We present ROBOTO2, an open-source, web-based platform for large language model (LLM)-assisted risk of bias (ROB) assessment of clinical trials. ROBOTO2 streamlines the traditionally labor-intensive ROB v2 (ROB2) annotation process via an interactive interface that combines PDF parsing, retrieval-augmented LLM prompting, and human-in-the-loop review. Users can upload clinical trial reports, receive preliminary answers and supporting evidence for ROB2 signaling questions, and provide real-time feedback or corrections to system suggestions. ROBOTO2 is publicly available at https://roboto2.vercel.app/, with code and data released to foster reproducibility and adoption. We construct and release a dataset of 521 pediatric clinical trial reports (8954 signaling questions with 1202 evidence passages), annotated using both manually and LLM-assisted methods, serving as a benchmark and enabling future research. Using this dataset, we benchmark ROB2 performance for 4 LLMs and provide an analysis into current model capabilities and ongoing challenges in automating this critical aspect of systematic review.

This paper describes the inference system of FZI-WIM at the SemEval-2024 Task 2: Safe Biomedical Natural Language Inference for Clinical Trials. Our system utilizes the chain of thought (CoT) paradigm to tackle this complex reasoning problem and further improves the CoT performance with self-consistency. Instead of greedy decoding, we sample multiple reasoning chains with the same prompt and make the final verification with majority voting. The self-consistent CoT system achieves a baseline F1 score of 0.80 (1st), faithfulness score of 0.90 (3rd), and consistency score of 0.73 (12th). We release the code and data publicly https://github.com/jens5588/FZI-WIM-NLI4CT.

Meta-analyses statistically aggregate the findings of different randomized controlled trials (RCTs) to assess treatment effectiveness. Because this yields robust estimates of treatment effectiveness, results from meta-analyses are considered the strongest form of evidence. However, rigorous evidence syntheses are time-consuming and labor-intensive, requiring manual extraction of data from individual trials to be synthesized. Ideally, language technologies would permit fully automatic meta-analysis, on demand. This requires accurately extracting numerical results from individual trials, which has been beyond the capabilities of natural language processing (NLP) models to date. In this work, we evaluate whether modern large language models (LLMs) can reliably perform this task. We annotate (and release) a modest but granular evaluation dataset of clinical trial reports with numerical findings attached to interventions, comparators, and outcomes. Using this dataset, we evaluate the performance of seven LLMs applied zero-shot for the task of conditionally extracting numerical findings from trial reports. We find that massive LLMs that can accommodate lengthy inputs are tantalizingly close to realizing fully automatic meta-analysis, especially for dichotomous (binary) outcomes (e.g., mortality). However, LLMs -- including ones trained on biomedical texts -- perform poorly when the outcome measures are complex and tallying the results requires inference. This work charts a path toward fully automatic meta-analysis of RCTs via LLMs, while also highlighting the limitations of existing models for this aim.

Results from Randomized Controlled Trials (RCTs) establish the comparative effectiveness of interventions, and are in turn critical inputs for evidence-based care. However, results from RCTs are presented in (often unstructured) natural language articles describing the design, execution, and outcomes of trials; clinicians must manually extract findings pertaining to interventions and outcomes of interest from such articles. This onerous manual process has motivated work on (semi-)automating extraction of structured evidence from trial reports. In this work we propose and evaluate a text-to-text model built on instruction-tuned Large Language Models (LLMs) to jointly extract Interventions, Outcomes, and Comparators (ICO elements) from clinical abstracts, and infer the associated results reported. Manual (expert) and automated evaluations indicate that framing evidence extraction as a conditional generation task and fine-tuning LLMs for this purpose realizes considerable ($\sim$20 point absolute F1 score) gains over the previous SOTA. We perform ablations and error analyses to assess aspects that contribute to model performance, and to highlight potential directions for further improvements. We apply our model to a collection of published RCTs through mid-2022, and release a searchable database of structured findings: http://ico-relations.ebm-nlp.com

With the increasing number of clinical trial reports generated every day, it is becoming hard to keep up with novel discoveries that inform evidence-based healthcare recommendations. To help automate this process and assist medical experts, NLP solutions are being developed. This motivated the SemEval-2023 Task 7, where the goal was to develop an NLP system for two tasks: evidence retrieval and natural language inference from clinical trial data. In this paper, we describe our two developed systems. The first one is a pipeline system that models the two tasks separately, while the second one is a joint system that learns the two tasks simultaneously with a shared representation and a multi-task learning approach. The final system combines their outputs in an ensemble system. We formalize the models, present Figure 1: The task consists of predicting whether a their characteristics and challenges, and provide given claim entails or contradicts the clinical trial report an analysis of achieved results. Our system based on the evidence found in it.