All Stories

  1. MiRInter-Trans: a Transformer-Based Framework for microRNA Interaction Prediction

    Article • Bioinformatics Advances, March 2026, Oxford University Press (OUP)

    Professor Giorgio Valentini

  2. A Transformer-Based Model to Predict Micro RNA Interactions

    Article • October 2025, Springer Science + Business Media

    Professor Giorgio Valentini

  3. Modular Deep Neural Networks with Residual Connections for Predicting the Pathogenicity of Genetic Variants in Non Coding Genomic Regions

    Article • October 2025, Springer Science + Business Media

    Professor Giorgio Valentini

  4. AI methods and biologically informed data curation enable accurate RNA m5C prediction

    Article • September 2025, Cold Spring Harbor Laboratory Press

    Professor Giorgio Valentini

  5. Replacing non-biomedical concepts improves embedding of biomedical concepts

    Article • PLOS One, May 2025, PLOS

    Professor Giorgio Valentini

  6. miss-SNF: a multimodal patient similarity network integration approach to handle completely missing data sources

    Article • Bioinformatics, March 2025, Oxford University Press (OUP)

    Professor Giorgio Valentini

  7. miss-SNF: a multimodal patient similarity network integration approach to handle completely missing data sources

    Article • February 2025, Cold Spring Harbor Laboratory Press

    Professor Giorgio Valentini

  8. RNA Knowledge-Graph analysis through homogeneous embedding methods

    Article • February 2025, Cold Spring Harbor Laboratory Press

    Professor Giorgio Valentini

  9. Fine-tuning of conditional Transformers improves in silico enzyme prediction and generation

    Article • Computational and Structural Biotechnology Journal, January 2025, Elsevier

    Professor Giorgio Valentini

  10. RNA knowledge-graph analysis through homogeneous embedding methods

    Article • Bioinformatics Advances, December 2024, Oxford University Press (OUP)

    Professor Giorgio Valentini

  11. Leveraging generative AI to assist biocuration of medical actions for rare disease

    Article • Bioinformatics Advances, December 2024, Oxford University Press (OUP)

    Professor Giorgio Valentini

  12. Fine-tuning of conditional Transformers for the generation of functionally characterized enzymes

    Article • September 2024, Springer Science + Business Media

    Professor Giorgio Valentini

  13. An ontology-based knowledge graph for representing interactions involving RNA molecules

    Article • Scientific Data, August 2024, Springer Science + Business Media

    Professor Giorgio Valentini

  14. Systematic benchmarking demonstrates large language models have not reached the diagnostic accuracy of traditional rare-disease decision support tools

    Article • July 2024, Cold Spring Harbor Laboratory Press

    Professor Giorgio Valentini

  15. Replacing non-biomedical concepts improves embedding of biomedical concepts

    Article • July 2024, Cold Spring Harbor Laboratory Press

    Professor Giorgio Valentini

  16. Predicting nutrition and environmental factors associated with female reproductive disorders using a knowledge graph and random forests

    Article • International Journal of Medical Informatics, July 2024, Elsevier

    Professor Giorgio Valentini

  17. Association of post-COVID phenotypic manifestations with new-onset psychiatric disease

    Article • Translational Psychiatry, June 2024, Springer Science + Business Media

    Professor Giorgio Valentini

  18. An open source knowledge graph ecosystem for the life sciences

    Article • Scientific Data, April 2024, Springer Science + Business Media

    Professor Giorgio Valentini

  19. Exploring the similarity between genetic diseases improves their differential diagnosis and the understanding of their etiology

    Article • European Journal of Human Genetics, January 2024, Springer Science + Business Media

    Professor Giorgio Valentini

  20. Intrinsic-Dimension analysis for guiding dimensionality reduction and data-fusion in multi-omics data processing

    Article • January 2024, Cold Spring Harbor Laboratory Press

    Professor Giorgio Valentini

  21. Node-degree aware edge sampling mitigates inflated classification performance in biomedical random walk-based graph representation learning

    Article • Bioinformatics Advances, January 2024, Oxford University Press (OUP)

    Professor Giorgio Valentini

  22. The promises of large language models for protein design and modeling

    Article • Frontiers in Bioinformatics, November 2023, Frontiers

    Professor Giorgio Valentini

  23. Predictive models of long COVID

    Article • EBioMedicine, October 2023, Elsevier

    Professor Giorgio Valentini

  24. Predicting nutrition and environmental factors associated with female reproductive disorders using a knowledge graph and random forests

    Article • July 2023, Cold Spring Harbor Laboratory Press

    Professor Giorgio Valentini

  25. A software resource for large graph processing and analysis

    Article • Nature Computational Science, June 2023, Springer Science + Business Media

    Professor Giorgio Valentini

  26. GRAPE for fast and scalable graph processing and random-walk-based embedding

    Article • Nature Computational Science, June 2023, Springer Science + Business Media

    Professor Giorgio Valentini

  27. An expectation–maximization framework for comprehensive prediction of isoform-specific functions

    Article • Bioinformatics, March 2023, Oxford University Press (OUP)

    Professor Giorgio Valentini

  28. Combining Clinical and Genetic Data to Predict Response to Fingolimod Treatment in Relapsing Remitting Multiple Sclerosis Patients: A Precision Medicine Approach

    Article • Journal of Personalized Medicine, January 2023, MDPI AG

    Professor Giorgio Valentini

  29. A Meta-Graph for the Construction of an RNA-Centered Knowledge Graph

    Article • January 2023, Springer Science + Business Media

    Professor Giorgio Valentini

  30. Degree-Normalization Improves Random-Walk-Based Embedding Accuracy in PPI Graphs

    Article • January 2023, Springer Science + Business Media

    Professor Giorgio Valentini

  31. Integration and Visual Analysis of Biomolecular Networks Through UNIPred-Web

    Article • January 2023, Springer Science + Business Media

    Professor Giorgio Valentini

  32. Boosting tissue-specific prediction of active cis-regulatory regions through deep learning and Bayesian optimization techniques

    Article • BMC Bioinformatics, December 2022, Springer Science + Business Media

    Professor Giorgio Valentini

  33. Metformin is Associated with Reduced COVID-19 Severity in Patients with Prediabetes

    Article • August 2022, Cold Spring Harbor Laboratory Press

    Professor Giorgio Valentini

  34. GraPE: fast and scalable Graph Processing and Embedding

    Article • August 2022, Springer Science + Business Media

    Professor Giorgio Valentini

  35. Automated image analysis to assess hygienic behaviour of honeybees

    Article • PLOS One, January 2022, PLOS

    elena casiraghi, Professor Giorgio Valentini

  36. ParSMURF-NG: A Machine Learning High Performance Computing System for the Analysis of Imbalanced Big Omics Data

    Article • January 2022, Springer Science + Business Media

    Professor Giorgio Valentini

  37. Abdominal Computed Tomography Imaging Findings in Hospitalized COVID-19 Patients: A Year-Long Experience and Associations Revealed by Explainable Artificial Intelligence

    Article • Journal of Imaging, December 2021, MDPI AG

    Professor Giorgio Valentini

  38. HEMDAG: a family of modular and scalable hierarchical ensemble methods to improve Gene Ontology term prediction

    Article • Bioinformatics, July 2021, Oxford University Press (OUP)

    Professor Giorgio Valentini

  39. NSAID use and clinical outcomes in COVID-19 patients: A 38-center retrospective cohort study

    Article • April 2021, Cold Spring Harbor Laboratory Press

    Professor Giorgio Valentini

  40. Interpretable prioritization of splice variants in diagnostic next-generation sequencing

    Article • January 2021, Cold Spring Harbor Laboratory Press

    Professor Giorgio Valentini

  41. Semi-automatic Column Type Inference for CSV Table Understanding

    Article • January 2021, Springer Science + Business Media

    Professor Giorgio Valentini

  42. Multi-resolution visualization and analysis of biomolecular networks through hierarchical community detection and web-based graphical tools

    Article • PLOS One, December 2020, PLOS

    Professor Giorgio Valentini

  43. Protein function prediction as a graph-transduction game

    Article • Pattern Recognition Letters, June 2020, Elsevier

    Professor Giorgio Valentini

  44. Complex Data Imputation by Auto-Encoders and Convolutional Neural Networks—A Case Study on Genome Gap-Filling

    Article • Computers, May 2020, MDPI AG

    Professor Giorgio Valentini

  45. Multitask Hopfield Networks

    Article • January 2020, Springer Science + Business Media

    Professor Giorgio Valentini

  46. Disease–Genes Must Guide Data Source Integration in the Gene Prioritization Process

    Article • January 2019, Springer Science + Business Media

    Professor Giorgio Valentini

  47. Ensembling Descendant Term Classifiers to Improve Gene - Abnormal Phenotype Predictions

    Article • January 2019, Springer Science + Business Media

    Professor Giorgio Valentini

  48. Prediction of Human Phenotype Ontology terms by means of hierarchical ensemble methods

    Article • BMC Bioinformatics, October 2017, Springer Science + Business Media

    Professor Giorgio Valentini

  49. Imbalance-Aware Machine Learning for Predicting Rare and Common Disease-Associated Non-Coding Variants

    Article • Scientific Reports, June 2017, Springer Science + Business Media

    Professor Giorgio Valentini

  50. COSNet: An R package for label prediction in unbalanced biological networks

    Article • Neurocomputing, May 2017, Elsevier

    Professor Giorgio Valentini

  51. Within network learning on big graphs using secondary memory-based random walk kernels

    Article • November 2016, Springer Science + Business Media

    Professor Giorgio Valentini

  52. Multi-species protein function prediction

    Article • November 2016, ACM (Association for Computing Machinery)

    Professor Giorgio Valentini

  53. An expanded evaluation of protein function prediction methods shows an improvement in accuracy

    Article • September 2016, Springer Science + Business Media

    Professor Casey Greene, Dr Christophe Dessimoz, Dr Tunca Dogan, Professor Giorgio Valentini

  54. A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease

    Article • The American Journal of Human Genetics, September 2016, Elsevier

    Professor Giorgio Valentini

  55. RANKS: a flexible tool for node label ranking and classification in biological networks

    Article • Bioinformatics, June 2016, Oxford University Press (OUP)

    Professor Giorgio Valentini

  56. UNIPred: Unbalance-Aware Network Integration and Prediction of Protein Functions

    Article • Journal of Computational Biology, December 2015, Mary Ann Liebert Inc

    Professor Giorgio Valentini

  57. Learning node labels with multi-category Hopfield networks

    Article • Neural Computing and Applications, June 2015, Springer Science + Business Media

    Professor Giorgio Valentini

  58. A Hierarchical Ensemble Method for DAG-Structured Taxonomies

    Article • January 2015, Springer Science + Business Media

    Professor Giorgio Valentini

  59. An extensive analysis of disease-gene associations using network integration and fast kernel-based gene prioritization methods

    Article • Artificial Intelligence in Medicine, June 2014, Elsevier

    Professor Giorgio Valentini

  60. Hierarchical Ensemble Methods for Protein Function Prediction

    Article • ISRN Bioinformatics, May 2014, Wiley

    Professor Giorgio Valentini

  61. Think globally and solve locally: secondary memory-based network learning for automated multi-species function prediction

    Article • GigaScience, April 2014, Oxford University Press (OUP)

    Professor Giorgio Valentini

  62. GOssTo: a stand-alone application and a web tool for calculating semantic similarities on the Gene Ontology

    Article • Bioinformatics, March 2014, Oxford University Press (OUP)

    Professor Giorgio Valentini

  63. Network-Based Drug Ranking and Repositioning with Respect to DrugBank Therapeutic Categories

    Article • IEEE/ACM Transactions on Computational Biology and Bioinformatics, November 2013, Institute of Electrical & Electronics Engineers (IEEE)

    Professor Giorgio Valentini

  64. Energy‐Efficient Resource Utilization in Cloud Computing

    Article • October 2013, Wiley

    Professor Giorgio Valentini

  65. A neural network algorithm for semi-supervised node label learning from unbalanced data

    Article • Neural Networks, July 2013, Elsevier

    Professor Giorgio Valentini

  66. A Novel Approach to the Problem of Non-uniqueness of the Solution in Hierarchical Clustering

    Article • IEEE Transactions on Neural Networks and Learning Systems, July 2013, Institute of Electrical & Electronics Engineers (IEEE)

    Professor Giorgio Valentini

  67. Regeneration-associated WNT Signaling Is Activated in Long-term Reconstituting AC133bright Acute Myeloid Leukemia Cells

    Article • Neoplasia, December 2012, Elsevier

    Professor Giorgio Valentini

  68. A Fast Ranking Algorithm for Predicting Gene Functions in Biomolecular Networks

    Article • IEEE/ACM Transactions on Computational Biology and Bioinformatics, November 2012, Institute of Electrical & Electronics Engineers (IEEE)

    Professor Giorgio Valentini

  69. Cancer module genes ranking using kernelized score functions

    Article • BMC Bioinformatics, September 2012, Springer Science + Business Media

    Professor Giorgio Valentini

  70. Ensemble Methods

    Article • March 2012, Taylor & Francis

    Professor Giorgio Valentini

  71. Large Scale Ranking and Repositioning of Drugs with Respect to DrugBank Therapeutic Categories

    Article • January 2012, Springer Science + Business Media

    Professor Giorgio Valentini

  72. Random Walking on Functional Interaction Networks to Rank Genes Involved in Cancer

    Article • January 2012, Springer Science + Business Media

    Professor Giorgio Valentini

  73. Synergy of multi-label hierarchical ensembles, data fusion, and cost-sensitive methods for gene functional inference

    Article • Machine Learning, December 2011, Springer Science + Business Media

    Professor Giorgio Valentini

  74. A Mathematical Model for the Validation of Gene Selection Methods

    Article • IEEE/ACM Transactions on Computational Biology and Bioinformatics, September 2011, Institute of Electrical & Electronics Engineers (IEEE)

    Professor Giorgio Valentini

  75. True Path Rule Hierarchical Ensembles for Genome-Wide Gene Function Prediction

    Article • IEEE/ACM Transactions on Computational Biology and Bioinformatics, May 2011, Institute of Electrical & Electronics Engineers (IEEE)

    Professor Giorgio Valentini

  76. XML-Based Approaches for the Integration of Heterogeneous Bio-Molecular Data

    Article • April 2011, Taylor & Francis

    Professor Giorgio Valentini

  77. Ensembles in Machine Learning Applications

    Article • January 2011

    Professor Giorgio Valentini

  78. COSNet: A Cost Sensitive Neural Network for Semi-supervised Learning in Graphs

    Article • January 2011, Springer Science + Business Media

    Professor Giorgio Valentini

  79. A Novel Ensemble Technique for Protein Subcellular Location Prediction

    Article • January 2011, Springer Science + Business Media

    Professor Giorgio Valentini

  80. Learning functional linkage networks with a cost-sensitive approach

    Article • January 2011, IOS Press

    Professor Giorgio Valentini

  81. Dynamic multi-objective routing algorithm: a multi-objective routing algorithm for the simple hybrid routing protocol on wireless sensor networks

    Article • IET Communications, September 2010, the Institution of Engineering and Technology (the IET)

    Professor Giorgio Valentini

  82. Integration of heterogeneous data sources for gene function prediction using decision templates and ensembles of learning machines

    Article • Neurocomputing, March 2010, Elsevier

    Professor Giorgio Valentini

  83. An Experimental Comparison of Hierarchical Bayes and True Path Rule Ensembles for Protein Function Prediction

    Article • January 2010, Springer Science + Business Media

    Professor Giorgio Valentini

  84. XML-based approaches for the integration of heterogeneous bio-molecular data

    Article • BMC Bioinformatics, October 2009, Springer Science + Business Media

    Professor Giorgio Valentini

  85. Classification of co-expressed genes from DNA regulatory regions

    Article • Information Fusion, July 2009, Elsevier

    Professor Giorgio Valentini

  86. Computational intelligence and machine learning in bioinformatics

    Article • Artificial Intelligence in Medicine, February 2009, Elsevier

    Professor Giorgio Valentini

  87. Fuzzy ensemble clustering based on random projections for DNA microarray data analysis

    Article • Artificial Intelligence in Medicine, February 2009, Elsevier

    Professor Giorgio Valentini

  88. Applications of Supervised and Unsupervised Ensemble Methods

    Article • January 2009, Springer Science + Business Media

    Professor Giorgio Valentini

  89. True Path Rule Hierarchical Ensembles

    Article • January 2009, Springer Science + Business Media

    Professor Giorgio Valentini

  90. Ensemble Based Data Fusion for Gene Function Prediction

    Article • January 2009, Springer Science + Business Media

    Professor Giorgio Valentini

  91. A stability-based algorithm to validate hierarchical clusters of genes

    Article • International Journal of Knowledge Engineering and Soft Data Paradigms, January 2009, Inderscience Publishers

    Professor Giorgio Valentini

  92. Unsupervised Stability-Based Ensembles to Discover Reliable Structures in Complex Bio-molecular Data

    Article • January 2009, Springer Science + Business Media

    Professor Giorgio Valentini

  93. Prediction of Gene Function Using Ensembles of SVMs and Heterogeneous Data Sources

    Article • January 2009, Springer Science + Business Media

    Professor Giorgio Valentini

  94. Classification of DNA microarray data with Random Projection Ensembles of Polynomial SVMs

    Article • January 2009, IOS Press

    Professor Giorgio Valentini

  95. Comparing early and late data fusion methods for gene function prediction

    Article • January 2009, IOS Press

    Professor Giorgio Valentini

  96. Dataset complexity can help to generate accurate ensembles of k-nearest neighbors

    Article • June 2008, Institute of Electrical & Electronics Engineers (IEEE)

    Professor Giorgio Valentini

  97. Discovering multi–level structures in bio-molecular data through the Bernstein inequality

    Article • BMC Bioinformatics, March 2008, Springer Science + Business Media

    Professor Giorgio Valentini

  98. HCGene: a software tool to support the hierarchical classification of genes

    Article • Bioinformatics, January 2008, Oxford University Press (OUP)

    Professor Giorgio Valentini

  99. Supervised and Unsupervised Ensemble Methods and their Applications

    Article • January 2008, Springer Science + Business Media

    Professor Giorgio Valentini

  100. Ensemble Clustering with a Fuzzy Approach

    Article • January 2008, Springer Science + Business Media

    Professor Giorgio Valentini

  101. Gene expression modeling through positive boolean functions

    Article • International Journal of Approximate Reasoning, January 2008, Elsevier

    Professor Giorgio Valentini

  102. Model order selection for bio-molecular data clustering

    Article • BMC Bioinformatics, May 2007, Springer Science + Business Media

    Professor Giorgio Valentini

  103. Discovering Significant Structures in Clustered Bio-molecular Data Through the Bernstein Inequality

    Article • January 2007, Springer Science + Business Media

    Professor Giorgio Valentini

  104. Mosclust: a software library for discovering significant structures in bio-molecular data

    Article • Bioinformatics, November 2006, Oxford University Press (OUP)

    Professor Giorgio Valentini

  105. Randomized maps for assessing the reliability of patients clusters in DNA microarray data analyses

    Article • Artificial Intelligence in Medicine, June 2006, Elsevier

    Professor Giorgio Valentini

  106. Characterization of lung tumor subtypes through gene expression cluster validity assessment

    Article • RAIRO - Theoretical Informatics and Applications, April 2006, EDP Sciences

    Professor Giorgio Valentini

  107. Ensembles Based on Random Projections to Improve the Accuracy of Clustering Algorithms

    Article • January 2006, Springer Science + Business Media

    Professor Giorgio Valentini

  108. Biological Specifications for a Synthetic Gene Expression Data Generation Model

    Article • January 2006, Springer Science + Business Media

    Professor Giorgio Valentini

  109. Clusterv: a tool for assessing the reliability of clusters discovered in DNA microarray data

    Article • Bioinformatics, December 2005, Oxford University Press (OUP)

    Professor Giorgio Valentini

  110. An Experimental Bias-Variance Analysis of SVM Ensembles Based on Resampling Techniques

    Article • IEEE Transactions on Systems Man and Cybernetics Part B (Cybernetics), December 2005, Institute of Electrical & Electronics Engineers (IEEE)

    Professor Giorgio Valentini

  111. Support vector machines for candidate nodules classification

    Article • Neurocomputing, October 2005, Elsevier

    Professor Giorgio Valentini

  112. Bio-molecular cancer prediction with random subspace ensembles of support vector machines

    Article • Neurocomputing, January 2005, Elsevier

    Professor Giorgio Valentini

  113. Lung nodules detection and classification

    Article • January 2005, Institute of Electrical & Electronics Engineers (IEEE)

    Professor Giorgio Valentini

  114. An experimental analysis of the dependence among codeword bit errors in ECOC learning machines

    Article • Neurocomputing, March 2004, Elsevier

    Professor Giorgio Valentini

  115. Effectiveness of error correcting output coding methods in ensemble and monolithic learning machines

    Article • Pattern Analysis and Applications, February 2004, Springer Science + Business Media

    Professor Giorgio Valentini

  116. Cancer recognition with bagged ensembles of support vector machines

    Article • Neurocomputing, January 2004, Elsevier

    Professor Giorgio Valentini

  117. Random Aggregated and Bagged Ensembles of SVMs: An Empirical Bias–Variance Analysis

    Article • January 2004, Springer Science + Business Media

    Professor Giorgio Valentini

  118. Effectiveness of error correcting output coding methods in ensemble and monolithic learning machines

    Article • Pattern Analysis and Applications, February 2003, Springer Science + Business Media

    Professor Giorgio Valentini

  119. An Application of Low Bias Bagged SVMs to the Classification of Heterogeneous Malignant Tissues

    Article • January 2003, Springer Science + Business Media

    Professor Giorgio Valentini

  120. Gene expression data analysis of human lymphoma using support vector machines and output coding ensembles

    Article • Artificial Intelligence in Medicine, November 2002, Elsevier

    Professor Giorgio Valentini

  121. NEURObjects: an object-oriented library for neural network development

    Article • Neurocomputing, October 2002, Elsevier

    Professor Giorgio Valentini

  122. Ensembles of Learning Machines

    Article • January 2002, Springer Science + Business Media

    Professor Giorgio Valentini

  123. Boosting and Classification of Electronic Nose Data

    Article • January 2002, Springer Science + Business Media

    Professor Giorgio Valentini

  124. Bias—Variance Analysis and Ensembles of SVM

    Article • January 2002, Springer Science + Business Media

    Professor Giorgio Valentini

  125. Decompositive classification models for electronic noses

    Article • Analytica Chimica Acta, November 2001, Elsevier

    Professor Giorgio Valentini

  126. Dependence among Codeword Bits Errors in ECOC Learning Machines: An Experimental Analysis

    Article • January 2001, Springer Science + Business Media

    Professor Giorgio Valentini

  127. Effectiveness of Error Correcting Output Codes in Multiclass Learning Problems

    Article • January 2000, Springer Science + Business Media

    Professor Giorgio Valentini

  128. Feature Selection Combined with Random Subspace Ensemble for Gene Expression Based Diagnosis of Malignancies

    Article • Springer Science + Business Media

    Professor Giorgio Valentini

  129. Fuzzy Ensemble Clustering for DNA Microarray Data Analysis

    Article • Springer Science + Business Media

    Professor Giorgio Valentini

  130. An Algorithm to Assess the Reliability of Hierarchical Clusters in Gene Expression Data

    Article • Springer Science + Business Media

    Professor Giorgio Valentini

  131. Data Integration Issues and Opportunities in Biological XML Data Management

    Article • IGI Global

    Professor Giorgio Valentini

  132. Bagged ensembles of Support Vector Machines for gene expression data analysis

    Article • Institute of Electrical & Electronics Engineers (IEEE)

    Professor Giorgio Valentini

  133. Random projections for assessing gene expression cluster stability

    Article • Institute of Electrical & Electronics Engineers (IEEE)

    Professor Giorgio Valentini