical records. Hygieia features a router-based and knowledge-enhanced framework that mitigates hallucination and tailors diagnostic strategies to different disease categories. Notably, it prioritizes risk-related genomic factors for rare diseases and provides confidence scores to assist clinical decision-making. We conducted a comprehensive evaluation demonstrating that Hygieia achieves state-of-the-art performance across multiple diagnostic benchmarks. In collaboration with clinical experts from Yale School of Medicine and Duke-NUS Medical School, we further validated its practical utility by showing (1) Hygieia's superior diagnostic performance compared to physicians with an improvement from 12%-60% and (2) its effectiveness in assisting clinicians with medical records for handling real-world cases. Our findings indicate that Hygieia not only enhances diagnostic accuracy and interpretability but also significantly reduces clinician workload, highlighting its potential as a valuable tool in clinical decision support systems.