Developing effective biomedical retrieval models is important for excelling at knowledge-intensive biomedical tasks but still challenging due to the lack of sufficient publicly annotated biomedical data and computational resources. We present BMRetriever, a series of dense retrievers for enhancing biomedical retrieval via unsupervised pre-training on large biomedical corpora, followed by instruction fine-tuning on a combination of labeled datasets and synthetic pairs. Experiments on 5 biomedical tasks across 11 datasets verify BMRetriever’s efficacy on various biomedical applications. BMRetriever also exhibits strong parameter efficiency, with the 410M variant outperforming baselines up to 11.7 times larger, and the 2B variant matching the performance of models with over 5B parameters. The training data and model checkpoints are released at https://huggingface.co/BMRetriever to ensure transparency, reproducibility, and application to new domains.

Despite their improved capabilities in generation and reasoning, adapting large language models (LLMs) to the biomedical domain remains challenging due to their immense size and privacy concerns. In this study, we propose MedAdapter, a unified post-hoc adapter for test-time adaptation of LLMs towards biomedical applications. Instead of fine-tuning the entire LLM, MedAdapter effectively adapts the original model by fine-tuning only a small BERT-sized adapter to rank candidate solutions generated by LLMs. Experiments on four biomedical tasks across eight datasets demonstrate that MedAdapter effectively adapts both white-box and black-box LLMs in biomedical reasoning, achieving average performance improvements of 18.24% and 10.96%, respectively, without requiring extensive computational resources or sharing data with third parties. MedAdapter also yields enhanced performance when combined with train-time adaptation, highlighting a flexible and complementary solution to existing adaptation methods. Faced with the challenges of balancing model performance, computational resources, and data privacy, MedAdapter provides an efficient, privacy-preserving, cost-effective, and transparent solution for adapting LLMs to the biomedical domain.

Clinicians often rely on data engineers to retrieve complex patient information from electronic health record (EHR) systems, a process that is both inefficient and time-consuming. We propose EHRAgent, a large language model (LLM) agent empowered with accumulative domain knowledge and robust coding capability. EHRAgent enables autonomous code generation and execution to facilitate clinicians in directly interacting with EHRs using natural language. Specifically, we formulate a multi-tabular reasoning task based on EHRs as a tool-use planning process, efficiently decomposing a complex task into a sequence of manageable actions with external toolsets. We first inject relevant medical information to enable EHRAgent to effectively reason about the given query, identifying and extracting the required records from the appropriate tables. By integrating interactive coding and execution feedback, EHRAgent then effectively learns from error messages and iteratively improves its originally generated code. Experiments on three real-world EHR datasets show that EHRAgent outperforms the strongest baseline by up to 29.6% in success rate, verifying its strong capacity to tackle complex clinical tasks with minimal demonstrations.

Clinical natural language processing faces challenges like complex medical terminology and clinical contexts. Recently, large language models (LLMs) have shown promise in this domain. Yet, their direct deployment can lead to privacy issues and are constrained by resources. To address this challenge, we delve into synthetic clinical text generation with LLMs for clinical NLP tasks. We propose an innovative, resource-efficient approach, ClinGen, which infuses knowledge into the process. Our model involves clinical knowledge extraction and context-informed LLM prompting. Both clinical topics and writing styles are drawn from external domain-specific knowledge graphs and LLMs to guide data generation. Our extensive empirical study across 8 clinical NLP tasks and 18 datasets reveals that ClinGen consistently enhances performance across various tasks by 7.7%-8.7% on average, effectively aligning the distribution of real datasets and enriching the diversity of generated training instances.

We present RAM-EHR, a Retrieval AugMentation pipeline to improve clinical predictions on Electronic Health Records (EHRs). RAM-EHR first collects multiple knowledge sources, converts them into text format, and uses dense retrieval to obtain information related to medical concepts. This strategy addresses the difficulties associated with complex names for the concepts. RAM-EHR then augments the local EHR predictive model co-trained with consistency regularization to capture complementary information from patient visits and summarized knowledge. Experiments on two EHR datasets show the efficacy of RAM-EHR over previous knowledge-enhanced baselines (3.4% gain in AUROC and 7.2% gain in AUPR), emphasizing the effectiveness of the summarized knowledge from RAM-EHR for clinical prediction tasks.

Information extraction, e.g., attribute value extraction, has been extensively studied and formulated based only on text. However, many attributes can benefit from image-based extraction, like color, shape, pattern, among others. The visual modality has long been underutilized, mainly due to multimodal annotation difficulty. In this paper, we aim to patch the visual modality to the textual-established attribute in- formation extractor. The cross-modality integration faces several unique challenges: (C1) images and textual descriptions are loosely paired intra-sample and inter-samples; (C2) images usually contain rich backgrounds that can mislead the prediction; (C3) weakly supervised labels from textual-established ex- tractors are biased for multimodal training. We present PV2TEA, an encoder-decoder architecture equipped with three bias reduction schemes: (S1) Augmented label-smoothed contrast to improve the cross-modality alignment for loosely-paired image and text; (S2) Attention-pruning that adaptively distinguishes the visual foreground; (S3) Two-level neighborhood regularization that mitigates the label textual bias via reliability estimation. Empirical results on real-world e-Commerce datasets1 demonstrate up to 11.74% absolute (20.97% relatively) F1 increase over unimodal baselines.

Previous research has demonstrated the advantages of integrating data from multiple sources over traditional unimodal data, leading to the emergence of numerous novel multimodal applications. We propose a multimodal classification benchmark MuG with eight datasets that allows researchers to evaluate and improve their models. These datasets are collected from four various genres of games that cover tabular, textual, and visual modalities. We conduct multi-aspect data analysis to provide insights into the benchmark, including label balance ratios, percentages of missing features, distributions of data within each modality, and the correlations between labels and input modalities. We further present experimental results obtained by several state-of-the-art unimodal classifiers and multimodal classifiers, which demonstrate the challenging and multimodal-dependent properties of the benchmark. MuG is released at https://github.com/lujiaying/MUG-Bench with the data, tutorials, and implemented baselines.

Stepping from sentence-level to document-level, the research on relation extraction (RE) confronts increasing text length and more complicated entity interactions. Consequently, it is more challenging to encode the key information sources—relevant contexts and entity types. However, existing methods only implicitly learn to model these critical information sources while being trained for RE. As a result, they suffer the problems of ineffective supervision and uninterpretable model predictions. In contrast, we propose to explicitly teach the model to capture relevant contexts and entity types by supervising and augmenting intermediate steps (SAIS) for RE. Based on a broad spectrum of carefully designed tasks, our proposed SAIS method not only extracts relations of better quality due to more effective supervision, but also retrieves the corresponding supporting evidence more accurately so as to enhance interpretability. By assessing model uncertainty, SAIS further boosts the performance via evidence-based data augmentation and ensemble inference while reducing the computational cost. Eventually, SAIS delivers state-of-the-art RE results on three benchmarks (DocRED, CDR, and GDA) and outperforms the runner-up by 5.04% relatively in F1 score in evidence retrieval on DocRED.

Federated learning (FL) can be essential in knowledge representation, reasoning, and data mining applications over multi-source knowledge graphs (KGs). A recent study FedE first proposes an FL framework that shares entity embeddings of KGs across all clients. However, entity embedding sharing from FedE would incur a severe privacy leakage. Specifically, the known entity embedding can be used to infer whether a specific relation between two entities exists in a private client. In this paper, we introduce a novel attack method that aims to recover the original data based on the embedding information, which is further used to evaluate the vulnerabilities of FedE. Furthermore, we propose a Federated learning paradigm with privacy-preserving Relation embedding aggregation (FedR) to tackle the privacy issue in FedE. Besides, relation embedding sharing can significantly reduce the communication cost due to its smaller size of queries. We conduct extensive experiments to evaluate FedR with five different KG embedding models and three datasets. Compared to FedE, FedR achieves similar utility and significant improvements regarding privacy-preserving effect and communication efficiency on the link prediction task.