Automatic evaluation of natural language generation (NLG) tasks has gained extensive research interests, since it can rapidly assess the performance of large language models (LLMs). However, automatic NLG evaluation struggles with medical QA because it fails to focus on the crucial correctness of medical facts throughout the generated text. To address this, this paper introduces a new data structure, imap, designed to capture key information in questions and answers, enabling evaluators to focus on essential details. The imap comprises three components: Query, Constraint, and Inform, each of which is in the form of term-value pairs to represent medical facts in a structural manner. We then introduce imapScore, which compares the corresponding medical term-value pairs in the imap to score generated texts. We utilize GPT-4 to extract imap from questions, human-annotated answers, and generated responses. To mitigate the diversity in medical terminology for fair term-value pairs comparison, we use a medical knowledge graph to assist GPT-4 in determining matches. To compare imapScore with existing NLG metrics, we establish a new benchmark dataset. The experimental results show that imapScore consistently outperforms state-of-the-art metrics, demonstrating an average improvement of 79.8% in correlation with human scores. Furthermore, incorporating imap into n-gram, embedding, and LLM metrics boosts the base versions, increasing correlation with human scores by averages of 89.9%, 81.7%, and 32.6%, respectively.

The impressive capabilities of large language models (LLMs) have attracted extensive interests of applying LLMs to medical field. However, the complex nature of clinical environments presents significant hallucination challenges for LLMs, hindering their widespread adoption. In this paper, we address these hallucination issues in the context of Medical Information Extraction (MIE) tasks by introducing ALternate Contrastive Decoding (ALCD). We begin by redefining MIE tasks as an identify-and-classify process. We then separate the identification and classification functions of LLMs by selectively masking the optimization of tokens during fine-tuning. During the inference stage, we alternately contrast output distributions derived from sub-task models. This approach aims to selectively enhance the identification and classification capabilities while minimizing the influence of other inherent abilities in LLMs. Additionally, we propose an alternate adaptive constraint strategy to more effectively adjust the scale and scope of contrastive tokens. Through comprehensive experiments on two different backbones and six diverse medical information extraction tasks, ALCD demonstrates significant improvements in resolving hallucination issues compared to conventional decoding methods.

The bias of disease prediction in Large Language Models (LLMs) is a critical yet underexplored issue, with potential implications for healthcare outcomes and equity. As LLMs increasingly find applications in healthcare, understanding and addressing their biases becomes paramount. This study focuses on this crucial topic, investigating the bias of disease prediction in models such as GPT-4, ChatGPT, and Qwen1.5-72b across gender, age range, and disease judgment behaviors. Utilizing a comprehensive real-clinical health record dataset of over 330,000 entries, we uncover that all three models exhibit distinct biases, indicating a pervasive issue of unfairness. To measure this, we introduce a novel metric–the diagnosis bias score, which reflects the ratio of prediction numbers to label numbers. Our in-depth analysis, based on this score, sheds light on the inherent biases in these models. In response to these findings, we propose a simple yet effective prompt-based solution to alleviate the observed bias in disease prediction with LLMs. This research underscores the importance of fairness in AI, particularly in healthcare applications, and offers a practical approach to enhance the equity of disease prediction models.

The visual question localized-answering (VQLA) system has garnered increasing attention due to its potential as a knowledgeable assistant in surgical education. Apart from providing text-based answers, VQLA can also pinpoint the specific region of interest for better surgical scene understanding. Although recent Transformer-based models for VQLA have obtained promising results, they (1) conduct vanilla text-to-image cross attention, leading to unidirectional and coarse-grained alignment; (2) ignore exploiting the semantics of answers to further boost performance. In this paper, we propose a novel model termed OTAS, which first introduces optimal transport to achieve bidirectional and fine-grained alignment between images and questions, enabling more precise localization. Besides, OTAS incorporates a set of learnable candidate answer embeddings to query the probability of each answer class for a given image-question pair. Through Transformer attention, the candidate answer embeddings interact with the fused features of the image-question pair to make the answer decision. Extensive experiments on two widely-used benchmark datasets demonstrate the superiority of our model over state-of-the-art methods.

Although biomedical entity linking (BioEL) has made significant progress with pre-trained language models, challenges still exist for fine-grained and long-tailed entities. To address these challenges, we present BioELQA, a novel model that treats Biomedical Entity Linking as Multiple Choice Question Answering. BioELQA first obtains candidate entities with a fast retriever, jointly presents the mention and candidate entities to a generator, and then outputs the predicted symbol associated with its chosen entity. This formulation enables explicit comparison of different candidate entities, thus capturing fine-grained interactions between mentions and entities, as well as among entities themselves. To improve generalization for long-tailed entities, we retrieve similar labeled training instances as clues and concatenate the input with retrieved instances for the generator. Extensive experimental results show that BioELQA outperforms state-of-the-art baselines on several datasets.

Dialogue policy learning (DPL) aims to determine an abstract representation (also known as action) to guide what the response should be. Typically, DPL is cast as a sequential decision problem across a series of predefined action candidates. However, such static and narrow actions can limit response diversity and impede the dialogue agent’s adaptability to new scenarios and edge cases. To overcome these challenges, we introduce a novel Joint Transformer Reinforcement Learning framework, coined as JoTR, where a text-to-text Transformer-based model is employed to directly generate dialogue actions. More concretely, JoTR formulates a token-grained policy, facilitating more dynamic and adaptable dialogue action generation without the need for predefined action candidates. This method not only enhances the diversity of responses but also significantly improves the system’s capability to manage unfamiliar scenarios. Furthermore, JoTR utilizes Reinforcement Learning with a reward-shaping mechanism to efficiently fine-tune the token-grained policy. This allows the model to evolve through interactions, thereby enhancing its performance over time. Our extensive evaluation demonstrates that JoTR surpasses previous state-of-the-art models, showing improvements of 9% and 13% in success rate, and 34% and 37% in the diversity of dialogue actions across two benchmark dialogue modeling tasks respectively. These results have been validated by both user simulators and human evaluators. Code and data are available at ://github.com/KwanWaiChung/JoTR.

The first 24 hours’ medication plan is critical to patients with serious or life-threatening illnesses and injuries. An appropriate medication can result in a lower mortality, a shorter length stay and a higher APACHE score. However, in clinical practice, the medication plan is often error-prone, especially when a decision must be made quickly for life-threatening situations in Intensive Care Unit (ICU). Therefore, predicting the effectiveness of the first 24 hours’ medication plan is of great importance in assisting doctors to make proper decisions. Existing effectiveness prediction works usually focus on one specific medicine, one specific disease, or one specific lab test, making it hard to extend to general medicines and diseases in hospital/ICU scenarios. In this paper, we propose to predict medication effectiveness of the first 24 hours in hospital/ICU based on patients’ information. Specifically, we use a knowledge enhanced module to incorporate external knowledge about medications and a medical feature learning module to determine the interaction between diagnosis and medications. To handle the data imbalance problem, we further optimize the proposed model with a contrastive loss. Extensive experimental results on a public dataset show that our model can significantly outperform state-of-the-art methods.

Artificial intelligence (AI)-aided disease prediction has gained extensive research interest due to its capability to support clinical decision-making. Existing works mainly formulate disease prediction as a multi-label classification problem and use historical Electronic Medical Records (EMR) to train supervised models. However, in real-world clinics, such purely data-driven approaches pose two main challenges: 1) long tail problem: there are excessive EMRs for common diseases and insufficient EMRs for rare diseases, thus training over an imbalanced data set could result in a biased model that ignores rare diseases in diagnosis; 2) easily misdiagnosed diseases: some diseases can be easily distinguished while others sharing analogous conditions are much more difficult. General classification models without emphasizing easily misdiagnosed diseases may generate incorrect predictions. To tackle these two problems, we propose a Medical Knowledge-Enhanced Contrastive Learning (MKeCL) approach to disease diagnosis in this paper. MKeCL incorporates medical knowledge graphs and medical licensing exams in modeling in order to compensate for the insufficient information on rare diseases; To handle hard-to-diagnose diseases, MKeCL introduces a contrastive learning strategy to separate diseases that are easily misdiagnosed. Moreover, we establish a new benchmark, named Jarvis-D, which contains clinical EMRs collected from various hospitals. Experiments on real clinical EMRs show that the proposed MKeCL outperforms existing disease prediction approaches, especially in the setting of few-shot and zero-shot scenarios.

Knowledge graph completion (KGC) is a widely used method to tackle incompleteness in knowledge graphs (KGs) by making predictions for missing links. Description-based KGC leverages pre-trained language models to learn entity and relation representations with their names or descriptions, which shows promising results. However, the performance of description-based KGC is still limited by the quality of text and the incomplete structure, as it lacks sufficient entity descriptions and relies solely on relation names, leading to sub-optimal results. To address this issue, we propose MPIKGC, a general framework to compensate for the deficiency of contextualized knowledge and improve KGC by querying large language models (LLMs) from various perspectives, which involves leveraging the reasoning, explanation, and summarization capabilities of LLMs to expand entity descriptions, understand relations, and extract structures, respectively. We conducted extensive evaluation of the effectiveness and improvement of our framework based on four description-based KGC models, for both link prediction and triplet classification tasks. All codes and generated data will be publicly available after review.

Automatic diagnosis (AD), a critical application of AI in healthcare, employs machine learning techniques to assist doctors in gathering patient symptom information for precise disease diagnosis. The Transformer-based method utilizes an input symptom sequence, predicts itself through auto-regression, and employs the hidden state of the final symptom to determine the disease. Despite its simplicity and superior performance demonstrated, a decline in disease diagnosis accuracy is observed caused by 1) a mismatch between symptoms observed during training and generation, and 2) the effect of different symptom orders on disease prediction. To address the above obstacles, we introduce the CoAD, a novel disease and symptom collaborative generation framework, which incorporates several key innovations to improve AD: 1) aligning sentence-level disease labels with multiple possible symptom inquiry steps to bridge the gap between training and generation; 2) expanding symptom labels for each sub-sequence of symptoms to enhance annotation and eliminate the effect of symptom order; 3) developing a repeated symptom input schema to effectively and efficiently learn the expanded disease and symptom labels. We evaluate the CoAD framework using four datasets, including three public and one private, and demonstrate that it achieves an average 2.3% improvement over previous state-of-the-art results in automatic disease diagnosis. For reproducibility, we release the code and data at https://github.com/KwanWaiChung/coad.

In the task of incremental few-shot relation classification, model performance is always limited by the incompatibility between the base feature embedding space and the novel feature embedding space. To tackle the issue, we propose a novel model named ICA-Proto: Iterative Cross Alignment prototypical network. Specifically, we incorporate the query representation into the encoding of novel prototypes and utilize the query-aware prototypes to update the query representation at the same time. Further, we implement the above process iteratively to achieve more interaction. In addition, a novel prototype quadruplet loss is designed to regulate the spatial distributions of embedding space, so as to make it easier for the relation classification. Experimental results on two benchmark datasets demonstrate that ICA-Proto significantly outperforms the state-of-the-art baseline model.

The cross-domain text-to-SQL task aims to build a system that can parse user questions into SQL on complete unseen databases, and the single-domain text-to-SQL task evaluates the performance on identical databases. Both of these setups confront unavoidable difficulties in real-world applications. To this end, we introduce the cross-schema text-to-SQL task, where the databases of evaluation data are different from that in the training data but come from the same domain. Furthermore, we present CSS, a large-scale CrosS-Schema Chinese text-to-SQL dataset, to carry on corresponding studies. CSS originally consisted of 4,340 question/SQL pairs across 2 databases. In order to generalize models to different medical systems, we extend CSS and create 19 new databases along with 29,280 corresponding dataset examples. Moreover, CSS is also a large corpus for single-domain Chinese text-to-SQL studies. We present the data collection approach and a series of analyses of the data statistics. To show the potential and usefulness of CSS, benchmarking baselines have been conducted and reported. Our dataset is publicly available at https://huggingface.co/datasets/zhanghanchong/css.

The multi-turn doctor-patient dialogue includes rich medical knowledge, like the symptoms of the patient, the diagnosis and medication suggested by the doctor. If mined and represented properly, such medical knowledge can benefit a large range of clinical applications, including diagnosis assistance and medication recommendation. To derive structured knowledge from free text dialogues, we target a critical task: the Dialogue Medical Information Extraction (DMIE). DMIE aims to detect pre-defined clinical meaningful medical items (symptoms, surgery, etc.) as well as their statuses (positive, negative, etc.) from the dialogue. Existing approaches mainly formulate DMIE as a multi-label classification problem and ignore the relationships among medical items and statuses. Different from previous approaches, we propose a heterogeneous graph to model the relationship between items. We further propose two consecutive attention based modules to enrich the item representation with the dialogue and status. In this manner, we are able to model the relationships among medical items and statuses in the DMIE task. Experimental results on the public benchmark data set show that the proposed model outperforms previous works and achieves the state-of-the-art performance.

Knowledge graph (KG) embedding is a fundamental task in natural language processing, and various methods have been proposed to explore semantic patterns in distinctive ways. In this paper, we propose to learn an ensemble by leveraging existing methods in a relation-aware manner. However, exploring these semantics using relation-aware ensemble leads to a much larger search space than general ensemble methods. To address this issue, we propose a divide-search-combine algorithm RelEns-DSC that searches the relation-wise ensemble weights independently. This algorithm has the same computation cost as general ensemble methods but with much better performance. Experimental results on benchmark datasets demonstrate the effectiveness of the proposed method in efficiently searching relation-aware ensemble weights and achieving state-of-the-art embedding performance. The code is public at https://github.com/LARS-research/RelEns.

Providing Emotional Support (ES) to soothe people in emotional distress is an essential capability in social interactions. Most existing researches on building ES conversation systems only considered single-turn interactions with users, which was over-simplified. In comparison, multi-turn ES conversation systems can provide ES more effectively, but face several new technical challenges, including: (1) how to adopt appropriate support strategies to achieve the long-term dialogue goal of comforting the user’s emotion; (2) how to dynamically model the user’s state. In this paper, we propose a novel system MultiESC to address these issues. For strategy planning, drawing inspiration from the A* search algorithm, we propose lookahead heuristics to estimate the future user feedback after using particular strategies, which helps to select strategies that can lead to the best long-term effects. For user state modeling, MultiESC focuses on capturing users’ subtle emotional expressions and understanding their emotion causes. Extensive experiments show that MultiESC significantly outperforms competitive baselines in both dialogue generation and strategy planning.

Prompt-based fine-tuning for pre-trained models has proven effective for many natural language processing tasks under few-shot settings in general domain. However, tuning with prompt in biomedical domain has not been investigated thoroughly. Biomedical words are often rare in general domain, but quite ubiquitous in biomedical contexts, which dramatically deteriorates the performance of pre-trained models on downstream biomedical applications even after fine-tuning, especially in low-resource scenarios. We propose a simple yet effective approach to helping models learn rare biomedical words during tuning with prompt. Experimental results show that our method can achieve up to 6% improvement in biomedical natural language inference task without any extra parameters or training steps using few-shot vanilla prompt settings.

Multi-modal entity alignment aims to identify equivalent entities between two different multi-modal knowledge graphs, which consist of structural triples and images associated with entities. Most previous works focus on how to utilize and encode information from different modalities, while it is not trivial to leverage multi-modal knowledge in entity alignment because of the modality heterogeneity. In this paper, we propose MCLEA, a Multi-modal Contrastive Learning based Entity Alignment model, to obtain effective joint representations for multi-modal entity alignment. Different from previous works, MCLEA considers task-oriented modality and models the inter-modal relationships for each entity representation. In particular, MCLEA firstly learns multiple individual representations from multiple modalities, and then performs contrastive learning to jointly model intra-modal and inter-modal interactions. Extensive experimental results show that MCLEA outperforms state-of-the-art baselines on public datasets under both supervised and unsupervised settings.

Distant supervision (DS) is a strong way to expand the datasets for enhancing relation extraction (RE) models but often suffers from high label noise. Current works based on attention, reinforcement learning, or GAN are black-box models so they neither provide meaningful interpretation of sample selection in DS nor stability on different domains. On the contrary, this work proposes a novel model-agnostic instance sampling method for DS by influence function (IF), namely REIF. Our method identifies favorable/unfavorable instances in the bag based on IF, then does dynamic instance sampling. We design a fast influence sampling algorithm that reduces the computational complexity from 𝒪(mn) to 𝒪(1), with analyzing its robustness on the selected sampling function. Experiments show that by simply sampling the favorable instances during training, REIF is able to win over a series of baselines which have complicated architectures. We also demonstrate that REIF can support interpretable instance selection.

Fast screening and diagnosis are critical in COVID-19 patient treatment. In addition to the gold standard RT-PCR, radiological imaging like X-ray and CT also works as an important means in patient screening and follow-up. However, due to the excessive number of patients, writing reports becomes a heavy burden for radiologists. To reduce the workload of radiologists, we propose DeltaNet to generate medical reports automatically. Different from typical image captioning approaches that generate reports with an encoder and a decoder, DeltaNet applies a conditional generation process. In particular, given a medical image, DeltaNet employs three steps to generate a report: 1) first retrieving related medical reports, i.e., the historical reports from the same or similar patients; 2) then comparing retrieved images and current image to find the differences; 3) finally generating a new report to accommodate identified differences based on the conditional report. We evaluate DeltaNet on a COVID-19 dataset, where DeltaNet outperforms state-of-the-art approaches. Besides COVID-19, the proposed DeltaNet can be applied to other diseases as well. We validate its generalization capabilities on the public IU-Xray and MIMIC-CXR datasets for chest-related diseases.

This paper presents our wining contribution to SemEval 2021 Task 8: MeasEval. The purpose of this task is identifying the counts and measurements from clinical scientific discourse, including quantities, entities, properties, qualifiers, units, modifiers, and their mutual relations. This task can be induced to a joint entity and relation extraction problem. Accordingly, we propose CONNER, a cascade count and measurement extraction tool that can identify entities and the corresponding relations in a two-step pipeline model. We provide a detailed description of the proposed model hereinafter. Furthermore, the impact of the essential modules and our in-process technical schemes are also investigated.

With the need of fast retrieval speed and small memory footprint, document hashing has been playing a crucial role in large-scale information retrieval. To generate high-quality hashing code, both semantics and neighborhood information are crucial. However, most existing methods leverage only one of them or simply combine them via some intuitive criteria, lacking a theoretical principle to guide the integration process. In this paper, we encode the neighborhood information with a graph-induced Gaussian distribution, and propose to integrate the two types of information with a graph-driven generative model. To deal with the complicated correlations among documents, we further propose a tree-structured approximation method for learning. Under the approximation, we prove that the training objective can be decomposed into terms involving only singleton or pairwise documents, enabling the model to be trained as efficiently as uncorrelated ones. Extensive experimental results on three benchmark datasets show that our method achieves superior performance over state-of-the-art methods, demonstrating the effectiveness of the proposed model for simultaneously preserving semantic and neighborhood information.

This paper explores the task of Difficulty-Controllable Question Generation (DCQG), which aims at generating questions with required difficulty levels. Previous research on this task mainly defines the difficulty of a question as whether it can be correctly answered by a Question Answering (QA) system, lacking interpretability and controllability. In our work, we redefine question difficulty as the number of inference steps required to answer it and argue that Question Generation (QG) systems should have stronger control over the logic of generated questions. To this end, we propose a novel framework that progressively increases question difficulty through step-by-step rewriting under the guidance of an extracted reasoning chain. A dataset is automatically constructed to facilitate the research, on which extensive experiments are conducted to test the performance of our method.

Joint extraction of entities and relations from unstructured texts is a crucial task in information extraction. Recent methods achieve considerable performance but still suffer from some inherent limitations, such as redundancy of relation prediction, poor generalization of span-based extraction and inefficiency. In this paper, we decompose this task into three subtasks, Relation Judgement, Entity Extraction and Subject-object Alignment from a novel perspective and then propose a joint relational triple extraction framework based on Potential Relation and Global Correspondence (PRGC). Specifically, we design a component to predict potential relations, which constrains the following entity extraction to the predicted relation subset rather than all relations; then a relation-specific sequence tagging component is applied to handle the overlapping problem between subjects and objects; finally, a global correspondence component is designed to align the subject and object into a triple with low-complexity. Extensive experiments show that PRGC achieves state-of-the-art performance on public benchmarks with higher efficiency and delivers consistent performance gain on complex scenarios of overlapping triples. The source code has been submitted as the supplementary material and will be made publicly available after the blind review.

For task-oriented dialog systems, training a Reinforcement Learning (RL) based Dialog Management module suffers from low sample efficiency and slow convergence speed due to the sparse rewards in RL. To solve this problem, many strategies have been proposed to give proper rewards when training RL, but their rewards lack interpretability and cannot accurately estimate the distribution of state-action pairs in real dialogs. In this paper, we propose a multi-level reward modeling approach that factorizes a reward into a three-level hierarchy: domain, act, and slot. Based on inverse adversarial reinforcement learning, our designed reward model can provide more accurate and explainable reward signals for state-action pairs. Extensive evaluations show that our approach can be applied to a wide range of reinforcement learning-based dialog systems and significantly improves both the performance and the speed of convergence.

Existing unsupervised document hashing methods are mostly established on generative models. Due to the difficulties of capturing long dependency structures, these methods rarely model the raw documents directly, but instead to model the features extracted from them (e.g. bag-of-words (BOG), TFIDF). In this paper, we propose to learn hash codes from BERT embeddings after observing their tremendous successes on downstream tasks. As a first try, we modify existing generative hashing models to accommodate the BERT embeddings. However, little improvement is observed over the codes learned from the old BOG or TFIDF features. We attribute this to the reconstruction requirement in the generative hashing, which will enforce irrelevant information that is abundant in the BERT embeddings also compressed into the codes. To remedy this issue, a new unsupervised hashing paradigm is further proposed based on the mutual information (MI) maximization principle. Specifically, the method first constructs appropriate global and local codes from the documents and then seeks to maximize their mutual information. Experimental results on three benchmark datasets demonstrate that the proposed method is able to generate hash codes that outperform existing ones learned from BOG features by a substantial margin.

Embedding-based entity alignment has been widely investigated in recent years, but most proposed methods still rely on an ideal supervised learning setting with a large number of unbiased seed mappings for training and validation, which significantly limits their usage. In this study, we evaluate those state-of-the-art methods in an industrial context, where the impact of seed mappings with different sizes and different biases is explored. Besides the popular benchmarks from DBpedia and Wikidata, we contribute and evaluate a new industrial benchmark that is extracted from two heterogeneous knowledge graphs (KGs) under deployment for medical applications. The experimental results enable the analysis of the advantages and disadvantages of these alignment methods and the further discussion of suitable strategies for their industrial deployment.