Automated medical image captioning translates complex radiological images into diagnostic narratives that can support reporting workflows. We present a Swin-BART encoder-decoder system with a lightweight regional attention module that amplifies diagnostically salient regions before cross-attention. Trained and evaluated on ROCO, our model achieves state-of-the-art semantic fidelity while remaining compact and interpretable. We report results as mean$\pm$std over three seeds and include $95\%$ confidence intervals. Compared with baselines, our approach improves ROUGE (proposed 0.603, ResNet-CNN 0.356, BLIP2-OPT 0.255) and BERTScore (proposed 0.807, BLIP2-OPT 0.645, ResNet-CNN 0.623), with competitive BLEU, CIDEr, and METEOR. We further provide ablations (regional attention on/off and token-count sweep), per-modality analysis (CT/MRI/X-ray), paired significance tests, and qualitative heatmaps that visualize the regions driving each description. Decoding uses beam search (beam size $=4$), length penalty $=1.1$, $no\_repeat\_ngram\_size$ $=3$, and max length $=128$. The proposed design yields accurate, clinically phrased captions and transparent regional attributions, supporting safe research use with a human in the loop.

Clinical conversations mix explicit directives (order a chest X-ray) with implicit reasoning (the cough worsened overnight, we should check for pneumonia). Many systems rely on LLM rewriting, adding latency, instability, and opacity that hinder real-time ordering. We present JEDA (Joint Embedding for Direct and Ambient clinical orders), a domain-initialized bi-encoder that retrieves canonical orders directly and, in a query-free mode, encodes a short rolling window of ambient dialogue to trigger retrieval. Initialized from PubMedBERT and fine-tuned with a duplicate-safe contrastive objective, JEDA aligns heterogeneous expressions of intent to shared order concepts. Training uses constrained LLM guidance to tie each signed order to complementary formulations (command only, context only, command+context, context+reasoning), producing clearer inter-order separation, tighter query extendash order coupling, and stronger generalization. The query-free mode is noise-resilient, reducing sensitivity to disfluencies and ASR errors by conditioning on a short window rather than a single utterance. Deployed in practice, JEDA yields large gains and substantially outperforms its base encoder and recent open embedders (Linq Embed Mistral, SFR Embedding, GTE Qwen, BGE large, Embedding Gemma). The result is a fast, interpretable, LLM-free retrieval layer that links ambient context to actionable clinical orders in real time.

Topic modeling is a useful tool for analyzing large corpora of written documents, particularly academic papers. Despite a wide variety of proposed topic modeling techniques, these techniques do not perform well when applied to medical texts. This can be due to the low number of documents available for some topics in the healthcare domain. In this paper, we propose ProtoTopic, a prototypical network-based topic model used for topic generation for a set of medical paper abstracts. Prototypical networks are efficient, explainable models that make predictions by computing distances between input datapoints and a set of prototype representations, making them particularly effective in low-data or few-shot learning scenarios. With ProtoTopic, we demonstrate improved topic coherence and diversity compared to two topic modeling baselines used in the literature, demonstrating the ability of our model to generate medically relevant topics even with limited data.

Academic misconduct detection in biomedical research remains challenging due to algorithmic narrowness in existing methods and fragmented analytical pipelines. We present BMDetect, a multimodal deep learning framework that integrates journal metadata (SJR, institutional data), semantic embeddings (PubMedBERT), and GPT-4o-mined textual attributes (methodological statistics, data anomalies) for holistic manuscript evaluation. Key innovations include: (1) multimodal fusion of domain-specific features to reduce detection bias; (2) quantitative evaluation of feature importance, identifying journal authority metrics (e.g., SJR-index) and textual anomalies (e.g., statistical outliers) as dominant predictors; and (3) the BioMCD dataset, a large-scale benchmark with 13,160 retracted articles and 53,411 controls. BMDetect achieves 74.33% AUC, outperforming single-modality baselines by 8.6%, and demonstrates transferability across biomedical subfields. This work advances scalable, interpretable tools for safeguarding research integrity.

Identifying immune checkpoint inhibitor (ICI) studies in genomic repositories like Gene Expression Omnibus (GEO) is vital for cancer research yet remains challenging due to semantic ambiguity, extreme class imbalance, and limited labeled data in low-resource settings. We present ProtoBERT-LoRA, a hybrid framework that combines PubMedBERT with prototypical networks and Low-Rank Adaptation (LoRA) for efficient fine-tuning. The model enforces class-separable embeddings via episodic prototype training while preserving biomedical domain knowledge. Our dataset was divided as: Training (20 positive, 20 negative), Prototype Set (10 positive, 10 negative), Validation (20 positive, 200 negative), and Test (71 positive, 765 negative). Evaluated on test dataset, ProtoBERT-LoRA achieved F1-score of 0.624 (precision: 0.481, recall: 0.887), outperforming the rule-based system, machine learning baselines and finetuned PubMedBERT. Application to 44,287 unlabeled studies reduced manual review efforts by 82%. Ablation studies confirmed that combining prototypes with LoRA improved performance by 29% over stand-alone LoRA.

Biomedical queries have become increasingly prevalent in web searches, reflecting the growing interest in accessing biomedical literature. Despite recent research on large-language models (LLMs) motivated by endeavours to attain generalized intelligence, their efficacy in replacing task and domain-specific natural language understanding approaches remains questionable. In this paper, we address this question by conducting a comprehensive empirical evaluation of intent detection and named entity recognition (NER) tasks from biomedical text. We show that Supervised Fine Tuned approaches are still relevant and more effective than general-purpose LLMs. Biomedical transformer models such as PubMedBERT can surpass ChatGPT on NER task with only 5 supervised examples.

Information extraction techniques, including named entity recognition (NER) and relation extraction (RE), are crucial in many domains to support making sense of vast amounts of unstructured text data by identifying and connecting relevant information. Such techniques can assist researchers in extracting valuable insights. In this paper, we introduce the Entity-aware Masking for Biomedical Relation Extraction (EMBRE) method for biomedical relation extraction, as applied in the context of the BioRED challenge Task 1, in which human-annotated entities are provided as input. Specifically, we integrate entity knowledge into a deep neural network by pretraining the backbone model with an entity masking objective. We randomly mask named entities for each instance and let the model identify the masked entity along with its type. In this way, the model is capable of learning more specific knowledge and more robust representations. Then, we utilize the pre-trained model as our backbone to encode language representations and feed these representations into two multilayer perceptron (MLPs) to predict the logits for relation and novelty, respectively. The experimental results demonstrate that our proposed method can improve the performances of entity pair, relation and novelty extraction over our baseline.

Objectives Extraction of PICO (Populations, Interventions, Comparison, and Outcomes) entities is fundamental to evidence retrieval. We present a novel method PICOX to extract overlapping PICO entities. Materials and Methods PICOX first identifies entities by assessing whether a word marks the beginning or conclusion of an entity. Then it uses a multi-label classifier to assign one or more PICO labels to a span candidate. PICOX was evaluated using one of the best-performing baselines, EBM-NLP, and three more datasets, i.e., PICO-Corpus, and RCT publications on Alzheimer's Disease or COVID-19, using entity-level precision, recall, and F1 scores. Results PICOX achieved superior precision, recall, and F1 scores across the board, with the micro F1 score improving from 45.05 to 50.87 (p << 0.01). On the PICO-Corpus, PICOX obtained higher recall and F1 scores than the baseline and improved the micro recall score from 56.66 to 67.33. On the COVID-19 dataset, PICOX also outperformed the baseline and improved the micro F1 score from 77.10 to 80.32. On the AD dataset, PICOX demonstrated comparable F1 scores with higher precision when compared to the baseline. Conclusion PICOX excels in identifying overlapping entities and consistently surpasses a leading baseline across multiple datasets. Ablation studies reveal that its data augmentation strategy effectively minimizes false positives and improves precision.

Pre-trained transformers are often fine-tuned to aid clinical decision-making using limited clinical notes. Model interpretability is crucial, especially in high-stakes domains like medicine, to establish trust and ensure safety, which requires human engagement. We introduce SUFO, a systematic framework that enhances interpretability of fine-tuned transformer feature spaces. SUFO utilizes a range of analytic and visualization techniques, including Supervised probing, Unsupervised similarity analysis, Feature dynamics, and Outlier analysis to address key questions about model trust and interpretability. We conduct a case study investigating the impact of pre-training data where we focus on real-world pathology classification tasks, and validate our findings on MedNLI. We evaluate five 110M-sized pre-trained transformer models, categorized into general-domain (BERT, TNLR), mixed-domain (BioBERT, Clinical BioBERT), and domain-specific (PubMedBERT) groups. Our SUFO analyses reveal that: (1) while PubMedBERT, the domain-specific model, contains valuable information for fine-tuning, it can overfit to minority classes when class imbalances exist. In contrast, mixed-domain models exhibit greater resistance to overfitting, suggesting potential improvements in domain-specific model robustness; (2) in-domain pre-training accelerates feature disambiguation during fine-tuning; and (3) feature spaces undergo significant sparsification during this process, enabling clinicians to identify common outlier modes among fine-tuned models as demonstrated in this paper. These findings showcase the utility of SUFO in enhancing trust and safety when using transformers in medicine, and we believe SUFO can aid practitioners in evaluating fine-tuned language models for other applications in medicine and in more critical domains.

Clinical classification of chest radiography is particularly challenging for standard machine learning algorithms due to its inherent long-tailed and multi-label nature. However, few attempts take into account the coupled challenges posed by both the class imbalance and label co-occurrence, which hinders their value to boost the diagnosis on chest X-rays (CXRs) in the real-world scenarios. Besides, with the prevalence of pretraining techniques, how to incorporate these new paradigms into the current framework lacks of the systematical study. This technical report presents a brief description of our solution in the ICCV CVAMD 2023 CXR-LT Competition. We empirically explored the effectiveness for CXR diagnosis with the integration of several advanced designs about data augmentation, feature extractor, classifier design, loss function reweighting, exogenous data replenishment, etc. In addition, we improve the performance through simple test-time data augmentation and ensemble. Our framework finally achieves 0.349 mAP on the competition test set, ranking in the top five.