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Xavier Tannier

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Computation and Language Machine Learning Artificial Intelligence Information Retrieval

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preprint2026arXiv

LongBEL: Long-Context and Document-Consistent Biomedical Entity Linking

Biomedical entity linking maps textual mentions to concepts in structured knowledge bases such as UMLS or SNOMED CT. Most existing systems link each mention independently, using only the mention or its surrounding sentence. This ignores dependencies between mentions in the same document and can lead to inconsistent predictions, especially when the same concept appears under different surface forms. We introduce LongBEL, a document-level generative framework that combines full-document context with a memory of previous predictions. To make this memory robust, LongBEL is trained with cross-validated predictions rather than gold labels, reducing the mismatch between training and inference and limiting cascading errors. Experiments on five biomedical benchmarks across English, French, and Spanish show that LongBEL improves over sentence-level generative baselines, with the largest gains on datasets where concepts frequently recur within documents. An ensemble of local, global, and memory-based variants achieves the best results across all benchmarks. Further analysis shows that the largest gains occur on recurring concepts, suggesting that LongBEL mainly improves document-level consistency rather than isolated mention disambiguation.

preprint2022arXiv

Identifying causal relations in tweets using deep learning: Use case on diabetes-related tweets from 2017-2021

Objective: Leveraging machine learning methods, we aim to extract both explicit and implicit cause-effect associations in patient-reported, diabetes-related tweets and provide a tool to better understand opinion, feelings and observations shared within the diabetes online community from a causality perspective. Materials and Methods: More than 30 million diabetes-related tweets in English were collected between April 2017 and January 2021. Deep learning and natural language processing methods were applied to focus on tweets with personal and emotional content. A cause-effect-tweet dataset was manually labeled and used to train 1) a fine-tuned Bertweet model to detect causal sentences containing a causal association 2) a CRF model with BERT based features to extract possible cause-effect associations. Causes and effects were clustered in a semi-supervised approach and visualised in an interactive cause-effect-network. Results: Causal sentences were detected with a recall of 68% in an imbalanced dataset. A CRF model with BERT based features outperformed a fine-tuned BERT model for cause-effect detection with a macro recall of 68%. This led to 96,676 sentences with cause-effect associations. "Diabetes" was identified as the central cluster followed by "Death" and "Insulin". Insulin pricing related causes were frequently associated with "Death". Conclusions: A novel methodology was developed to detect causal sentences and identify both explicit and implicit, single and multi-word cause and corresponding effect as expressed in diabetes-related tweets leveraging BERT-based architectures and visualised as cause-effect-network. Extracting causal associations on real-life, patient reported outcomes in social media data provides a useful complementary source of information in diabetes research.

preprint2022arXiv

Learning structures of the French clinical language:development and validation of word embedding models using 21 million clinical reports from electronic health records

Background Clinical studies using real-world data may benefit from exploiting clinical reports, a particularly rich albeit unstructured medium. To that end, natural language processing can extract relevant information. Methods based on transfer learning using pre-trained language models have achieved state-of-the-art results in most NLP applications; however, publicly available models lack exposure to speciality-languages, especially in the medical field. Objective We aimed to evaluate the impact of adapting a language model to French clinical reports on downstream medical NLP tasks. Methods We leveraged a corpus of 21M clinical reports collected from August 2017 to July 2021 at the Greater Paris University Hospitals (APHP) to produce two CamemBERT architectures on speciality language: one retrained from scratch and the other using CamemBERT as its initialisation. We used two French annotated medical datasets to compare our language models to the original CamemBERT network, evaluating the statistical significance of improvement with the Wilcoxon test. Results Our models pretrained on clinical reports increased the average F1-score on APMed (an APHP-specific task) by 3 percentage points to 91%, a statistically significant improvement. They also achieved performance comparable to the original CamemBERT on QUAERO. These results hold true for the fine-tuned and from-scratch versions alike, starting from very few pre-training samples. Conclusions We confirm previous literature showing that adapting generalist pre-train language models such as CamenBERT on speciality corpora improves their performance for downstream clinical NLP tasks. Our results suggest that retraining from scratch does not induce a statistically significant performance gain compared to fine-tuning.

preprint2014arXiv

Evaluating Temporal Graphs Built from Texts via Transitive Reduction

Temporal information has been the focus of recent attention in information extraction, leading to some standardization effort, in particular for the task of relating events in a text. This task raises the problem of comparing two annotations of a given text, because relations between events in a story are intrinsically interdependent and cannot be evaluated separately. A proper evaluation measure is also crucial in the context of a machine learning approach to the problem. Finding a common comparison referent at the text level is not obvious, and we argue here in favor of a shift from event-based measures to measures on a unique textual object, a minimal underlying temporal graph, or more formally the transitive reduction of the graph of relations between event boundaries. We support it by an investigation of its properties on synthetic data and on a well-know temporal corpus.