Anthony Yazdani

Anthony Yazdani, Dimitrios Proios, Hossein Rouhizadeh et al.

Current approaches for clinical information extraction are inefficient in terms of computational costs and memory consumption, hindering their application to process large-scale electronic health records (EHRs). We propose an efficient end-to-end model, the Joint-NER-RE-Fourier (JNRF), to jointly learn the tasks of named entity recognition and relation extraction for documents of variable length. The architecture uses positional encoding and unitary batch sizes to process variable length documents and uses a weight-shared Fourier network layer for low-complexity token mixing. Finally, we reach the theoretical computational complexity lower bound for relation extraction using a selective pooling strategy and distance-aware attention weights with trainable polynomial distance functions. We evaluated the JNRF architecture using the 2018 N2C2 ADE benchmark to jointly extract medication-related entities and relations in variable-length EHR summaries. JNRF outperforms rolling window BERT with selective pooling by 0.42%, while being twice as fast to train. Compared to state-of-the-art BiLSTM-CRF architectures on the N2C2 ADE benchmark, results show that the proposed approach trains 22 times faster and reduces GPU memory consumption by 1.75 folds, with a reasonable performance tradeoff of 90%, without the use of external tools, hand-crafted rules or post-processing. Given the significant carbon footprint of deep learning models and the current energy crises, these methods could support efficient and cleaner information extraction in EHRs and other types of large-scale document databases.

Anthony Yazdani, Hossein Rouhizadeh, David Vicente Alvarez et al.

This paper outlines the performance evaluation of a system for adverse drug event normalization, developed by the Data Science for Digital Health (DS4DH) group for the Social Media Mining for Health Applications (SMM4H) 2023 shared task 5. Shared task 5 targeted the normalization of adverse drug event mentions in Twitter to standard concepts of the Medical Dictionary for Regulatory Activities terminology. Our system hinges on a two-stage approach: BERT fine-tuning for entity recognition, followed by zero-shot normalization using sentence transformers and reciprocal-rank fusion. The approach yielded a precision of 44.9%, recall of 40.5%, and an F1-score of 42.6%. It outperformed the median performance in shared task 5 by 10% and demonstrated the highest performance among all participants. These results substantiate the effectiveness of our approach and its potential application for adverse drug event normalization in the realm of social media text mining.

Félicien Hêche, Sohrab Ferdowsi, Anthony Yazdani et al.

Objective: The objective of this study is to develop a machine learning (ML)-based framework for early risk stratification of clinical trials (CTs) according to their likelihood of exhibiting a high rate of dosing errors, using information available prior to trial initiation. Materials and Methods: We constructed a dataset from ClinicalTrials.gov comprising 42,112 CTs. Structured, semi-structured trial data, and unstructured protocol-related free-text data were extracted. CTs were assigned binary labels indicating elevated dosing error rate, derived from adverse event reports, MedDRA terminology, and Wilson confidence intervals. We evaluated an XGBoost model trained on structured features, a ClinicalModernBERT model using textual data, and a simple late-fusion model combining both modalities. Post-hoc probability calibration was applied to enable interpretable, trial-level risk stratification. Results: The late-fusion model achieved the highest AUC-ROC (0.862). Beyond discrimination, calibrated outputs enabled robust stratification of CTs into predefined risk categories. The proportion of trials labeled as having an excessively high dosing error rate increased monotonically across higher predicted risk groups and aligned with the corresponding predicted probability ranges. Discussion: These findings indicate that dosing error risk can be anticipated at the trial level using pre-initiation information. Probability calibration was essential for translating model outputs into reliable and interpretable risk categories, while simple multimodal integration yielded performance gains without requiring complex architectures. Conclusion: This study introduces a reproducible and scalable ML framework for early, trial-level risk stratification of CTs at risk of high dosing error rates, supporting proactive, risk-based quality management in clinical research.

Anthony Yazdani, Ihor Stepanov, Douglas Teodoro

Biomedical named entity recognition (NER) presents unique challenges due to specialized vocabularies, the sheer volume of entities, and the continuous emergence of novel entities. Traditional NER models, constrained by fixed taxonomies and human annotations, struggle to generalize beyond predefined entity types. To address these issues, we introduce GLiNER-BioMed, a domain-adapted suite of Generalist and Lightweight Model for NER (GLiNER) models specifically tailored for biomedicine. In contrast to conventional approaches, GLiNER uses natural language labels to infer arbitrary entity types, enabling zero-shot recognition. Our approach first distills the annotation capabilities of large language models (LLMs) into a smaller, more efficient model, enabling the generation of high-coverage synthetic biomedical NER data. We subsequently train two GLiNER architectures, uni- and bi-encoder, at multiple scales to balance computational efficiency and recognition performance. Experiments on several biomedical datasets demonstrate that GLiNER-BioMed outperforms the state-of-the-art in both zero- and few-shot scenarios, achieving 5.96% improvement in F1-score over the strongest baseline (p-value < 0.001). Ablation studies highlight the effectiveness of our synthetic data generation strategy and emphasize the complementary benefits of synthetic biomedical pre-training combined with fine-tuning on general-domain annotations. All datasets, models, and training pipelines are publicly available at https://github.com/ds4dh/GLiNER-biomed.

Anthony Yazdani, Alban Bornet, Philipp Khlebnikov et al.

Adverse drug events (ADEs) are a major safety issue in clinical trials. Thus, predicting ADEs is key to developing safer medications and enhancing patient outcomes. To support this effort, we introduce CT-ADE, a dataset for multilabel ADE prediction in monopharmacy treatments. CT-ADE encompasses 2,497 drugs and 168,984 drug-ADE pairs from clinical trial results, annotated using the MedDRA ontology. Unlike existing resources, CT-ADE integrates treatment and target population data, enabling comparative analyses under varying conditions, such as dosage, administration route, and demographics. In addition, CT-ADE systematically collects all ADEs in the study population, including positive and negative cases. To provide a baseline for ADE prediction performance using the CT-ADE dataset, we conducted analyses using large language models (LLMs). The best LLM achieved an F1-score of 56%, with models incorporating treatment and patient information outperforming by 21%-38% those relying solely on the chemical structure. These findings underscore the importance of contextual information in ADE prediction and establish CT-ADE as a robust resource for safety risk assessment in pharmaceutical research and development.