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.

This paper presents FoFo, a pioneering benchmark for evaluating large language models’ (LLMs) ability to follow complex, domain-specific formats, a crucial yet under-examined capability for their application as AI agents. Despite LLMs’ advancements, existing benchmarks fail to assess their format-following proficiency adequately. FoFo fills this gap with a diverse range of real-world formats and instructions, developed through an AI-Human collaborative method. Our evaluation across both open-source (e.g., Llama 2, WizardLM) and closed-source (e.g., GPT-4, PALM2, Gemini) LLMs highlights three key findings: open-source models significantly lag behind closed-source ones in format adherence; LLMs’ format-following performance is independent of their content generation quality; and LLMs’ format proficiency varies across different domains. These insights suggest the need for specialized tuning for format-following skills and highlight FoFo’s role in guiding the selection of domain-specific AI agents. FoFo will be publicly released, contributing a critical tool for advancing LLM evaluation and application.

Embodied agents equipped with GPT as their brain have exhibited extraordinary decision-making and generalization abilities across various tasks. However, existing zero-shot agents for vision-and-language navigation (VLN) only prompt the GPT-4 to select potential locations within localized environments, without constructing an effective “global-view” for the agent to understand the overall environment. In this work, we present a novel **map**-guided **GPT**-based agent, dubbed **MapGPT**, which introduces an online linguistic-formed map to encourage the global exploration. Specifically, we build an online map and incorporate it into the prompts that include node information and topological relationships, to help GPT understand the spatial environment. Benefiting from this design, we further propose an adaptive planning mechanism to assist the agent in performing multi-step path planning based on a map, systematically exploring multiple candidate nodes or sub-goals step by step. Extensive experiments demonstrate that our MapGPT is applicable to both GPT-4 and GPT-4V, achieving state-of-the-art zero-shot performance on the R2R and REVERIE simultaneously (~10% and ~12% improvements in SR), and showcasing the newly emergent global thinking and path planning abilities of the GPT.

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.

We present PATRON, a prompt-based data selection method for pre-trained language model fine-tuning under cold-start scenarios, i.e., no initial labeled data are available. In PATRON, we design (1) a prompt-based uncertainty propagation approach to estimate the importance of data points and (2) a partition-then-rewrite (PTR) strategy to promote sample diversity when querying for annotations. Experiments on six text classification datasets show that PATRON outperforms the strongest cold-start data selection baselines by up to 6.9%. Besides, with 128 labels only, PATRON achieves 91.0% and 92.1% of the fully supervised performance based on vanilla fine-tuning and prompt-based learning respectively. Our implementation of PATRON will be published upon acceptance.

We propose a novel framework to conduct field extraction from forms with unlabeled data. To bootstrap the training process, we develop a rule-based method for mining noisy pseudo-labels from unlabeled forms. Using the supervisory signal from the pseudo-labels, we extract a discriminative token representation from a transformer-based model by modeling the interaction between text in the form. To prevent the model from overfitting to label noise, we introduce a refinement module based on a progressive pseudo-label ensemble. Experimental results demonstrate the effectiveness of our framework.

We propose, DocQueryNet, a value retrieval method with arbitrary queries for form-like documents to reduce human effort of processing forms. Unlike previous methods that only address a fixed set of field items, our method predicts target value for an arbitrary query based on the understanding of the layout and semantics of a form. To further boost model performance, we propose a simple document language modeling (SimpleDLM) strategy to improve document understanding on large-scale model pre-training. Experimental results show that DocQueryNet outperforms previous designs significantly and the SimpleDLM further improves our performance on value retrieval by around 17% F1 score compared with the state-of-the-art pre-training method. Code is available here, https://github.com/salesforce/QVR-SimpleDLM.