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.

Machine learning (ML) exhibits promise in the clinical domain. However, it is constrained by data scarcity and ethical considerations, as the generation of clinical trials presents significant challenges due to stringent privacy regulations, high costs, and the extended duration required for conducting studies with human participants. Despite the advancements of large language models (LLMs) in general generation tasks, their potential in facilitating the generation of synthetic clinical trials is under-explored. To address this gap, we introduce a novel Retrieval-Reasoning few-shot framework that leverages LLMs to generate artificial yet realistic and diverse clinical trials with binary success/failure labels. Experiments conducted on real clinical trials from the \url{ClinicalTrials.gov} database demonstrate that our synthetic data can effectively augment real datasets. Furthermore, by fine-tuning a pre-trained model as a binary classifier on synthetic clinical trial datasets, we demonstrate that this augmentation enhances model training for downstream tasks such as trial outcome prediction. Our findings suggest that LLMs for synthetic clinical trial generation hold promise for accelerating clinical research and upholding ethical standards for patient privacy. The code is publicly available at https://anonymous.4open.science/r/Retrieval_Reasoning_Clinical_Trial_Generation-3EC4.

Language Processing (NLP) tasks, including in the Our overall best submission to the task achieved assessment of textual entailment relations. However, a macro F1-score of 0.80 (1st place on the leaderboard), these models are heavily susceptible to shortcut a consistency score of 0.72 (15th), and a learning (Du et al., 2023), factual inconsistency faithfulness score of 0.83 (11th). Our method excels (Xie et al., 2023), and performance degradation in classification accuracy, but fails at being when exposed to data from specialized domains, robust to perturbations on the statements, i.e. predicting such as in the case of medical data.

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.

While BERT-like models have proven identifying the inference relationship (entailment to be effective in various NLP tasks such as Named vs. contradiction) between Clinical Trial Report Entity Recognition (Devlin et al., 2019), scaling up (CTR) statement pairs. These statements and the the number of parameters in transformer models supporting evidence are crafted by individuals not only enhances their capabilities but also endows with expertise in the clinical domain, including them with new abilities not seen in smaller clinical trial organizers and research oncologists.

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.

Abstruse learning algorithms and complex datasets increasingly characterize modern clinical decision support systems (CDSS). As a result, clinicians cannot easily or rapidly scrutinize the CDSS recommendation when facing a difficult diagnosis or treatment decision in practice. Over-trust or under-trust are frequent. Prior research has explored supporting such assessments by explaining DST data inputs and algorithmic mechanisms. This paper explores a different approach: Providing precisely relevant, scientific evidence from biomedical literature. We present a proof-of-concept system, Clinical Evidence Engine, to demonstrate the technical and design feasibility of this approach across three domains (cardiovascular diseases, autism, cancer). Leveraging Clinical BioBERT, the system can effectively identify clinical trial reports based on lengthy clinical questions (e.g., "risks of catheter infection among adult patients in intensive care unit who require arterial catheters, if treated with povidone iodine-alcohol"). This capability enables the system to identify clinical trials relevant to diagnostic/treatment hypotheses -- a clinician's or a CDSS's. Further, Clinical Evidence Engine can identify key parts of a clinical trial abstract, including patient population (e.g., adult patients in intensive care unit who require arterial catheters), intervention (povidone iodine-alcohol), and outcome (risks of catheter infection). This capability opens up the possibility of enabling clinicians to 1) rapidly determine the match between a clinical trial and a clinical question, and 2) understand the result and contexts of the trial without extensive reading. We demonstrate this potential by illustrating two example use scenarios of the system. We discuss the idea of designing DST explanations not as specific to a DST or an algorithm, but as a domain-agnostic decision support infrastructure.