Low-resource Information Extraction with the European Clinical Case Corpus

We present E3C-3.0, a multilingual dataset in the medical domain, comprising clinical cases annotated with diseases and test-result relations. The dataset includes both native texts in five languages (English, French, Italian, Spanish and Basque) and texts translated and projected from the English source into five target languages (Greek, Italian, Polish, Slovak, and Slovenian). A semi-automatic approach has been implemented, including automatic annotation projection based on Large Language Models (LLMs) and human revision. We present several experiments showing that current state-of-the-art LLMs can benefit from being fine-tuned on the E3C-3.0 dataset. We also show that transfer learning in different languages is very effective, mitigating the scarcity of data. Finally, we compare performance both on native data and on projected data. We release the data at https://huggingface.co/collections/NLP-FBK/e3c-projected-676a7d6221608d60e4e9fd89 .

CoRLD: Contrastive Representation Learning Of Deformable Shapes In Images

Deformable shape representations, parameterized by deformations relative to a given template, have proven effective for improved image analysis tasks. However, their broader applicability is hindered by two major challenges. First, existing methods mainly rely on a known template during testing, which is impractical and limits flexibility. Second, they often struggle to capture fine-grained, voxel-level distinctions between similar shapes (e.g., anatomical variations among healthy individuals, those with mild cognitive impairment, and diseased states). To address these limitations, we propose a novel framework - Contrastive Representation Learning of Deformable shapes (CoRLD) in learned deformation spaces and demonstrate its effectiveness in the context of image classification. Our CoRLD leverages a class-aware contrastive supervised learning objective in latent deformation spaces, promoting proximity among representations of similar classes while ensuring separation of dissimilar groups. In contrast to previous deep learning networks that require a reference image as input to predict deformation changes, our approach eliminates this dependency. Instead, template images are utilized solely as ground truth in the loss function during the training process, making our model more flexible and generalizable to a wide range of medical applications. We validate CoRLD on diverse datasets, including real brain magnetic resonance imaging (MRIs) and adrenal shapes derived from computed tomography (CT) scans. Experimental results show that our model effectively extracts deformable shape features, which can be easily integrated with existing classifiers to substantially boost the classification accuracy. Our code is available at GitHub.

Causal Tree Extraction from Medical Case Reports: A Novel Task for Experts-like Text Comprehension

Extracting causal relationships from a medical case report is essential for comprehending the case, particularly its diagnostic process. Since the diagnostic process is regarded as a bottom-up inference, causal relationships in cases naturally form a multi-layered tree structure. The existing tasks, such as medical relation extraction, are insufficient for capturing the causal relationships of an entire case, as they treat all relations equally without considering the hierarchical structure inherent in the diagnostic process. Thus, we propose a novel task, Causal Tree Extraction (CTE), which receives a case report and generates a causal tree with the primary disease as the root, providing an intuitive understanding of a case's diagnostic process. Subsequently, we construct a Japanese case report CTE dataset, J-Casemap, propose a generation-based CTE method that outperforms the baseline by 20.2 points in the human evaluation, and introduce evaluation metrics that reflect clinician preferences. Further experiments also show that J-Casemap enhances the performance of solving other medical tasks, such as question answering.

PlainQAFact: Automatic Factuality Evaluation Metric for Biomedical Plain Language Summaries Generation

Hallucinated outputs from language models pose risks in the medical domain, especially for lay audiences making health-related decisions. Existing factuality evaluation methods, such as entailment- and question-answering-based (QA), struggle with plain language summary (PLS) generation due to elaborative explanation phenomenon, which introduces external content (e.g., definitions, background, examples) absent from the source document to enhance comprehension. To address this, we introduce PlainQAFact, a framework trained on a fine-grained, human-annotated dataset PlainFact, to evaluate the factuality of both source-simplified and elaboratively explained sentences. PlainQAFact first classifies factuality type and then assesses factuality using a retrieval-augmented QA-based scoring method. Our approach is lightweight and computationally efficient. Empirical results show that existing factuality metrics fail to effectively evaluate factuality in PLS, especially for elaborative explanations, whereas PlainQAFact achieves state-of-the-art performance. We further analyze its effectiveness across external knowledge sources, answer extraction strategies, overlap measures, and document granularity levels, refining its overall factuality assessment.

Leveraging Semantic Type Dependencies for Clinical Named Entity Recognition

Previous work on clinical relation extraction from free-text sentences leveraged information about semantic types from clinical knowledge bases as a part of entity representations. In this paper, we exploit additional evidence by also making use of domain-specific semantic type dependencies. We encode the relation between a span of tokens matching a Unified Medical Language System (UMLS) concept and other tokens in the sentence. We implement our method and compare against different named entity recognition (NER) architectures (i.e., BiLSTM-CRF and BiLSTM-GCN-CRF) using different pre-trained clinical embeddings (i.e., BERT, BioBERT, UMLSBert). Our experimental results on clinical datasets show that in some cases NER effectiveness can be significantly improved by making use of domain-specific semantic type dependencies. Our work is also the first study generating a matrix encoding to make use of more than three dependencies in one pass for the NER task.

EPEE: Towards Efficient and Effective Foundation Models in Biomedicine

Foundation models, including language models, e.g., GPT, and vision models, e.g., CLIP, have significantly advanced numerous biomedical tasks. Despite these advancements, the high inference latency and the "overthinking" issues in model inference impair the efficiency and effectiveness of foundation models, thus limiting their application in real-time clinical settings. To address these challenges, we proposed EPEE (Entropy- and Patience-based Early Exiting), a novel hybrid strategy designed to improve the inference efficiency of foundation models. The core idea was to leverage the strengths of entropy-based and patience-based early exiting methods to overcome their respective weaknesses. To evaluate EPEE, we conducted experiments on three core biomedical tasks-classification, relation extraction, and event extraction-using four foundation models (BERT, ALBERT, GPT-2, and ViT) across twelve datasets, including clinical notes and medical images. The results showed that EPEE significantly reduced inference time while maintaining or improving accuracy, demonstrating its adaptability to diverse datasets and tasks. EPEE addressed critical barriers to deploying foundation models in healthcare by balancing efficiency and effectiveness. It potentially provided a practical solution for real-time clinical decision-making with foundation models, supporting reliable and efficient workflows.

To Vaccinate or not to Vaccinate? Analyzing $\mathbb{X}$ Power over the Pandemic

The COVID-19 pandemic has profoundly affected the normal course of life -- from lock-downs and virtual meetings to the unprecedentedly swift creation of vaccines. To halt the COVID-19 pandemic, the world has started preparing for the global vaccine roll-out. In an effort to navigate the immense volume of information about COVID-19, the public has turned to social networks. Among them, $\mathbb{X}$ (formerly Twitter) has played a key role in distributing related information. Most people are not trained to interpret medical research and remain skeptical about the efficacy of new vaccines. Measuring their reactions and perceptions is gaining significance in the fight against COVID-19. To assess the public perception regarding the COVID-19 vaccine, our work applies a sentiment analysis approach, using natural language processing of $\mathbb{X}$ data. We show how to use textual analytics and textual data visualization to discover early insights (for example, by analyzing the most frequently used keywords and hashtags). Furthermore, we look at how people's sentiments vary across the countries. Our results indicate that although the overall reaction to the vaccine is positive, there are also negative sentiments associated with the tweets, especially when examined at the country level. Additionally, from the extracted tweets, we manually labeled 100 tweets as positive and 100 tweets as negative and trained various One-Class Classifiers (OCCs). The experimental results indicate that the S-SVDD classifiers outperform other OCCs.

A Novel Retinial Image Contrast Enhancement -- Fuzzy-Based Method

The vascular structure in retinal images plays a crucial role in ophthalmic diagnostics, and its accuracies are directly influenced by the quality of the retinal image. Contrast enhancement is one of the crucial steps in any segmentation algorithm - the more so since the retinal images are related to medical diagnosis. Contrast enhancement is a vital step that not only intensifies the darkness of the blood vessels but also prevents minor capillaries from being disregarded during the process. This paper proposes a novel model that utilizes the linear blending of Fuzzy Contrast Enhancement (FCE) and Contrast Limited Adaptive Histogram Equalization (CLAHE) to enhance the retinal image for retinal vascular structure segmentation. The scheme is tested using the Digital Retinal Images for Vessel Extraction (DRIVE) dataset. The assertion was then evaluated through performance comparison among other methodologies which are Gray-scaling, Histogram Equalization (HE), FCE, and CLAHE. It was evident in this paper that the combination of FCE and CLAHE methods showed major improvement. Both FCE and CLAHE methods dominating with 88% as better enhancement methods proved that preprocessing through fuzzy logic is effective.

The Joint Entity-Relation Extraction Model Based on Span and Interactive Fusion Representation for Chinese Medical Texts with Complex Semantics

Joint entity-relation extraction is a critical task in transforming unstructured or semi-structured text into triplets, facilitating the construction of large-scale knowledge graphs, and supporting various downstream applications. Despite its importance, research on Chinese text, particularly with complex semantics in specialized domains like medicine, remains limited. To address this gap, we introduce the CH-DDI, a Chinese drug-drug interactions dataset designed to capture the intricacies of medical text. Leveraging the strengths of attention mechanisms in capturing long-range dependencies, we propose the SEA module, which enhances the extraction of complex contextual semantic information, thereby improving entity recognition and relation extraction. Additionally, to address the inefficiencies of existing methods in facilitating information exchange between entity recognition and relation extraction, we present an interactive fusion representation module. This module employs Cross Attention for bidirectional information exchange between the tasks and further refines feature extraction through BiLSTM. Experimental results on both our CH-DDI dataset and public CoNLL04 dataset demonstrate that our model exhibits strong generalization capabilities. On the CH-DDI dataset, our model achieves an F1-score of 96.73% for entity recognition and 78.43% for relation extraction. On the CoNLL04 dataset, it attains an entity recognition precision of 89.54% and a relation extraction accuracy of 71.64%.

MKE-Coder: Multi-Axial Knowledge with Evidence Verification in ICD Coding for Chinese EMRs

The task of automatically coding the International Classification of Diseases (ICD) in the medical field has been well-established and has received much attention. Automatic coding of the ICD in the medical field has been successful in English but faces challenges when dealing with Chinese electronic medical records (EMRs). The first issue lies in the difficulty of extracting disease code-related information from Chinese EMRs, primarily due to the concise writing style and specific internal structure of the EMRs. The second problem is that previous methods have failed to leverage the disease-based multi-axial knowledge and lack of association with the corresponding clinical evidence. This paper introduces a novel framework called MKE-Coder: Multi-axial Knowledge with Evidence verification in ICD coding for Chinese EMRs. Initially, we identify candidate codes for the diagnosis and categorize each of them into knowledge under four coding axes.Subsequently, we retrieve corresponding clinical evidence from the comprehensive content of EMRs and filter credible evidence through a scoring model. Finally, to ensure the validity of the candidate code, we propose an inference module based on the masked language modeling strategy. This module verifies that all the axis knowledge associated with the candidate code is supported by evidence and provides recommendations accordingly. To evaluate the performance of our framework, we conduct experiments using a large-scale Chinese EMR dataset collected from various hospitals. The experimental results demonstrate that MKE-Coder exhibits significant superiority in the task of automatic ICD coding based on Chinese EMRs. In the practical evaluation of our method within simulated real coding scenarios, it has been demonstrated that our approach significantly aids coders in enhancing both their coding accuracy and speed.