In the past decade a surge in the amount of electronic health record (EHR) data in the United States, attributed to a favorable policy environment created by the Health Information Technology for Economic and Clinical Health (HITECH) Act of 2009 and the 21st Century Cures Act of 2016. Clinical notes for patients' assessments, diagnoses, and treatments are captured in these EHRs in free-form text by physicians, who spend a considerable amount of time entering and editing them. Manually writing clinical notes takes a considerable amount of a doctor's valuable time, increasing the patient's waiting time and possibly delaying diagnoses. Large language models (LLMs) possess the ability to generate news articles that closely resemble human-written ones. We investigate the usage of Chain-of-Thought (CoT) prompt engineering to improve the LLM's response in clinical note generation. In our prompts, we use as input International Classification of Diseases (ICD) codes and basic patient information. We investigate a strategy that combines the traditional CoT with semantic search results to improve the quality of generated clinical notes. Additionally, we infuse a knowledge graph (KG) built from clinical ontology to further enrich the domain-specific knowledge of generated clinical notes. We test our prompting technique on six clinical cases from the CodiEsp test dataset using GPT-4 and our results show that it outperformed the clinical notes generated by standard one-shot prompts.

As concerns around data privacy in machine learning grow, the ability to unlearn, or remove, specific data points from trained models becomes increasingly important. While state of the art unlearning methods have emerged in response, they typically treat all points in the forget set equally. In this work, we challenge this approach by asking whether points that have a negligible impact on the model's learning need to be removed. Through a comparative analysis of influence functions across language and vision tasks, we identify subsets of training data with negligible impact on model outputs. Leveraging this insight, we propose an efficient unlearning framework that reduces the size of datasets before unlearning leading to significant computational savings (up to approximately 50 percent) on real world empirical examples.

Accurate prediction of protein function is essential for elucidating molecular mechanisms and advancing biological and therapeutic discovery. Yet experimental annotation lags far behind the rapid growth of protein sequence data. Computational approaches address this gap by associating proteins with Gene Ontology (GO) terms, which encode functional knowledge through hierarchical relations and textual definitions. However, existing models often emphasize one modality over the other, limiting their ability to generalize, particularly to unseen or newly introduced GO terms that frequently arise as the ontology evolves, and making the previously trained models outdated. We present STAR-GO, a Transformer-based framework that jointly models the semantic and structural characteristics of GO terms to enhance zero-shot protein function prediction. STAR-GO integrates textual definitions with ontology graph structure to learn unified GO representations, which are processed in hierarchical order to propagate information from general to specific terms. These representations are then aligned with protein sequence embeddings to capture sequence-function relationships. STAR-GO achieves state-of-the-art performance and superior zero-shot generalization, demonstrating the utility of integrating semantics and structure for robust and adaptable protein function prediction. Code is available at https://github.com/boun-tabi-lifelu/stargo.

-- Prompt engineering has emerged as a useful way studying the algorithmic tendencies and biases of large language models (LLMs). Meanwhile c reatives and academics have leveraged LLMs to develop creative works and explore the boundaries of their writing capabilities through text - generation and code. This study suggests that creative text prompting, specifically "Poetry Prompt Patterns," may be a useful addition to the prompt engineer's toolbox, and outlines the process by which this approach may be taken. Then, the paper uses poetic prompts to assess three models' descriptions and evaluations of a renowned poet and test the consequences of models' willingness to adapt or rewrite original creative works for presumed audiences. Since the release of public - facing chat - style large language model (LLM) natural language generators (NLGs) like ChatGPT and Claude, public debate has acknowledged their great potential for creativity, as well as the ways in which they can be leveraged to make representations that don't reflect reality.

The rapid emergence of generative AI tools is transforming the way software is developed. Consequently, software engineering education must adapt to ensure that students not only learn traditional development methods but also understand how to meaningfully and responsibly use these new technologies. In particular, project-based courses offer an effective environment to explore and evaluate the integration of AI assistance into real-world development practices. This paper presents our approach and a user study conducted within a university programming project in which students collaboratively developed computer games. The study investigates how participants used generative AI tools throughout different phases of the software development process, identifies the types of tasks where such tools were most effective, and analyzes the challenges students encountered. Building on these insights, we further examine a repository-aware, locally deployed large language model (LLM) assistant designed to provide project-contextualized support. The system employs Retrieval-Augmented Generation (RAG) to ground responses in relevant documentation and source code, enabling qualitative analysis of model behavior, parameter sensitivity, and common failure modes. The findings deepen our understanding of context-aware AI support in educational software projects and inform future integration of AI-based assistance into software engineering curricula.

Developers are widely using AI code-generation models, aiming to increase productivity and efficiency. However, there are also quality concerns regarding the AI-generated code. The generated code is produced by models trained on publicly available code, which are known to contain bugs and quality issues. Those issues can cause trust and maintenance challenges during the development process. Several quality issues associated with AI-generated code have been reported, including bugs and defects. However, these findings are often scattered and lack a systematic summary. A comprehensive review is currently lacking to reveal the types and distribution of these errors, possible remediation strategies, as well as their correlation with the specific models. In this paper, we systematically analyze the existing AI-generated code literature to establish an overall understanding of bugs and defects in generated code, providing a reference for future model improvement and quality assessment. We aim to understand the nature and extent of bugs in AI-generated code, and provide a classification of bug types and patterns present in code generated by different models. We also discuss possible fixes and mitigation strategies adopted to eliminate bugs from the generated code.

The convergence of next-generation wireless systems and distributed Machine Learning (ML) demands Federated Learning (FL) methods that remain efficient and robust with wireless connected peers and under network churn. Peer-to-peer (P2P) FL removes the bottleneck of a central coordinator, but existing approaches suffer from excessive communication complexity, limiting their scalability in practice. We introduce MAR-FL, a novel P2P FL system that leverages iterative group-based aggregation to substantially reduce communication overhead while retaining resilience to churn. MAR-FL achieves communication costs that scale as O(N log N), contrasting with the O(N^2) complexity of previously existing baselines, and thereby maintains effectiveness especially as the number of peers in an aggregation round grows. The system is robust towards unreliable FL clients and can integrate private computing.

Domain shift remains a key challenge in deploying machine learning models to the real world. Unsupervised domain adaptation (UDA) aims to address this by minimising domain discrepancy during training, but the discrepancy estimates suffer from high variance in stochastic settings, which can stifle the theoretical benefits of the method. This paper proposes Variance-Reduced Domain Adaptation via Stratified Sampling (VaRDASS), the first specialised stochastic variance reduction technique for UDA. We consider two specific discrepancy measures -- correlation alignment and the maximum mean discrepancy (MMD) -- and derive ad hoc stratification objectives for these terms. We then present expected and worst-case error bounds, and prove that our proposed objective for the MMD is theoretically optimal (i.e., minimises the variance) under certain assumptions. Finally, a practical k-means style optimisation algorithm is introduced and analysed. Experiments on three domain shift datasets demonstrate improved discrepancy estimation accuracy and target domain performance.

Influenza A viruses (IAVs) evolve antigenically at a pace that requires frequent vaccine updates, yet the haemagglutination inhibition (HI) assays used to quantify antigenicity are labor-intensive and unscalable. As a result, genomic data vastly outpace available phenotypic labels, limiting the effectiveness of traditional supervised models. We hypothesize that combining pre-trained Protein Language Models (PLMs) with Semi-Supervised Learning (SSL) can retain high predictive accuracy even when labeled data are scarce. We evaluated two SSL strategies, Self-training and Label Spreading, against fully supervised baselines using four PLM-derived embeddings (ESM-2, ProtVec, ProtT5, ProtBert) applied to haemagglutinin (HA) sequences. A nested cross-validation framework simulated low-label regimes (25%, 50%, 75%, and 100% label availability) across four IAV subtypes (H1N1, H3N2, H5N1, H9N2). SSL consistently improved performance under label scarcity. Self-training with ProtVec produced the largest relative gains, showing that SSL can compensate for lower-resolution representations. ESM-2 remained highly robust, achieving F1 scores above 0.82 with only 25% labeled data, indicating that its embeddings capture key antigenic determinants. While H1N1 and H9N2 were predicted with high accuracy, the hypervariable H3N2 subtype remained challenging, although SSL mitigated the performance decline. These findings demonstrate that integrating PLMs with SSL can address the antigenicity labeling bottleneck and enable more effective use of unlabeled surveillance sequences, supporting rapid variant prioritization and timely vaccine strain selection.

Tokenization strategies shape how models process electronic health records, yet fair comparisons of their effectiveness remain limited. We present a systematic evaluation of tokenization approaches for clinical time series modeling using transformer-based architectures, revealing task-dependent and sometimes counterintuitive findings about temporal and value feature importance. Through controlled ablations across four clinical prediction tasks on MIMIC-IV, we demonstrate that explicit time encodings provide no consistent statistically significant benefit for the evaluated downstream tasks. Value features show task-dependent importance, affecting mortality prediction but not readmission, suggesting code sequences alone can carry sufficient predictive signal. We further show that frozen pretrained code encoders dramatically outperform their trainable counterparts while requiring dramatically fewer parameters. Larger clinical encoders provide consistent improvements across tasks, benefiting from frozen embeddings that eliminate computational overhead. Our controlled evaluation enables fairer tokenization comparisons and demonstrates that simpler, parameter-efficient approaches can, in many cases, achieve strong performance, though the optimal tokenization strategy remains task-dependent.