Daily Papers

Large language models (LLMs) hold great promise in summarizing medical evidence. Most recent studies focus on the application of proprietary LLMs. Using proprietary LLMs introduces multiple risk factors, including a lack of transparency and vendor dependency. While open-source LLMs allow better transparency and customization, their performance falls short compared to proprietary ones. In this study, we investigated to what extent fine-tuning open-source LLMs can further improve their performance in summarizing medical evidence. Utilizing a benchmark dataset, MedReview, consisting of 8,161 pairs of systematic reviews and summaries, we fine-tuned three broadly-used, open-sourced LLMs, namely PRIMERA, LongT5, and Llama-2. Overall, the fine-tuned LLMs obtained an increase of 9.89 in ROUGE-L (95% confidence interval: 8.94-10.81), 13.21 in METEOR score (95% confidence interval: 12.05-14.37), and 15.82 in CHRF score (95% confidence interval: 13.89-16.44). The performance of fine-tuned LongT5 is close to GPT-3.5 with zero-shot settings. Furthermore, smaller fine-tuned models sometimes even demonstrated superior performance compared to larger zero-shot models. The above trends of improvement were also manifested in both human and GPT4-simulated evaluations. Our results can be applied to guide model selection for tasks demanding particular domain knowledge, such as medical evidence summarization.

Developing artificial intelligence (AI) for vertical domains requires a solid data foundation for both training and evaluation. In this work, we introduce TrialPanorama, a large-scale, structured database comprising 1,657,476 clinical trial records aggregated from 15 global sources. The database captures key aspects of trial design and execution, including trial setups, interventions, conditions, biomarkers, and outcomes, and links them to standard biomedical ontologies such as DrugBank and MedDRA. This structured and ontology-grounded design enables TrialPanorama to serve as a unified, extensible resource for a wide range of clinical trial tasks, including trial planning, design, and summarization. To demonstrate its utility, we derive a suite of benchmark tasks directly from the TrialPanorama database. The benchmark spans eight tasks across two categories: three for systematic review (study search, study screening, and evidence summarization) and five for trial design (arm design, eligibility criteria, endpoint selection, sample size estimation, and trial completion assessment). The experiments using five state-of-the-art large language models (LLMs) show that while general-purpose LLMs exhibit some zero-shot capability, their performance is still inadequate for high-stakes clinical trial workflows. We release TrialPanorama database and the benchmark to facilitate further research on AI for clinical trials.

Understanding temporal relations and answering time-sensitive questions is crucial yet a challenging task for question-answering systems powered by large language models (LLMs). Existing approaches either update the parametric knowledge of LLMs with new facts, which is resource-intensive and often impractical, or integrate LLMs with external knowledge retrieval (i.e., retrieval-augmented generation). However, off-the-shelf retrievers often struggle to identify relevant documents that require intensive temporal reasoning. To systematically study time-sensitive question answering, we introduce the TempRAGEval benchmark, which repurposes existing datasets by incorporating temporal perturbations and gold evidence labels. As anticipated, all existing retrieval methods struggle with these temporal reasoning-intensive questions. We further propose Modular Retrieval (MRAG), a trainless framework that includes three modules: (1) Question Processing that decomposes question into a main content and a temporal constraint; (2) Retrieval and Summarization that retrieves evidence and uses LLMs to summarize according to the main content; (3) Semantic-Temporal Hybrid Ranking that scores each evidence summarization based on both semantic and temporal relevance. On TempRAGEval, MRAG significantly outperforms baseline retrievers in retrieval performance, leading to further improvements in final answer accuracy.

Large Language Models (LLMs) have been extensively evaluated for general summarization tasks as well as medical research assistance, but they have not been specifically evaluated for the task of summarizing real-world evidence (RWE) from structured output of RWE studies. We introduce RWESummary, a proposed addition to the MedHELM framework (Bedi, Cui, Fuentes, Unell et al., 2025) to enable benchmarking of LLMs for this task. RWESummary includes one scenario and three evaluations covering major types of errors observed in summarization of medical research studies and was developed using Atropos Health proprietary data. Additionally, we use RWESummary to compare the performance of different LLMs in our internal RWE summarization tool. At the time of publication, with 13 distinct RWE studies, we found the Gemini 2.5 models performed best overall (both Flash and Pro). We suggest RWESummary as a novel and useful foundation model benchmark for real-world evidence study summarization.

Evaluating the truthfulness of online content is critical for combating misinformation. This study examines the efficiency and effectiveness of crowdsourced truthfulness assessments through a comparative analysis of two approaches: one involving full-length webpages as evidence for each claim, and another using summaries for each evidence document generated with a large language model. Using an A/B testing setting, we engage a diverse pool of participants tasked with evaluating the truthfulness of statements under these conditions. Our analysis explores both the quality of assessments and the behavioral patterns of participants. The results reveal that relying on summarized evidence offers comparable accuracy and error metrics to the Standard modality while significantly improving efficiency. Workers in the Summary setting complete a significantly higher number of assessments, reducing task duration and costs. Additionally, the Summary modality maximizes internal agreement and maintains consistent reliance on and perceived usefulness of evidence, demonstrating its potential to streamline large-scale truthfulness evaluations.

Following each patient visit, physicians draft long semi-structured clinical summaries called SOAP notes. While invaluable to clinicians and researchers, creating digital SOAP notes is burdensome, contributing to physician burnout. In this paper, we introduce the first complete pipelines to leverage deep summarization models to generate these notes based on transcripts of conversations between physicians and patients. After exploring a spectrum of methods across the extractive-abstractive spectrum, we propose Cluster2Sent, an algorithm that (i) extracts important utterances relevant to each summary section; (ii) clusters together related utterances; and then (iii) generates one summary sentence per cluster. Cluster2Sent outperforms its purely abstractive counterpart by 8 ROUGE-1 points, and produces significantly more factual and coherent sentences as assessed by expert human evaluators. For reproducibility, we demonstrate similar benefits on the publicly available AMI dataset. Our results speak to the benefits of structuring summaries into sections and annotating supporting evidence when constructing summarization corpora.

Large language models (LLMs) are capable of generating coherent summaries from very long contexts given a user query. Extracting and properly citing evidence spans could help improve the transparency and reliability of these summaries. At the same time, LLMs suffer from positional biases in terms of which information they understand and attend to, which could affect evidence citation. Whereas previous work has focused on evidence citation with predefined levels of granularity (e.g. sentence, paragraph, document, etc.), we propose the task of long-context query focused summarization with unstructured evidence citation. We show how existing systems struggle to generate and properly cite unstructured evidence from their context, and that evidence tends to be "lost-in-the-middle". To help mitigate this, we create the Summaries with Unstructured Evidence Text dataset (SUnsET), a synthetic dataset generated using a novel domain-agnostic pipeline which can be used as supervision to adapt LLMs to this task. We demonstrate across 5 LLMs of different sizes and 4 datasets with varying document types and lengths that LLMs adapted with SUnsET data generate more relevant and factually consistent evidence than their base models, extract evidence from more diverse locations in their context, and can generate more relevant and consistent summaries.

Plain language summarization with LLMs can be useful for improving textual accessibility of technical content. But how factual are these summaries in a high-stakes domain like medicine? This paper presents FactPICO, a factuality benchmark for plain language summarization of medical texts describing randomized controlled trials (RCTs), which are the basis of evidence-based medicine and can directly inform patient treatment. FactPICO consists of 345 plain language summaries of RCT abstracts generated from three LLMs (i.e., GPT-4, Llama-2, and Alpaca), with fine-grained evaluation and natural language rationales from experts. We assess the factuality of critical elements of RCTs in those summaries: Populations, Interventions, Comparators, Outcomes (PICO), as well as the reported findings concerning these. We also evaluate the correctness of the extra information (e.g., explanations) added by LLMs. Using FactPICO, we benchmark a range of existing factuality metrics, including the newly devised ones based on LLMs. We find that plain language summarization of medical evidence is still challenging, especially when balancing between simplicity and factuality, and that existing metrics correlate poorly with expert judgments on the instance level.

Sifting through vast textual data and summarizing key information imposes a substantial burden on how clinicians allocate their time. Although large language models (LLMs) have shown immense promise in natural language processing (NLP) tasks, their efficacy across diverse clinical summarization tasks has not yet been rigorously examined. In this work, we employ domain adaptation methods on eight LLMs, spanning six datasets and four distinct summarization tasks: radiology reports, patient questions, progress notes, and doctor-patient dialogue. Our thorough quantitative assessment reveals trade-offs between models and adaptation methods in addition to instances where recent advances in LLMs may not lead to improved results. Further, in a clinical reader study with six physicians, we depict that summaries from the best adapted LLM are preferable to human summaries in terms of completeness and correctness. Our ensuing qualitative analysis delineates mutual challenges faced by both LLMs and human experts. Lastly, we correlate traditional quantitative NLP metrics with reader study scores to enhance our understanding of how these metrics align with physician preferences. Our research marks the first evidence of LLMs outperforming human experts in clinical text summarization across multiple tasks. This implies that integrating LLMs into clinical workflows could alleviate documentation burden, empowering clinicians to focus more on personalized patient care and other irreplaceable human aspects of medicine.

Prior work in Argument Mining frequently alludes to its potential applications in automatic debating systems. Despite this focus, almost no datasets or models exist which apply natural language processing techniques to problems found within competitive formal debate. To remedy this, we present the DebateSum dataset. DebateSum consists of 187,386 unique pieces of evidence with corresponding argument and extractive summaries. DebateSum was made using data compiled by competitors within the National Speech and Debate Association over a 7-year period. We train several transformer summarization models to benchmark summarization performance on DebateSum. We also introduce a set of fasttext word-vectors trained on DebateSum called debate2vec. Finally, we present a search engine for this dataset which is utilized extensively by members of the National Speech and Debate Association today. The DebateSum search engine is available to the public here: http://www.debate.cards

We consider the problem of automatically generating a narrative biomedical evidence summary from multiple trial reports. We evaluate modern neural models for abstractive summarization of relevant article abstracts from systematic reviews previously conducted by members of the Cochrane collaboration, using the authors conclusions section of the review abstract as our target. We enlist medical professionals to evaluate generated summaries, and we find that modern summarization systems yield consistently fluent and relevant synopses, but that they are not always factual. We propose new approaches that capitalize on domain-specific models to inform summarization, e.g., by explicitly demarcating snippets of inputs that convey key findings, and emphasizing the reports of large and high-quality trials. We find that these strategies modestly improve the factual accuracy of generated summaries. Finally, we propose a new method for automatically evaluating the factuality of generated narrative evidence syntheses using models that infer the directionality of reported findings.

To assess the effectiveness of any medical intervention, researchers must conduct a time-intensive and highly manual literature review. NLP systems can help to automate or assist in parts of this expensive process. In support of this goal, we release MS^2 (Multi-Document Summarization of Medical Studies), a dataset of over 470k documents and 20k summaries derived from the scientific literature. This dataset facilitates the development of systems that can assess and aggregate contradictory evidence across multiple studies, and is the first large-scale, publicly available multi-document summarization dataset in the biomedical domain. We experiment with a summarization system based on BART, with promising early results. We formulate our summarization inputs and targets in both free text and structured forms and modify a recently proposed metric to assess the quality of our system's generated summaries. Data and models are available at https://github.com/allenai/ms2

Traditionally, Text Simplification is treated as a monolingual translation task where sentences between source texts and their simplified counterparts are aligned for training. However, especially for longer input documents, summarizing the text (or dropping less relevant content altogether) plays an important role in the simplification process, which is currently not reflected in existing datasets. Simultaneously, resources for non-English languages are scarce in general and prohibitive for training new solutions. To tackle this problem, we pose core requirements for a system that can jointly summarize and simplify long source documents. We further describe the creation of a new dataset for joint Text Simplification and Summarization based on German Wikipedia and the German children's lexicon "Klexikon", consisting of almost 2900 documents. We release a document-aligned version that particularly highlights the summarization aspect, and provide statistical evidence that this resource is well suited to simplification as well. Code and data are available on Github: https://github.com/dennlinger/klexikon

The goal of automated summarization techniques (Paice, 1990; Kupiec et al, 1995) is to condense text by focusing on the most critical information. Generative large language models (LLMs) have shown to be robust summarizers, yet traditional metrics struggle to capture resulting performance (Goyal et al, 2022) in more powerful LLMs. In safety-critical domains such as medicine, more rigorous evaluation is required, especially given the potential for LLMs to omit important information in the resulting summary. We propose MED-OMIT, a new omission benchmark for medical summarization. Given a doctor-patient conversation and a generated summary, MED-OMIT categorizes the chat into a set of facts and identifies which are omitted from the summary. We further propose to determine fact importance by simulating the impact of each fact on a downstream clinical task: differential diagnosis (DDx) generation. MED-OMIT leverages LLM prompt-based approaches which categorize the importance of facts and cluster them as supporting or negating evidence to the diagnosis. We evaluate MED-OMIT on a publicly-released dataset of patient-doctor conversations and find that MED-OMIT captures omissions better than alternative metrics.

Language models (LMs) often struggle to pay enough attention to the input context, and generate texts that are unfaithful or contain hallucinations. To mitigate this issue, we present context-aware decoding (CAD), which follows a contrastive output distribution that amplifies the difference between the output probabilities when a model is used with and without context. Our experiments show that CAD, without additional training, significantly improves the faithfulness of different LM families, including OPT, GPT, LLaMA and FLAN-T5 for summarization tasks (e.g., 14.3% gain for LLaMA in factuality metrics). Furthermore, CAD is particularly effective in overriding a model's prior knowledge when it contradicts the provided context, leading to substantial improvements in tasks where resolving the knowledge conflict is essential.

Query-focused summarization (QFS) aims to provide a summary of a single document/multi documents that can satisfy the information needs of a given query. It is useful for various real-world applications, such as abstractive snippet generation or more recent retrieval augmented generation (RAG). A prototypical QFS pipeline consists of a retriever (sparse or dense retrieval) and a generator (usually a large language model). However, applying large language models (LLM) potentially leads to hallucinations, especially when the evidence contradicts the prior belief of LLMs. There has been growing interest in developing new decoding methods to improve generation quality and reduce hallucination. In this work, we conduct a large-scale reproducibility study on one recently proposed decoding method -- Context-aware Decoding (CAD). In addition to replicating CAD's experiments on news summarization datasets, we include experiments on QFS datasets, and conduct more rigorous analysis on computational complexity and hyperparameter sensitivity. Experiments with eight different language models show that performance-wise, CAD improves QFS quality by (1) reducing factuality errors/hallucinations while (2) mostly retaining the match of lexical patterns, measured by ROUGE scores, while also at a cost of increased inference-time FLOPs and reduced decoding speed. The code implementation based on Huggingface Library is made available https://github.com/zhichaoxu-shufe/context-aware-decoding-qfs

Very large language models (LLMs), such as GPT-3 and Codex have achieved state-of-the-art performance on several natural-language tasks, and show great promise also for code. A particularly exciting aspect of LLMs is their knack for few-shot and zero-shot learning: they can learn to perform a task with very few examples. Few-shotting has particular synergies in software engineering, where there are a lot of phenomena (identifier names, APIs, terminology, coding patterns) that are known to be highly project-specific. However, project-specific data can be quite limited, especially early in the history of a project; thus the few-shot learning capacity of LLMs might be very relevant. In this paper, we investigate the use few-shot training with the very large GPT (Generative Pre-trained Transformer) Codex model, and find evidence suggesting that one can significantly surpass state-of-the-art models for code-summarization, leveraging project-specific training.

Abstractive summarization systems today produce fluent and relevant output, but often "hallucinate" statements not supported by the source text. We analyze the connection between hallucinations and training data, and find evidence that models hallucinate because they train on target summaries that are unsupported by the source. Based on our findings, we present PINOCCHIO, a new decoding method that improves the consistency of a transformer-based abstractive summarizer by constraining beam search to avoid hallucinations. Given the model states and outputs at a given step, PINOCCHIO detects likely model hallucinations based on various measures of attribution to the source text. PINOCCHIO backtracks to find more consistent output, and can opt to produce no summary at all when no consistent generation can be found. In experiments, we find that PINOCCHIO improves the consistency of generation (in terms of F1) by an average of~67% on two abstractive summarization datasets.

This paper presents HerO 2, Team HUMANE's system for the AVeriTeC shared task at the FEVER-25 workshop. HerO 2 is an enhanced version of HerO, the best-performing open-source model from the previous year's challenge. It improves evidence quality through document summarization and answer reformulation, optimizes veracity prediction via post-training quantization under computational constraints, and enhances overall system performance by integrating updated language model (LM) backbones. HerO 2 ranked second on the leaderboard while achieving the shortest runtime among the top three systems, demonstrating both high efficiency and strong potential for real-world fact verification. The code is available at https://github.com/ssu-humane/HerO2.

Multimodal retrieval-augmented generation (MM-RAG) is a key approach for applying large language models (LLMs) and agents to real-world knowledge bases, yet current evaluations are fragmented, focusing on either text or images in isolation or on simplified multimodal setups that fail to capture document-centric multimodal use cases. In this paper, we introduce UniDoc-Bench, the first large-scale, realistic benchmark for MM-RAG built from 70k real-world PDF pages across eight domains. Our pipeline extracts and links evidence from text, tables, and figures, then generates 1,600 multimodal QA pairs spanning factual retrieval, comparison, summarization, and logical reasoning queries. To ensure reliability, 20% of QA pairs are validated by multiple annotators and expert adjudication. UniDoc-Bench supports apples-to-apples comparison across four paradigms: (1) text-only, (2) image-only, (3) multimodal text-image fusion, and (4) multimodal joint retrieval -- under a unified protocol with standardized candidate pools, prompts, and evaluation metrics. Our experiments show that multimodal text-image fusion RAG systems consistently outperform both unimodal and jointly multimodal embedding-based retrieval, indicating that neither text nor images alone are sufficient and that current multimodal embeddings remain inadequate. Beyond benchmarking, our analysis reveals when and how visual context complements textual evidence, uncovers systematic failure modes, and offers actionable guidance for developing more robust MM-RAG pipelines.

Recognizing if LLM output can be grounded in evidence is central to many tasks in NLP: retrieval-augmented generation, summarization, document-grounded dialogue, and more. Current approaches to this kind of "fact-checking" are based on verifying each piece of a model generation against potential evidence using an LLM. However, this process can be very computationally expensive, requiring many calls to LLMs to check a single response. In this work, we show how to build small models that have GPT-4-level performance but for 400x lower cost. We do this by constructing synthetic training data with GPT-4, which involves creating realistic yet challenging instances of factual errors via a structured generation procedure. Training on this data teaches models to check each fact in the claim and recognize synthesis of information across sentences. For evaluation, we unify pre-existing datasets into a benchmark LLM-AggreFact, collected from recent work on fact-checking and grounding LLM generations. Our best system MiniCheck-FT5 (770M parameters) outperforms all systems of comparable size and reaches GPT-4 accuracy. We release LLM-AggreFact, code for data synthesis, and models.

Competitive Debate's increasingly technical nature has left competitors looking for tools to accelerate evidence production. We find that the unique type of extractive summarization performed by competitive debaters - summarization with a bias towards a particular target meaning - can be performed using the latest innovations in unsupervised pre-trained text vectorization models. We introduce CX_DB8, a queryable word-level extractive summarizer and evidence creation framework, which allows for rapid, biasable summarization of arbitarily sized texts. CX_DB8s usage of the embedding framework Flair means that as the underlying models improve, CX_DB8 will also improve. We observe that CX_DB8 also functions as a semantic search engine, and has application as a supplement to traditional "find" functionality in programs and webpages. CX_DB8 is currently used by competitive debaters and is made available to the public at https://github.com/Hellisotherpeople/CX_DB8

We introduce the Scratchpad Mechanism, a novel addition to the sequence-to-sequence (seq2seq) neural network architecture and demonstrate its effectiveness in improving the overall fluency of seq2seq models for natural language generation tasks. By enabling the decoder at each time step to write to all of the encoder output layers, Scratchpad can employ the encoder as a "scratchpad" memory to keep track of what has been generated so far and thereby guide future generation. We evaluate Scratchpad in the context of three well-studied natural language generation tasks --- Machine Translation, Question Generation, and Text Summarization --- and obtain state-of-the-art or comparable performance on standard datasets for each task. Qualitative assessments in the form of human judgements (question generation), attention visualization (MT), and sample output (summarization) provide further evidence of the ability of Scratchpad to generate fluent and expressive output.