Recent advancements in deep learning have shown transformative potential in medical imaging, yet concerns about fairness persist due to performance disparities across demographic subgroups. Existing methods aim to address these biases by mitigating sensitive attributes in image data; however, these attributes often carry clinically relevant information, and their removal can compromise model performance-a highly undesirable outcome. To address this challenge, we propose Fair Re-fusion After Disentanglement (FairREAD), a novel, simple, and efficient framework that mitigates unfairness by re-integrating sensitive demographic attributes into fair image representations. FairREAD employs orthogonality constraints and adversarial training to disentangle demographic information while using a controlled re-fusion mechanism to preserve clinically relevant details. Additionally, subgroup-specific threshold adjustments ensure equitable performance across demographic groups. Comprehensive evaluations on a large-scale clinical X-ray dataset demonstrate that FairREAD significantly reduces unfairness metrics while maintaining diagnostic accuracy, establishing a new benchmark for fairness and performance in medical image classification.

Training data attribution (TDA) methods aim to attribute model outputs back to specific training examples, and the application of these methods to large language model (LLM) outputs could significantly advance model transparency and data curation. However, it has been challenging to date to apply these methods to the full scale of LLM pretraining. In this paper, we refine existing gradient-based methods to work effectively at scale, allowing us to retrieve influential examples for an 8B-parameter language model from a pretraining corpus of over 160B tokens with no need for subsampling or pre-filtering. Our method combines several techniques, including optimizer state correction, a task-specific Hessian approximation, and normalized encodings, which we find to be critical for performance at scale. In quantitative evaluations on a fact tracing task, our method performs best at identifying examples that influence model predictions, but classical, model-agnostic retrieval methods such as BM25 still perform better at finding passages which explicitly contain relevant facts. These results demonstrate a misalignment between factual *attribution* and causal *influence*. With increasing model size and training tokens, we find that influence more closely aligns with factual attribution. Finally, we examine different types of examples identified as influential by our method, finding that while many directly entail a particular fact, others support the same output by reinforcing priors on relation types, common entities, and names. We release our prompt set and model outputs, along with a web-based visualization tool to explore influential examples for factual predictions, commonsense reasoning, arithmetic, and open-ended generation for an 8B-parameter LLM.

Background: Despite the current ubiquity of Large Language Models (LLMs) across the medical domain, there is a surprising lack of studies which address their reasoning behaviour. We emphasise the importance of understanding reasoning behaviour as opposed to high-level prediction accuracies, since it is equivalent to explainable AI (XAI) in this context. In particular, achieving XAI in medical LLMs used in the clinical domain will have a significant impact across the healthcare sector. Results: Therefore, we define the concept of reasoning behaviour in the specific context of medical LLMs. We then categorise and discuss the current state of the art of methods which evaluate reasoning behaviour in medical LLMs. Finally, we propose theoretical frameworks which can empower medical professionals or machine learning engineers to gain insight into the low-level reasoning operations of these previously obscure models. Conclusion: The subsequent increased transparency and trust in medical machine learning models by clinicians as well as patients will accelerate the integration, application as well as further development of medical AI for the healthcare system as a whole

Funding and support: The Generative AI Challenge is funded by grants from the Future Health Research and Innovation Fund (FHRIF), Grant ID IC2023-GAIA/11. Conflict of interest statement: The authors declare no conflicts of interest. Abstract This exploratory pilot study investigated the potential of combining a domain-specific model, BERN2, with large language models (LLMs) to enhance automated disease phenotyping from research survey data. Motivated by the need for efficient and accurate methods to harmonize the growing volume of survey data with standardized disease ontologies, we employed BERN2, a biomedical named entity recognition and normalization model, to extract disease information from the ORIGINS birth cohort survey data. After rigorously evaluating BERN2's performance against a manually curated ground truth dataset, we integrated various LLMs using prompt engineering, Retrieval-Augmented Generation (RAG), and Instructional Fine-Tuning (IFT) to refine the model's outputs. BERN2 demonstrated high performance in extracting and normalizing disease mentions, and the integration of LLMs, particularly with Few Shot Inference and RAG orchestration, further improved accuracy. This approach, especially when incorporating structured examples, logical reasoning prompts, and detailed context, offers a promising avenue for developing tools to enable efficient cohort profiling and data harmonization across large, heterogeneous research datasets. Introduction The increasing availability of research survey data from cohort studies and clinical trials offers unprecedented opportunities to advance biomedical research and improve healthcare (1).

Graphical model estimation from modern multi-omics data requires a balance between statistical estimation performance and computational scalability. We introduce a novel pseudolikelihood-based graphical model framework that reparameterizes the target precision matrix while preserving sparsity pattern and estimates it by minimizing an $\ell_1$-penalized empirical risk based on a new loss function. The proposed estimator maintains estimation and selection consistency in various metrics under high-dimensional assumptions. The associated optimization problem allows for a provably fast computation algorithm using a novel operator-splitting approach and communication-avoiding distributed matrix multiplication. A high-performance computing implementation of our framework was tested in simulated data with up to one million variables demonstrating complex dependency structures akin to biological networks. Leveraging this scalability, we estimated partial correlation network from a dual-omic liver cancer data set. The co-expression network estimated from the ultrahigh-dimensional data showed superior specificity in prioritizing key transcription factors and co-activators by excluding the impact of epigenomic regulation, demonstrating the value of computational scalability in multi-omic data analysis. %derived from the gene expression data.

The rapid identification of medical emergencies through digital communication channels remains a critical challenge in modern healthcare delivery, particularly with the increasing prevalence of telemedicine. This paper presents a novel approach leveraging large language models (LLMs) and prompt engineering techniques for automated emergency detection in medical communications. We developed and evaluated a comprehensive system using multiple LLaMA model variants (1B, 3B, and 7B parameters) to classify medical scenarios as emergency or non-emergency situations. Our methodology incorporated both system prompts and in-prompt training approaches, evaluated across different hardware configurations. The results demonstrate exceptional performance, with the LLaMA 2 (7B) model achieving 99.7% accuracy and the LLaMA 3.2 (3B) model reaching 99.6% accuracy with optimal prompt engineering. Through systematic testing of training examples within the prompts, we identified that including 10 example scenarios in the model prompts yielded optimal classification performance. Processing speeds varied significantly between platforms, ranging from 0.05 to 2.2 seconds per request. The system showed particular strength in minimizing high-risk false negatives in emergency scenarios, which is crucial for patient safety. The code implementation and evaluation framework are publicly available on GitHub, facilitating further research and development in this crucial area of healthcare technology.

In the digital age of today, the internet has become an indispensable platform for people's lives, work, and information exchange. However, the problem of violent text proliferation in the network environment has arisen, which has brought about many negative effects. In view of this situation, it is particularly important to build an effective system for cutting off violent text. The study of violent text cutting off based on the BERT-fasttext model has significant meaning. BERT is a pre-trained language model with strong natural language understanding ability, which can deeply mine and analyze text semantic information; Fasttext itself is an efficient text classification tool with low complexity and good effect, which can quickly provide basic judgments for text processing. By combining the two and applying them to the system for cutting off violent text, on the one hand, it can accurately identify violent text, and on the other hand, it can efficiently and reasonably cut off the content, preventing harmful information from spreading freely on the network. Compared with the single BERT model and fasttext, the accuracy was improved by 0.7% and 0.8%, respectively. Through this model, it is helpful to purify the network environment, maintain the health of network information, and create a positive, civilized, and harmonious online communication space for netizens, driving the development of social networking, information dissemination, and other aspects in a more benign direction.

Statistical protocols are often used for decision-making involving multiple parties, each with their own incentives, private information, and ability to influence the distributional properties of the data. We study a game-theoretic version of hypothesis testing in which a statistician, also known as a principal, interacts with strategic agents that can generate data. The statistician seeks to design a testing protocol with controlled error, while the data-generating agents, guided by their utility and prior information, choose whether or not to opt in based on expected utility maximization. This strategic behavior affects the data observed by the statistician and, consequently, the associated testing error. We analyze this problem for general concave and monotonic utility functions and prove an upper bound on the Bayes false discovery rate (FDR). Underlying this bound is a form of prior elicitation: we show how an agent's choice to opt in implies a certain upper bound on their prior null probability. Our FDR bound is unimprovable in a strong sense, achieving equality at a single point for an individual agent and at any countable number of points for a population of agents. We also demonstrate that our testing protocols exhibit a desirable maximin property when the principal's utility is considered. To illustrate the qualitative predictions of our theory, we examine the effects of risk aversion, reward stochasticity, and signal-to-noise ratio, as well as the implications for the Food and Drug Administration's testing protocols.

Recent advancements in NLP have spurred significant interest in analyzing social media text data for identifying linguistic features indicative of mental health issues. However, the domain of Expressive Narrative Stories (ENS)-deeply personal and emotionally charged narratives that offer rich psychological insights-remains underexplored. This study bridges this gap by utilizing a dataset sourced from Reddit, focusing on ENS from individuals with and without self-declared depression. Our research evaluates the utility of advanced language models, BERT and MentalBERT, against traditional models. We find that traditional models are sensitive to the absence of explicit topic-related words, which could risk their potential to extend applications to ENS that lack clear mental health terminology. Despite MentalBERT is design to better handle psychiatric contexts, it demonstrated a dependency on specific topic words for classification accuracy, raising concerns about its application when explicit mental health terms are sparse (P-value<0.05). In contrast, BERT exhibited minimal sensitivity to the absence of topic words in ENS, suggesting its superior capability to understand deeper linguistic features, making it more effective for real-world applications. Both BERT and MentalBERT excel at recognizing linguistic nuances and maintaining classification accuracy even when narrative order is disrupted. This resilience is statistically significant, with sentence shuffling showing substantial impacts on model performance (P-value<0.05), especially evident in ENS comparisons between individuals with and without mental health declarations. These findings underscore the importance of exploring ENS for deeper insights into mental health-related narratives, advocating for a nuanced approach to mental health text analysis that moves beyond mere keyword detection.

Classifying antimicrobial peptides(AMPs) from the vast array of peptides mined from metagenomic sequencing data is a significant approach to addressing the issue of antibiotic resistance. However, current AMP classification methods, primarily relying on sequence-based data, neglect the spatial structure of peptides, thereby limiting the accurate classification of AMPs. Additionally, the number of known AMPs is significantly lower than that of non-AMPs, leading to imbalanced datasets that reduce predictive accuracy for AMPs. To alleviate these two limitations, we first employ Omegafold to predict the three-dimensional spatial structures of AMPs and non-AMPs, constructing peptide graphs based on the amino acids' C$_\alpha$ positions. Building upon this, we propose a novel classification model named Spatial GNN-based AMP Classifier (SGAC). Our SGAC model employs a graph encoder based on Graph Neural Networks (GNNs) to process peptide graphs, generating high-dimensional representations that capture essential features from the three-dimensional spatial structure of amino acids. Then, to address the inherent imbalanced datasets, SGAC first incorporates Weight-enhanced Contrastive Learning, which clusters similar peptides while ensuring separation between dissimilar ones, using weighted contributions to emphasize AMP-specific features. Furthermore, SGAC employs Weight-enhanced Pseudo-label Distillation to dynamically generate high-confidence pseudo labels for ambiguous peptides, further refining predictions and promoting balanced learning between AMPs and non-AMPs. Experiments on publicly available AMP and non-AMP datasets demonstrate that SGAC significantly outperforms traditional sequence-based methods and achieves state-of-the-art performance among graph-based models, validating its effectiveness in AMP classification.