Richard Dufour

Yanis Labrak, Adrien Bazoge, Richard Dufour et al.

In recent years, pre-trained language models (PLMs) achieve the best performance on a wide range of natural language processing (NLP) tasks. While the first models were trained on general domain data, specialized ones have emerged to more effectively treat specific domains. In this paper, we propose an original study of PLMs in the medical domain on French language. We compare, for the first time, the performance of PLMs trained on both public data from the web and private data from healthcare establishments. We also evaluate different learning strategies on a set of biomedical tasks. In particular, we show that we can take advantage of already existing biomedical PLMs in a foreign language by further pre-train it on our targeted data. Finally, we release the first specialized PLMs for the biomedical field in French, called DrBERT, as well as the largest corpus of medical data under free license on which these models are trained.

Qingyu Chen, Alexis Allot, Robert Leaman et al.

The COVID-19 pandemic has been severely impacting global society since December 2019. Massive research has been undertaken to understand the characteristics of the virus and design vaccines and drugs. The related findings have been reported in biomedical literature at a rate of about 10,000 articles on COVID-19 per month. Such rapid growth significantly challenges manual curation and interpretation. For instance, LitCovid is a literature database of COVID-19-related articles in PubMed, which has accumulated more than 200,000 articles with millions of accesses each month by users worldwide. One primary curation task is to assign up to eight topics (e.g., Diagnosis and Treatment) to the articles in LitCovid. Despite the continuing advances in biomedical text mining methods, few have been dedicated to topic annotations in COVID-19 literature. To close the gap, we organized the BioCreative LitCovid track to call for a community effort to tackle automated topic annotation for COVID-19 literature. The BioCreative LitCovid dataset, consisting of over 30,000 articles with manually reviewed topics, was created for training and testing. It is one of the largest multilabel classification datasets in biomedical scientific literature. 19 teams worldwide participated and made 80 submissions in total. Most teams used hybrid systems based on transformers. The highest performing submissions achieved 0.8875, 0.9181, and 0.9394 for macro F1-score, micro F1-score, and instance-based F1-score, respectively. The level of participation and results demonstrate a successful track and help close the gap between dataset curation and method development. The dataset is publicly available via https://ftp.ncbi.nlm.nih.gov/pub/lu/LitCovid/biocreative/ for benchmarking and further development.

Yanis Labrak, Mickael Rouvier, Richard Dufour

We evaluate four state-of-the-art instruction-tuned large language models (LLMs) -- ChatGPT, Flan-T5 UL2, Tk-Instruct, and Alpaca -- on a set of 13 real-world clinical and biomedical natural language processing (NLP) tasks in English, such as named-entity recognition (NER), question-answering (QA), relation extraction (RE), etc. Our overall results demonstrate that the evaluated LLMs begin to approach performance of state-of-the-art models in zero- and few-shot scenarios for most tasks, and particularly well for the QA task, even though they have never seen examples from these tasks before. However, we observed that the classification and RE tasks perform below what can be achieved with a specifically trained model for the medical field, such as PubMedBERT. Finally, we noted that no LLM outperforms all the others on all the studied tasks, with some models being better suited for certain tasks than others.

Yanis Labrak, Adrien Bazoge, Emmanuel Morin et al.

Large Language Models (LLMs) have demonstrated remarkable versatility in recent years, offering potential applications across specialized domains such as healthcare and medicine. Despite the availability of various open-source LLMs tailored for health contexts, adapting general-purpose LLMs to the medical domain presents significant challenges. In this paper, we introduce BioMistral, an open-source LLM tailored for the biomedical domain, utilizing Mistral as its foundation model and further pre-trained on PubMed Central. We conduct a comprehensive evaluation of BioMistral on a benchmark comprising 10 established medical question-answering (QA) tasks in English. We also explore lightweight models obtained through quantization and model merging approaches. Our results demonstrate BioMistral's superior performance compared to existing open-source medical models and its competitive edge against proprietary counterparts. Finally, to address the limited availability of data beyond English and to assess the multilingual generalization of medical LLMs, we automatically translated and evaluated this benchmark into 7 other languages. This marks the first large-scale multilingual evaluation of LLMs in the medical domain. Datasets, multilingual evaluation benchmarks, scripts, and all the models obtained during our experiments are freely released.

Thibault Bañeras-Roux, Shashi Kumar, Driss Khalil et al.

Automatic Speech Recognition (ASR) is traditionally evaluated using Word Error Rate (WER), a metric that is insensitive to meaning. Embedding-based semantic metrics are better correlated with human perception, but decoder-based Large Language Models (LLMs) remain underexplored for this task. This paper evaluates their relevance through three approaches: (1) selecting the best hypothesis between two candidates, (2) computing semantic distance using generative embeddings, and (3) qualitative classification of errors. On the HATS dataset, the best LLMs achieve 92--94\% agreement with human annotators for hypothesis selection, compared to 63\% for WER, also outperforming semantic metrics. Embeddings from decoder-based LLMs show performance comparable to encoder models. Finally, LLMs offer a promising direction for interpretable and semantic ASR evaluation.

Arthur Amalvy, Vincent Labatut, Richard Dufour

Named Entity Recognition (NER) is a low-level task often used as a foundation for solving higher level NLP problems. In the context of character detection in novels, NER false negatives can be an issue as they possibly imply missing certain characters or relationships completely. In this article, we demonstrate that applying a straightforward data augmentation technique allows training a model achieving higher recall, at the cost of a certain amount of precision regarding ambiguous entities. We show that this decrease in precision can be mitigated by giving the model more local context, which resolves some of the ambiguities.

Thibault Bañeras-Roux, Mickaël Rouvier, Jane Wottawa et al.

Evaluating automatic speech recognition (ASR) systems is a classical but difficult and still open problem, which often boils down to focusing only on the word error rate (WER). However, this metric suffers from many limitations and does not allow an in-depth analysis of automatic transcription errors. In this paper, we propose to study and understand the impact of rescoring using language models in ASR systems by means of several metrics often used in other natural language processing (NLP) tasks in addition to the WER. In particular, we introduce two measures related to morpho-syntactic and semantic aspects of transcribed words: 1) the POSER (Part-of-speech Error Rate), which should highlight the grammatical aspects, and 2) the EmbER (Embedding Error Rate), a measurement that modifies the WER by providing a weighting according to the semantic distance of the wrongly transcribed words. These metrics illustrate the linguistic contributions of the language models that are applied during a posterior rescoring step on transcription hypotheses.

Thibault Bañeras Roux, Jane Wottawa, Mickael Rouvier et al.

Conventionally, Automatic Speech Recognition (ASR) systems are evaluated on their ability to correctly recognize each word contained in a speech signal. In this context, the word error rate (WER) metric is the reference for evaluating speech transcripts. Several studies have shown that this measure is too limited to correctly evaluate an ASR system, which has led to the proposal of other variants of metrics (weighted WER, BERTscore, semantic distance, etc.). However, they remain system-oriented, even when transcripts are intended for humans. In this paper, we firstly present Human Assessed Transcription Side-by-side (HATS), an original French manually annotated data set in terms of human perception of transcription errors produced by various ASR systems. 143 humans were asked to choose the best automatic transcription out of two hypotheses. We investigated the relationship between human preferences and various ASR evaluation metrics, including lexical and embedding-based ones, the latter being those that correlate supposedly the most with human perception.

Thibault Bañeras-Roux, Mickael Rouvier, Jane Wottawa et al.

The most commonly used metrics for evaluating automatic speech transcriptions, namely Word Error Rate (WER) and Character Error Rate (CER), have been heavily criticized for their poor correlation to human perception and their inability to take into account linguistic and semantic information. While metric-based embeddings, seeking to approximate human perception, have been proposed, their scores remain difficult to interpret, unlike WER and CER. In this article, we overcome this problem by proposing a paradigm that consists in incorporating a chosen metric into it in order to obtain an equivalent of the error rate: a Minimum Edit Distance (minED). This approach parallels transcription errors with their human perception, also allowing an original study of the severity of these errors from a human perspective.

Noé Cecillon, Vincent Labatut, Richard Dufour et al.

Graphs are ubiquitous for modeling complex systems involving structured data and relationships. Consequently, graph representation learning, which aims to automatically learn low-dimensional representations of graphs, has drawn a lot of attention in recent years. The overwhelming majority of existing methods handle unsigned graphs. However, signed graphs appear in an increasing number of application domains to model systems involving two types of opposed relationships. Several authors took an interest in signed graphs and proposed methods for providing vertex-level representations, but only one exists for whole-graph representations, and it can handle only fully connected graphs. In this article, we tackle this issue by proposing two approaches to learning whole-graph representations of general signed graphs. The first is a SG2V, a signed generalization of the whole-graph embedding method Graph2vec that relies on a modification of the Weisfeiler--Lehman relabelling procedure. The second one is WSGCN, a whole-graph generalization of the signed vertex embedding method SGCN that relies on the introduction of master nodes into the GCN. We propose several variants of both these approaches. A bottleneck in the development of whole-graph-oriented methods is the lack of data. We constitute a benchmark composed of three collections of signed graphs with corresponding ground truths. We assess our methods on this benchmark, and our results show that the signed whole-graph methods learn better representations for this task. Overall, the baseline obtains an F-measure score of 58.57, when SG2V and WSGCN reach 73.01 and 81.20, respectively. Our source code and benchmark dataset are both publicly available online.

Arthur Amalvy, Vincent Labatut, Richard Dufour

While recent pre-trained transformer-based models can perform named entity recognition (NER) with great accuracy, their limited range remains an issue when applied to long documents such as whole novels. To alleviate this issue, a solution is to retrieve relevant context at the document level. Unfortunately, the lack of supervision for such a task means one has to settle for unsupervised approaches. Instead, we propose to generate a synthetic context retrieval training dataset using Alpaca, an instructiontuned large language model (LLM). Using this dataset, we train a neural context retriever based on a BERT model that is able to find relevant context for NER. We show that our method outperforms several retrieval baselines for the NER task on an English literary dataset composed of the first chapter of 40 books.

Kélian Estève, Salima Mhdaffar, Mickael Rouvier et al.

Neural speech codecs are increasingly used as intermediate representations in codec-based speech generation systems. TiCodec introduces a factorized representation that separates time-varying speech content from time-invariant information through a Time-Invariant Representation Extraction (TIRE) module, potentially reducing the amount of information that must be modeled at the frame-level. In this work, we investigate the nature of the information captured by TIRE representations and their suitability for low-latency speech processing. Using a series of probing tasks, we analyze the influence of the encoder layer and show that intermediate layers capture complementary speaker- and environment-related information while containing little linguistic content. We further study several segment selection strategies for TIRE training and demonstrate that cross-file sampling improves the robustness of invariant representations. Based on these findings, we propose Dual-TIRE, a multi-level architecture that exploits the complementarity of different encoder layers and improves speech reconstruction quality and speaker similarity. Finally, we evaluate TiCodec in a streaming inference setting using successive 660ms processing blocks. Results show that streaming operation can be achieved without significant degradation in reconstruction performance, highlighting the potential of factorized neural codec representations for future low-latency speech generation systems.

Arthur Amalvy, Vincent Labatut, Richard Dufour

Renard (Relationships Extraction from NARrative Documents) is a Python library that allows users to define custom natural language processing (NLP) pipelines to extract character networks from narrative texts. Contrary to the few existing tools, Renard can extract dynamic networks, as well as the more common static networks. Renard pipelines are modular: users can choose the implementation of each NLP subtask needed to extract a character network. This allows users to specialize pipelines to particular types of texts and to study the impact of each subtask on the extracted network.

Yanis Labrak, Adrien Bazoge, Oumaima El Khettari et al.

The biomedical domain has sparked a significant interest in the field of Natural Language Processing (NLP), which has seen substantial advancements with pre-trained language models (PLMs). However, comparing these models has proven challenging due to variations in evaluation protocols across different models. A fair solution is to aggregate diverse downstream tasks into a benchmark, allowing for the assessment of intrinsic PLMs qualities from various perspectives. Although still limited to few languages, this initiative has been undertaken in the biomedical field, notably English and Chinese. This limitation hampers the evaluation of the latest French biomedical models, as they are either assessed on a minimal number of tasks with non-standardized protocols or evaluated using general downstream tasks. To bridge this research gap and account for the unique sensitivities of French, we present the first-ever publicly available French biomedical language understanding benchmark called DrBenchmark. It encompasses 20 diversified tasks, including named-entity recognition, part-of-speech tagging, question-answering, semantic textual similarity, and classification. We evaluate 8 state-of-the-art pre-trained masked language models (MLMs) on general and biomedical-specific data, as well as English specific MLMs to assess their cross-lingual capabilities. Our experiments reveal that no single model excels across all tasks, while generalist models are sometimes still competitive.

Léane Jourdan, Nicolas Hernandez, Richard Dufour et al.

Revision is a crucial step in scientific writing, where authors refine their work to improve clarity, structure, and academic quality. Existing approaches to automated writing assistance often focus on sentence-level revisions, which fail to capture the broader context needed for effective modification. In this paper, we explore the impact of shifting from sentence-level to paragraph-level scope for the task of scientific text revision. The paragraph level definition of the task allows for more meaningful changes, and is guided by detailed revision instructions rather than general ones. To support this task, we introduce ParaRev, the first dataset of revised scientific paragraphs with an evaluation subset manually annotated with revision instructions. Our experiments demonstrate that using detailed instructions significantly improves the quality of automated revisions compared to general approaches, no matter the model or the metric considered.

Yanis Labrak, Adrien Bazoge, Beatrice Daille et al.

Subword tokenization has become the prevailing standard in the field of natural language processing (NLP) over recent years, primarily due to the widespread utilization of pre-trained language models. This shift began with Byte-Pair Encoding (BPE) and was later followed by the adoption of SentencePiece and WordPiece. While subword tokenization consistently outperforms character and word-level tokenization, the precise factors contributing to its success remain unclear. Key aspects such as the optimal segmentation granularity for diverse tasks and languages, the influence of data sources on tokenizers, and the role of morphological information in Indo-European languages remain insufficiently explored. This is particularly pertinent for biomedical terminology, characterized by specific rules governing morpheme combinations. Despite the agglutinative nature of biomedical terminology, existing language models do not explicitly incorporate this knowledge, leading to inconsistent tokenization strategies for common terms. In this paper, we seek to delve into the complexities of subword tokenization in French biomedical domain across a variety of NLP tasks and pinpoint areas where further enhancements can be made. We analyze classical tokenization algorithms, including BPE and SentencePiece, and introduce an original tokenization strategy that integrates morpheme-enriched word segmentation into existing tokenization methods.

Yanis Labrak, Richard Dufour, Mickaël Rouvier

This paper investigates discrete unit representations in Speech Language Models (SLMs), focusing on optimizing speech modeling during continual pre-training. In this paper, we systematically examine how model architecture, data representation, and training robustness influence the pre-training stage in which we adapt existing pre-trained language models to the speech modality. Our experiments highlight the role of speech encoders and clustering granularity across different model scales, showing how optimal discretization strategies vary with model capacity. By examining cluster distribution and phonemic alignments, we investigate the effective use of discrete vocabulary, uncovering both linguistic and paralinguistic patterns. Additionally, we explore the impact of clustering data selection on model robustness, highlighting the importance of domain matching between discretization training and target applications.

Adrien Bazoge, Pacôme Constant dit Beaufils, Mohammed Hmitouch et al.

Social determinants of health (SDoH) significantly influence health outcomes, shaping disease progression, treatment adherence, and health disparities. However, their documentation in structured electronic health records (EHRs) is often incomplete or missing. This study presents an approach based on large language models (LLMs) for extracting 13 SDoH categories from French clinical notes. We trained Flan-T5-Large on annotated social history sections from clinical notes at Nantes University Hospital, France. We evaluated the model at two levels: (i) identification of SDoH categories and associated values, and (ii) extraction of detailed SDoH with associated temporal and quantitative information. The model performance was assessed across four datasets, including two that we publicly release as open resources. The model achieved strong performance for identifying well-documented categories such as living condition, marital status, descendants, job, tobacco, and alcohol use (F1 score > 0.80). Performance was lower for categories with limited training data or highly variable expressions, such as employment status, housing, physical activity, income, and education. Our model identified 95.8% of patients with at least one SDoH, compared to 2.8% for ICD-10 codes from structured EHR data. Our error analysis showed that performance limitations were linked to annotation inconsistencies, reliance on English-centric tokenizer, and reduced generalizability due to the model being trained on social history sections only. These results demonstrate the effectiveness of NLP in improving the completeness of real-world SDoH data in a non-English EHR system.

Antoine Tholly, Jane Wottawa, Mickael Rouvier et al.

Automatic Speech Recognition (ASR) transcription errors are commonly assessed using metrics that compare them with a reference transcription, such as Word Error Rate (WER), which measures spelling deviations from the reference, or semantic score-based metrics. However, these approaches often overlook what is understandable to humans when interpreting transcription errors. To address this limitation, a new evaluation is proposed that categorizes errors into four levels of severity, further divided into subtypes, based on objective linguistic criteria, contextual patterns, and the use of content words as the unit of analysis. This metric is applied to a benchmark of 10 state-of-the-art ASR systems on French language, encompassing both HMM-based and end-to-end models. Our findings reveal the strengths and weaknesses of each system, identifying those that provide the most comfortable reading experience for users.

Julien Aubert-Béduchaud, Florian Boudin, Béatrice Daille et al.

Familiarizing oneself with a new scientific field and its existing literature can be daunting due to the large amount of available articles. Curated lists of academic references, or reading lists, compiled by experts, offer a structured way to gain a comprehensive overview of a domain or a specific scientific challenge. In this work, we introduce ACL-rlg, the largest open expert-annotated reading list dataset. We also provide multiple baselines for evaluating reading list generation and formally define it as a retrieval task. Our qualitative study highlights the fact that traditional scholarly search engines and indexing methods perform poorly on this task, and GPT-4o, despite showing better results, exhibits signs of potential data contamination.

Arthur Amalvy, Vincent Labatut, Richard Dufour

The automatic extraction of character networks from literary texts is generally carried out using natural language processing (NLP) cascading pipelines. While this approach is widespread, no study exists on the impact of low-level NLP tasks on their performance. In this article, we conduct such a study on a literary dataset, focusing on the role of named entity recognition (NER) and coreference resolution when extracting co-occurrence networks. To highlight the impact of these tasks' performance, we start with gold-standard annotations, progressively add uniformly distributed errors, and observe their impact in terms of character network quality. We demonstrate that NER performance depends on the tested novel and strongly affects character detection. We also show that NER-detected mentions alone miss a lot of character co-occurrences, and that coreference resolution is needed to prevent this. Finally, we present comparison points with 2 methods based on large language models (LLMs), including a fully end-to-end one, and show that these models are outperformed by traditional NLP pipelines in terms of recall.

Yanis Labrak, Adel Moumen, Richard Dufour et al.

In the rapidly evolving landscape of spoken question-answering (SQA), the integration of large language models (LLMs) has emerged as a transformative development. Conventional approaches often entail the use of separate models for question audio transcription and answer selection, resulting in significant resource utilization and error accumulation. To tackle these challenges, we explore the effectiveness of end-to-end (E2E) methodologies for SQA in the medical domain. Our study introduces a novel zero-shot SQA approach, compared to traditional cascade systems. Through a comprehensive evaluation conducted on a new open benchmark of 8 medical tasks and 48 hours of synthetic audio, we demonstrate that our approach requires up to 14.7 times fewer resources than a combined 1.3B parameters LLM with a 1.55B parameters ASR model while improving average accuracy by 0.5\%. These findings underscore the potential of E2E methodologies for SQA in resource-constrained contexts.

Arthur Amalvy, Vincent Labatut, Richard Dufour

Pre-trained transformer-based models have recently shown great performance when applied to Named Entity Recognition (NER). As the complexity of their self-attention mechanism prevents them from processing long documents at once, these models are usually applied in a sequential fashion. Such an approach unfortunately only incorporates local context and prevents leveraging global document context in long documents such as novels, which might hinder performance. In this article, we explore the impact of global document context, and its relationships with local context. We find that correctly retrieving global document context has a greater impact on performance than only leveraging local context, prompting for further research on how to better retrieve that context.

Etienne Papegnies, Vincent Labatut, Richard Dufour et al.

Moderation of user-generated content in an online community is a challenge that has great socio-economical ramifications. However, the costs incurred by delegating this work to human agents are high. For this reason, an automatic system able to detect abuse in user-generated content is of great interest. There are a number of ways to tackle this problem, but the most commonly seen in practice are word filtering or regular expression matching. The main limitations are their vulnerability to intentional obfuscation on the part of the users, and their context-insensitive nature. Moreover, they are language-dependent and may require appropriate corpora for training. In this paper, we propose a system for automatic abuse detection that completely disregards message content. We first extract a conversational network from raw chat logs and characterize it through topological measures. We then use these as features to train a classifier on our abuse detection task. We thoroughly assess our system on a dataset of user comments originating from a French Massively Multiplayer Online Game. We identify the most appropriate network extraction parameters and discuss the discriminative power of our features, relatively to their topological and temporal nature. Our method reaches an F-measure of 83.89 when using the full feature set, improving on existing approaches. With a selection of the most discriminative features, we dramatically cut computing time while retaining most of the performance (82.65).

Etienne Papegnies, Vincent Labatut, Richard Dufour et al.

Online communities have gained considerable importance in recent years due to the increasing number of people connected to the Internet. Moderating user content in online communities is mainly performed manually, and reducing the workload through automatic methods is of great financial interest for community maintainers. Often, the industry uses basic approaches such as bad words filtering and regular expression matching to assist the moderators. In this article, we consider the task of automatically determining if a message is abusive. This task is complex since messages are written in a non-standardized way, including spelling errors, abbreviations, community-specific codes... First, we evaluate the system that we propose using standard features of online messages. Then, we evaluate the impact of the addition of pre-processing strategies, as well as original specific features developed for the community of an online in-browser strategy game. We finally propose to analyze the usefulness of this wide range of features using feature selection. This work can lead to two possible applications: 1) automatically flag potentially abusive messages to draw the moderator's attention on a narrow subset of messages ; and 2) fully automate the moderation process by deciding whether a message is abusive without any human intervention.

Mohamed Morchid, Juan-Manuel Torres-Moreno, Richard Dufour et al.

The number of documents available into Internet moves each day up. For this reason, processing this amount of information effectively and expressibly becomes a major concern for companies and scientists. Methods that represent a textual document by a topic representation are widely used in Information Retrieval (IR) to process big data such as Wikipedia articles. One of the main difficulty in using topic model on huge data collection is related to the material resources (CPU time and memory) required for model estimate. To deal with this issue, we propose to build topic spaces from summarized documents. In this paper, we present a study of topic space representation in the context of big data. The topic space representation behavior is analyzed on different languages. Experiments show that topic spaces estimated from text summaries are as relevant as those estimated from the complete documents. The real advantage of such an approach is the processing time gain: we showed that the processing time can be drastically reduced using summarized documents (more than 60\% in general). This study finally points out the differences between thematic representations of documents depending on the targeted languages such as English or latin languages.

Xavier Bost, Ilaria Brunetti, Luis Adrián Cabrera-Diego et al.

The 2013 Défi de Fouille de Textes (DEFT) campaign is interested in two types of language analysis tasks, the document classification and the information extraction in the specialized domain of cuisine recipes. We present the systems that the LIA has used in DEFT 2013. Our systems show interesting results, even though the complexity of the proposed tasks.

Mohamed Bouaziz, Mohamed Morchid, Richard Dufour et al.

Recently, machine learning methods have provided a broad spectrum of original and efficient algorithms based on Deep Neural Networks (DNN) to automatically predict an outcome with respect to a sequence of inputs. Recurrent hidden cells allow these DNN-based models to manage long-term dependencies such as Recurrent Neural Networks (RNN) and Long Short-Term Memory (LSTM). Nevertheless, these RNNs process a single input stream in one (LSTM) or two (Bidirectional LSTM) directions. But most of the information available nowadays is from multistreams or multimedia documents, and require RNNs to process these information synchronously during the training. This paper presents an original LSTM-based architecture, named Parallel LSTM (PLSTM), that carries out multiple parallel synchronized input sequences in order to predict a common output. The proposed PLSTM method could be used for parallel sequence classification purposes. The PLSTM approach is evaluated on an automatic telecast genre sequences classification task and compared with different state-of-the-art architectures. Results show that the proposed PLSTM method outperforms the baseline n-gram models as well as the state-of-the-art LSTM approach.