Table of Contents

• Clustering-Based Negative Sampling Approaches for Protein-Protein Interaction PredictionZehra Kesemen, Ilknur Karadeniz, Reyhan Aydogan. 3-14 [doi]
• Proteins Transcription Factor Prediction Using Graph Neural NetworksDomenico Amato, Salvatore Calderaro, Giosuè Lo Bosco, Filippo Vella, Riccardo Rizzo. 15-27 [doi]
• Identification of Differential Alternative Splicing Events: Assessing Tools Performance with Different Sequencing ParametersLuca Faretra, Antonio Ammendola, Massimo Pancione, Francesco Napolitano, Luigi Cerulo. 28-42 [doi]
• Methods and Tools to Facilitate RE:IN Modeling and Analysis of GRNsDaniel Grimland, Eitan Tannenbaum, Hillel Kugler. 43-57 [doi]
• Gene Set-Focused Analysis of RNA-Seq Data with MIEP (Make-It-Easy-Pipeline)Alberto Corradin, Francesco Ciccarese, Vittoria Raimondi, Loredana Urso, Micol Silic-Benussi, Vincenzo Ciminale. 58-68 [doi]
• Cross Sequencing Integration of Compositional Microbiome Data in CancerDiego Fernández-Edreira, Jose Liñares-Blanco, Carlos Fernandez-Lozano. 69-78 [doi]
• Private, Efficient and Scalable Kernel Learning for Medical Image AnalysisAnika Hannemann, Arjhun Swaminathan, Ali Burak Ünal, Mete Akgün. 81-95 [doi]
• Toward a Unified Graph-Based Representation of Medical Data for Precision Oncology MedicineDavide Belluomo, Tiziana Calamoneri, Giacomo Paesani, Ivano Salvo. 96-110 [doi]
• FP-Elegans M1: Feature Pyramid Reservoir Connectome Transformers and Multi-backbone Feature Extractors for MEDMNIST2D-V2Francesco Bardozzo, Pierpaolo Fiore, Pietro Liò, Roberto Tagliaferri. 111-120 [doi]
• Driver Gene Detection via Causal Inference on Single Cell EmbeddingsChengbo Fu, Lu Cheng 0004. 123-133 [doi]
• Assessing and Comparing Free Large Language Models' Responses to a Clinical Case: Accuracy, Safety, and ReliabilityElena Sblendorio, Alessio Lo Cascio, Daniele Napolitano, Francesco Germini, Vincenzo Dentamaro, Michela Piredda, Giancarlo Cicolini. 134-149 [doi]
• Three-Stage Data Science Methodology to Explore Genetic Heterogeneity of DiseasesSilvia Cascianelli, Cristina Iudica, Marco Masseroli. 150-164 [doi]
• Functional Data Analysis and Clustering of Haematological Parameters in SARS-CoV-2 PatientsDaniela Volpatto, Marco Frattarola, Simone Pernice, Francesca Cordero, Marco Beccuti, Giulio Mengozzi, Stefano De Angelis, Roberta Sirovich. 165-179 [doi]
• Gene Set Optimization for Single Cell TranscriptomicsH. Robert Frost. 183-195 [doi]
• MicroRNAs as Biomarkers for Ulcerative ColitisFlaminia Tani, Gloria Bertoli, Bruno Giovanni Galuzzi. 196-205 [doi]
• PHeP: TrustAlert Open-Source Platform for Enhancing Predictive Healthcare with Deep LearningSandro Gepiro Contaldo, Emanuele Pietropaolo, Lorenzo Bosio, Simone Pernice, Irene Terrone, Daniele Baccega, YuTing Wang, Rahul Kumar Sahoo, Giuseppe Rizzo 0002, Alessia Visconti, Paola Berchialla, Marco Beccuti. 206-216 [doi]
• Cutting Slices of Complexity in Cancer Therapy Design: An Agent-Based Model of Dabrafenib in MelanomaStefano Maestri. 217-229 [doi]
• Forward and Backward Feature Selection Guided by Prior Biological Knowledge for Enhanced InterpretabilitySofia Mongardi, Silvia Cascianelli, Marco Masseroli. 233-247 [doi]
• The Impact of Mis-Labeled Artefacts on Deep Learning Models for EEG Analysis: a Case StudyAlberto Zancanaro, Giulia Cisotto. 248-255 [doi]
• Benchmark Study on Supervised Relevance-Redundancy Assessment for Feature Selection in Genomic DataSimone Tomè, Silvia Cascianelli, Erika Salvi, Marco Masseroli. 256-265 [doi]
• Group Discovery in a Clinical Database of Patients with Psychosis Who Have Undergone Metacognitive TrainingCaroline König, Wafaa Guendouz, Pedro Copado, Cecilio Angulo, Àngela Nebot, Susana Ochoa, Maria Lamarca, Rabea Fischer, Fabrice Berna, Lucasz Gaweda, Vanessa Acuña, Alfredo Vellido. 269-280 [doi]
• Hierarchical Clustering with an Ensemble of Principle Component Trees for Interpretable Patient StratificationBastian Pfeifer, Marcus D. Bloice, Christel Sirocchi, Markus Loecher. 281-291 [doi]
• ESMCrystal : Enhancing Protein Crystallization Prediction Through Protein EmbeddingsJayanth Kumar, Kavya Jayakumar, Jayaprakash Sundararaj. 295-306 [doi]
• TARNAS, a TrAnslator for RNA Secondary Structure FormatsMichela Quadrini, Piero Hierro Canchari, Piermichele Rosati, Luca Tesei. 307-316 [doi]
• Novel Approaches for Spatially Resolving Gene Responses and Injection Site Localization in Transcriptomic DataAntonio Ammendola, Felicita Masone, Luigi Cerulo, Francesco Napolitano. 319-322 [doi]
• Deep Learning Approaches for Forensics DNA Profiling: a Replication StudyMirella Sangiovanni, Willem-Jan van den Heuvel, George Manias. 323-326 [doi]