Papers by James Thomas
A Framework for Flexible Extraction of Clinical Event Contextual Properties from Electronic Health Records (2025.acl-industry)
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| Challenge: | EHRs contain vast amounts of valuable clinical data, stored as unstructured text. |
| Approach: | They propose a method that uses existing NER+L methods to classify medical entities at scale using a named entity recognition and linking task. |
| Outcome: | The proposed model outperforms Bi-LSTM in minority class tasks with up to 28% of the time and 32% faster training time. |
RQUGE: Reference-Free Metric for Evaluating Question Generation by Answering the Question (2023.findings-acl)
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Alireza Mohammadshahi, Thomas Scialom, Majid Yazdani, Pouya Yanki, Angela Fan, James Henderson, Marzieh Saeidi
| Challenge: | Existing metrics for evaluating the quality of automatically generated questions are expensive and penalise valid questions that may not have high lexical or semantic similarity to the reference questions. |
| Approach: | They propose a question-answering and span scorer metric based on the answerability of the candidate question given the context. |
| Outcome: | The proposed metric has higher correlation with human judgment without relying on the reference question. |
Structured Multi-Label Biomedical Text Tagging via Attentive Neural Tree Decoding (D18-1)
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| Challenge: | Existing methods for tagging unstructured texts with arbitrary number of terms drawn from an ontology are lacking. |
| Approach: | They propose a model for tagging unstructured texts with an arbitrary number of terms drawn from an ontology. |
| Outcome: | The proposed model yields state-of-the-art results on the important task of assigning MeSH terms to biomedical abstracts. |