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or newly introduced GO terms that frequently arise as the ontology evolves, and making the previously trained models outdated.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.

As a classical approach on graph learning, the propagation-aggregation methodology is widely exploited by many of Graph Neural Networks (GNNs), wherein the representation of a node is updated by aggregating representations from itself and neighbor nodes recursively. Similar to the propagation-aggregation methodology, the Weisfeiler-Lehman (1-WL) algorithm tests isomorphism through color refinement according to color representations of a node and its neighbor nodes. However, 1-WL does not leverage any edge features (labels), presenting a potential improvement on exploiting edge features in some fields. To address this limitation, we proposed a novel Edged-WL algorithm (E-WL) which extends the original 1-WL algorithm to incorporate edge features. Building upon the E-WL algorithm, we also introduce an Edged Graph Isomorphism Network (EGIN) model for further exploiting edge features, which addresses one key drawback in many GNNs that do not utilize any edge features of graph data. We evaluated the performance of proposed models using 12 edge-featured benchmark graph datasets and compared them with some state-of-the-art baseline models. Experimental results indicate that our proposed EGIN models, in general, demonstrate superior performance in graph learning on graph classification tasks.

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.

In recent years we observed rapid and significant advancements in artificial intelligence (A.I.). So much so that many wonder how close humanity is to developing an A.I. model that can achieve human level of intelligence, also known as artificial general intelligence (A.G.I.). In this work we look at this question and we attempt to define the upper bounds, not just of A.I., but rather of any machine-computable process (a.k.a. an algorithm). To answer this question however, one must first precisely define A.G.I. We borrow prior work's definition of A.G.I. [1] that best describes the sentiment of the term, as used by the leading developers of A.I. That is, the ability to be creative and innovate in some field of study in a way that unlocks new and previously unknown functional capabilities in that field. Based on this definition we draw new bounds on the limits of computation. We formally prove that no algorithm can demonstrate new functional capabilities that were not already present in the initial algorithm itself. Therefore, no algorithm (and thus no A.I. model) can be truly creative in any field of study, whether that is science, engineering, art, sports, etc. In contrast, A.I. models can demonstrate existing functional capabilities, as well as combinations and permutations of existing functional capabilities. We conclude this work by discussing the implications of this proof both as it regards to the future of A.I. development, as well as to what it means for the origins of human intelligence.

Prior work on scientific question answering has largely emphasized chatbot-style systems, with limited exploration of fine-tuning foundation models for domain-specific reasoning. In this study, we developed a chatbot for the University of Limerick's Department of Electronic and Computer Engineering to provide course information to students. A custom dataset of 1,203 question-answer pairs in SQuAD format was constructed using the university book of modules, supplemented with manually and synthetically generated entries. We fine-tuned BERT (Devlin et al., 2019) using PyTorch and evaluated performance with Exact Match and F1 scores. Results show that even modest fine-tuning improves hypothesis framing and knowledge extraction, demonstrating the feasibility of adapting foundation models to educational domains. While domain-specific BERT variants such as BioBERT and SciBERT exist for biomedical and scientific literature, no foundation model has yet been tailored to university course materials. Our work addresses this gap by showing that fine-tuning BERT with academic QA pairs yields effective results, highlighting the potential to scale towards the first domain-specific QA model for universities and enabling autonomous educational knowledge systems.

Machine learning techniques face numerous challenges to achieve optimal performance. These include computational constraints, the limitations of single-view learning algorithms and the complexity of processing large datasets from different domains, sources or views. In this context, multi-view clustering (MVC), a class of unsupervised multi-view learning, emerges as a powerful approach to overcome these challenges. MVC compensates for the shortcomings of single-view methods and provides a richer data representation and effective solutions for a variety of unsupervised learning tasks. In contrast to traditional single-view approaches, the semantically rich nature of multi-view data increases its practical utility despite its inherent complexity. This survey makes a threefold contribution: (1) a systematic categorization of multi-view clustering methods into well-defined groups, including co-training, co-regularization, subspace, deep learning, kernel-based, anchor-based, and graph-based strategies; (2) an in-depth analysis of their respective strengths, weaknesses, and practical challenges, such as scalability and incomplete data; and (3) a forward-looking discussion of emerging trends, interdisciplinary applications, and future directions in MVC research. This study represents an extensive workload, encompassing the review of over 140 foundational and recent publications, the development of comparative insights on integration strategies such as early fusion, late fusion, and joint learning, and the structured investigation of practical use cases in the areas of healthcare, multimedia, and social network analysis. By integrating these efforts, this work aims to fill existing gaps in MVC research and provide actionable insights for the advancement of the field.