Abstract

Abstract
APAtizer is a tool designed to analyze alternative polyadenylation events on RNA-sequencing data. The tool handles different file formats, including BAM, htseq, and DaPars bedGraph files. It provides a user-friendly interface that allows users to generate informative visualizations, including Volcano plots, heatmaps, and gene lists. These outputs allow the user to retrieve useful biological insights such as the occurrence of polyadenylation events when comparing two biological conditions. In addition, it can perform differential gene expression, gene ontology analysis, visualization of Venn diagram intersections, and correlation analysis.

Abstract
Aging involves complex biological processes leading to the decline of living organisms. As population lifespan increases worldwide, the importance of identifying factors underlying healthy aging has become critical. Integration of multi-modal datasets is a powerful approach for the analysis of complex biological systems, with the potential to uncover novel aging biomarkers. In this study, we leveraged publicly available epigenomic, transcriptomic and telomere length data along with histological images from the Genotype-Tissue Expression project to build tissue-specific regression models for age prediction. Using data from two tissues, lung and ovary, we aimed to compare model performance across data modalities, as well as to assess the improvement resulting from integrating multiple data types. Our results demostrate that methylation outperformed the other data modalities, with a mean absolute error of 3.36 and 4.36 in the test sets for lung and ovary, respectively. These models achieved lower error rates when compared with established state-of-the-art tissue-agnostic methylation models, emphasizing the importance of a tissue-specific approach. Additionally, this work has shown how the application of Hierarchical Image Pyramid Transformers for feature extraction significantly enhances age modeling using histological images. Finally, we evaluated the benefits of integrating multiple data modalities into a single model. Combining methylation data with other data modalities only marginally improved performance likely due to the limited number of available samples. Combining gene expression with histological features yielded more accurate age predictions compared with the individual performance of these data types. Given these results, this study shows how machine learning applications can be extended to/in multi-modal aging research. Code used is available at https://github.com/zroger49/multi_modal_age_prediction.

Abstract
AbstractBreakthroughs in sequencing technologies led to an exponential growth of genomic data, providing unprecedented biological in-sights and new therapeutic applications. However, analyzing such large amounts of sensitive data raises key concerns regarding data privacy, specifically when the information is outsourced to third-party infrastructures for data storage and processing (e.g., cloud computing). Current solutions for data privacy protection resort to centralized designs or cryptographic primitives that impose considerable computational overheads, limiting their applicability to large-scale genomic analysis.We introduce Gyosa, a secure and privacy-preserving distributed genomic analysis solution. Unlike in previous work, Gyosafollows a distributed processing design that enables handling larger amounts of genomic data in a scalable and efficient fashion. Further, by leveraging trusted execution environments (TEEs), namely Intel SGX, Gyosaallows users to confidentially delegate their GWAS analysis to untrusted third-party infrastructures. To overcome the memory limitations of SGX, we implement a computation partitioning scheme within Gyosa. This scheme reduces the number of operations done inside the TEEs while safeguarding the users’ genomic data privacy. By integrating this security scheme inGlow, Gyosaprovides a secure and distributed environment that facilitates diverse GWAS studies. The experimental evaluation validates the applicability and scalability of Gyosa, reinforcing its ability to provide enhanced security guarantees. Further, the results show that, by distributing GWASes computations, one can achieve a practical and usable privacy-preserving solution.

Abstract
The main objective of this study is to contribute to multilingual discourse research by employing ISO-24617 Part 8 (Semantic Relations in Discourse, Core Annotation Schema – DR-core) for annotating discourse relations. Centering around a parallel discourse relations corpus that includes English, Polish, and European Portuguese, we initiate one of the few ISO-based comparative analyses through a multilingual corpus that aligns discourse relations across these languages. In this paper, we discuss the project’s contributions, including the annotated corpus, research findings, and statistics related to the use of discourse relations. The paper further discusses the challenges encountered in complying with the ISO standard, such as defining the scope of arguments and annotating specific relation types like Expansion. Our findings highlight the necessity for clearer definitions of certain discourse relations and more precise guidelines for argument spans, especially concerning the inclusion of connectives. Additionally, the study underscores the importance of ongoing collaborative efforts to broaden the inclusion of languages and more comprehensive datasets, with the objective of widening the reach of ISO-guided multilingual discourse research. © 2024 ELRA Language Resource Association: CC BY-NC 4.0.

Abstract
Recent advances in deep learning have promoted the advent of many computational systems capable of performing intelligent actions that, until then, were restricted to the human intellect. In the particular case of human languages, these advances allowed the introduction of applications like ChatGPT that are capable of generating coherent text without being explicitly programmed to do so. Instead, these models use large volumes of textual data to learn meaningful representations of human languages. Associated with these advances, concerns about copyright and data privacy infringements caused by these applications have emerged. Despite these concerns, the pace at which new natural language processing applications continued to be developed largely outperformed the introduction of new regulations. Today, communication barriers between legal experts and computer scientists motivate many unintentional legal infringements during the development of such applications. In this paper, a multidisciplinary team intends to bridge this communication gap and promote more compliant Portuguese NLP research by presenting a series of everyday NLP use cases, while highlighting the Portuguese legislation that may arise during its development. © 2024 ELRA Language Resource Association.