Papers by Thomas Lin
Joint Multimedia Event Extraction from Video and Article (2021.findings-emnlp)
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Brian Chen, Xudong Lin, Christopher Thomas, Manling Li, Shoya Yoshida, Lovish Chum, Heng Ji, Shih-Fu Chang
| Challenge: | Existing methods to extract multimedia events from video and text are limited to video and images. |
| Approach: | They propose a task to jointly extract events from video and text documents . they propose 'self-supervised' cross-modal event coreference model and cross-mod transformer architecture . |
| Outcome: | The proposed method achieves 6.0% and 5.8% absolute F-score gain on video-article pairs . the proposed method can resolve coreference and extract multimodal event frames more accurately than existing methods. |
MedicalSum: A Guided Clinical Abstractive Summarization Model for Generating Medical Reports from Patient-Doctor Conversations (2022.findings-emnlp)
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| Challenge: | Existing models for summarizing medical conversations do not take clinical knowledge into account and are difficult to control. |
| Approach: | They propose a transformer-based sequence-to-sequence architecture for summarizing medical conversations by integrating medical domain knowledge from the Unified Medical Language System (UMLS). |
| Outcome: | The proposed model achieves state-of-the-art ROUGE score improvements of 0.8-2.1 points (including 6.2% error reduction in the PE section) it incorporates medical domain knowledge from the Unified Medical Language System (UMLS). |
An Investigation of Evaluation Methods in Automatic Medical Note Generation (2023.findings-acl)
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| Challenge: | Recent studies show that doctors can save significant amounts of time when using automatic note generation. |
| Approach: | They propose task-specific metrics for automatic note generation from medical conversation summarization and generation, including knowledge-graph embedding-based metrics, customized model-based measures with domain-specific weights, and ensemble metrics. |
| Outcome: | The proposed evaluation metrics are compared to existing models and can have different behaviors on different types of clinical notes datasets. |
LLM Self-Correction with DeCRIM: Decompose, Critique, and Refine for Enhanced Following of Instructions with Multiple Constraints (2024.findings-emnlp)
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Thomas Palmeira Ferraz, Kartik Mehta, Yu-Hsiang Lin, Haw-Shiuan Chang, Shereen Oraby, Sijia Liu, Vivek Subramanian, Tagyoung Chung, Mohit Bansal, Nanyun Peng
| Challenge: | Recent studies have shown that LLMs struggle with instructions containing multiple constraints. |
| Approach: | They propose a self-correction pipeline that decomposes the original instruction into a list of constraints and uses a Critic model to decide when and where the LLM’s response needs refinement. |
| Outcome: | The proposed model outperforms GPT-4 on RealInstruct and IFEval even with weak feedback. |
Weakly-Supervised Temporal Article Grounding (2022.emnlp-main)
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Long Chen, Yulei Niu, Brian Chen, Xudong Lin, Guangxing Han, Christopher Thomas, Hammad Ayyubi, Heng Ji, Shih-Fu Chang
| Challenge: | Existing VG models make unrealistic assumptions about how to ground video segments . a recent study has shown that video grounding can be useful for downstream applications . |
| Approach: | They propose a new task: Weakly-Supervised temporal Article Grounding (WSAG) given an article and a relevant video, WSAG aims to localize all "groundable" sentences to the video. |
| Outcome: | The proposed method is simple but effective, and it can be used in real-world applications. |
Empowering Healthcare Practitioners with Language Models: Structuring Speech Transcripts in Two Real-World Clinical Applications (2025.emnlp-industry)
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Jean-Philippe Corbeil, Asma Ben Abacha, George Michalopoulos, Phillip Swazinna, Miguel Del-Agua, Jerome Tremblay, Akila Jeeson Daniel, Cari Bader, Kevin Cho, Pooja Krishnan, Nathan Bodenstab, Thomas Lin, Wenxuan Teng, Francois Beaulieu, Paul Vozila
| Challenge: | Large language models (LLMs) have demonstrated strong performance on clinical natural language processing tasks across multiple medical benchmarks. |
| Approach: | They propose an agentic pipeline for generating realistic, non-sensitive nurse dictations, enabling structured extraction of clinical observations. |
| Outcome: | The proposed pipeline generates realistic, non-sensitive nurse dictations, enabling structured extraction of clinical observations. |
Development of a Benchmark Corpus to Support Entity Recognition in Job Descriptions (2022.lrec-1)
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| Challenge: | Existing tools for identifying and extracting salient entities from job descriptions are limited by the lack of publicly available training data. |
| Approach: | They propose to use a standard definition of entities and a training corpus to develop a benchmark Entity Recognition (ER) model. |
| Outcome: | The proposed model achieves an F1 score of 0.59 from 18.6k entities comprising five types (Skill, Qualification, Experience, Occupation, and Domain). |
An Empirical Study of Clinical Note Generation from Doctor-Patient Encounters (2023.eacl-main)
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| Challenge: | Medical doctors spend 52 to 102 minutes per day writing clinical notes from patient encounters. |
| Approach: | They propose to use a new dataset to generate automated and manual clinical notes from doctor-patient conversations in a clinical setting. |
| Outcome: | The proposed model could reduce the time spent writing clinical notes from doctor-patient conversations in a clinical setting. |
A Modular Approach for Clinical SLMs Driven by Synthetic Data with Pre-Instruction Tuning, Model Merging, and Clinical-Tasks Alignment (2025.acl-long)
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Jean-Philippe Corbeil, Amin Dada, Jean-Michel Attendu, Asma Ben Abacha, Alessandro Sordoni, Lucas Caccia, Francois Beaulieu, Thomas Lin, Jens Kleesiek, Paul Vozila
| Challenge: | Large language models such as GPT-4 have limited their deployment in clinical settings . a novel framework for adapting SLMs into high-performing clinical models is needed . |
| Approach: | They propose a framework for adapting large language models into high-performing clinical models . they pre-instruct experts on relevant medical and clinical corpora and model merging . |
| Outcome: | The proposed framework outperforms the existing model on the CLUE+ benchmark on medical entities and radiology reports. |
MEDEC: A Benchmark for Medical Error Detection and Correction in Clinical Notes (2025.findings-acl)
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| Challenge: | Several studies have shown that large language models can answer medical questions correctly, outperforming the average human score in some medical exams. |
| Approach: | They introduce MEDEC, the first publicly available benchmark for medical error detection and correction in clinical notes. |
| Outcome: | The proposed model outperforms medical doctors in errors detection and correction tasks. |
Improving Precancerous Case Characterization via Transformer-based Ensemble Learning (2022.emnlp-industry)
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Yizhen Zhong, Jiajie Xiao, Thomas Vetterli, Mahan Matin, Ellen Loo, Jimmy Lin, Richard Bourgon, Ofer Shapira
| Challenge: | Application of natural language processing (NLP) to cancer pathology reports has been focused on detecting cancer cases, ignoring precancerous cases. |
| Approach: | They developed transformer-based deep neural network NLP models to perform the CRC phenotyping with the goal of extracting precancerous lesion attributes and distinguishing cancer and precancirous cases. |
| Outcome: | The proposed model achieves 0.914 macro-F1 scores for classifying patients into negative, non-advanced adenoma, advanced adénoma and CRC. |
Transforming Brainwaves into Language: EEG Microstates Meet Text Embedding Models for Dementia Detection (2025.acl-srw)
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| Challenge: | Dementia is recognised as the seventh leading cause of mortality globally and plays a major role in increasing disability and dependence among older adults. |
| Approach: | They propose to represent electroencephalography microstates as symbolic, language-like sequences and use text embedding and time-series deep learning models for classification. |
| Outcome: | The proposed method achieves a high accuracy of 94.31% on 1001 EEG data from multiple countries and eliminates fixed configurations and costly/invasive modalities. |