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2025-08-29: My article titled "The DBCV index is more informative than DCSI, CDbw, and VIASCKDE indices for unsupervised clustering internal assessment of concave-shaped and density-based clusters" was published in the PeerJ Computer Science journal.
2025-08-20: My article titled "A simple guide to the use of Student’s t-test, Mann-Whitney U test, Chi-squared test, and Kruskal-Wallis test in biostatistics" was published in the BioData Mining journal.
2025-08-18: My R software library geneExpressionFromGEO was included in the "Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics" CRAN Task View.
2025-07-25: My article titled "TaGra: an open Python package for easily generating graphs from data tables through manifold learning" was published in the PeerJ Computer Science journal.
2025-06-26: I attend the Artificial Intelligence in Oncology Workshop of the AIME 2025 conference in Pavia (Italy, EU), where I presented my work titled "DBSCAN applied to EHRs data from patients with glioblastoma clusters patients based on cytosolic Hsp70 protein, sex, and brain subventricular zone".
2025-06-20: My colleagues of the MMSP research group and I organize and attend the 2nd edition of the Milan Workshop on Computational Methods For Mental Health and Well Being 2025 at Università di Milano-Bicocca, Milan, Italy, EU.
2025-06-13: My article titled "DBSCAN and DBCV application to open medical records heterogeneous data for identifying clinically significant clusters of patients with neuroblastoma" was published in the BioData Mining journal.
2025-05-13: My article titled "Hyperdimensional computing in biomedical sciences: a brief review" was published in the PeerJ Computer Science journal.
2025-05-06: I contribute to the organization of and I participate in the 7th Milan Meeting on Next Generation Sequencing (MMNGS 2025) at Università di Milano-Bicocca.
2025-04-28: My chapter titled "Biological and Medical Ontologies: PRotein Ontology (PRO)" was published in the Encyclopedia of Bioinformatics and Computational Biology (2nd Edition).
2025-04-15: My article titled "A teaching proposal for a short course on biomedical data science" was published in the PLOS Computational Biology journal..
2025-04-09: I attend the Data Science for Health and Biology (DS4HB) workshop at Politecnico di Milano where I present a poster entitled "DBSCAN and DBCV applied to open medical records data of patients with neuroblastoma are capable of identifying clinically significant clusters".
2025-03-31: My article titled "Multivariate longitudinal clustering reveals neuropsychological factors as dementia predictors in an Alzheimer’s disease progression study" was published in the BioData Mining journal.
2025-02-17: My DBCVindex R package was published on CRAN.
2025-01-10: My article titled "Eight quick tips for biologically and medically informed machine learning" written with Luca Oneto was published in the PLOS Computational Biology journal.
2025-01-09: My article titled "The Venus score for the assessment of the quality and trustworthiness of biomedical datasets" was published in the BioData Mining journal.
2024-12-23: A preprint I wrote with David H. Brown titled "Interactive Classification Metrics: A graphical application to build robust intuition for classification model evaluation" was released on the arXiv preprint server.
2024-12-16: I publish the Python software package SaturnScore on PyPI and the R software package SaturnCoefficient on CRAN.
2024-11-29: I attend the AIxIA 2024 conference at Libera Università di Bolzano (Italy, EU) where I give an invited talk titled "How to assess my results? Evaluation metrics for supervised and unsupervised machine learning results" at the MLDM 2024 workshop and where I present a scientific poster titled "Analyzing trajectories of clinical markers in patients with sepsis through multivariate longitudinal clustering" at the HC@AIxIA 2024 workshop.
2024-11-15: My preprint titled "EHRs Data Harmonization Platform, an easy-to-use shiny app based on recodeflow for harmonizing and deriving clinical features" was released in the arXiv preprint server.
2024-11-07: I attend the Mathematics for our Health (M4H) Workshop 2024 at Politecnico di Milano.
2024-10-26: I give a talk titled "Open scientific research practices and their impact: open data, open software code, open publications" at Linux Day Milan 2024.
2024-10-24: My colleagues of the MMSP lab and I attend the NeuroMi 2024 conference, where I present a poster entitled "Longitudinal clustering on electronic mental health records reveals meaningful groups of disease trajectories".
2024-10-16: My article titled "Gene signatures for cancer research: a 25-year retrospective and future avenues" was published in the PLOS Computational Biology journal.
2024-09-30: A preprint I wrote with Nardin Samuel and other colleagues entitled "Data-driven probabilistic mapping of the spatial and molecular landscape of glioma" was released in the Social Science Research Network (SSRN) preprint server.
2024-09-04: I attend the CIBB 2024 conference at Università del Sannio in Benevento (Italy, EU) where I give two talks entitled "Longitudinal clustering on electronic mental health records reveals meaningful groups of disease trajectories" and "A method based on DBSCAN clustering to measure UMAP dimensionality reduction results".
2024-09-03: My article titled "Seven quick tips for gene-focused computational pangenomic analysis" was published in the BioData Mining journal.
2024-09-03: My article titled "Ten quick tips for clinical electroencephalographic (EEG) data acquisition and signal processing" was published in the PeerJ Computer Science journal, within the Revolutionizing Healthcare: The Role of AI and Machine Learning special issue.
2024-09-03: My article titled "Ten quick tips for electrocardiogram (ECG) signal processing" was published in the PeerJ Computer Science journal, within the Revolutionizing Healthcare: The Role of AI and Machine Learning special issue.
2024-06-13: My colleagues and I within the MMSP lab organize the 1st Milan Workshop on Computational Methods for Mental Health and Well Being 2024 at Università di Milano-Bicocca.
2024-06-05: The online Inside Precision Medicine magazine interviewed me on integration of multi-omics data and published the interview on their website.
2024-05-24: I organize a special session entitled "Machine learning for structured data in clinical informatics and medical biology" at the CIBB 2024 conference scheduled in September in Benevento (Italy, EU).
2024-03-15: My article "Identifying prognostic factors for survival in intensive care unit patients with SIRS or sepsis by machine learning analysis on electronic health records" was published in the PLOS Digital Health journal.
2024-02-26: My article "Ensemble machine learning reveals key features for diabetes duration from electronic health records" was published in the PeerJ Computer Science journal.
2023-12-21: My article "Ten quick tips for fuzzy logic modeling of biomedical systems" was published in the PLOS Computational Biology journal.
2023-09-20: My article "Clinical feature ranking based on ensemble machine learning reveals top survival factors for glioblastoma multiforme" was published in the Journal of Healthcare Informatics Research.
2023-08-18: My article "Computational intelligence analysis of high-risk neuroblastoma patient health records reveals time to maximum response as one of the most relevant factors for outcome prediction" was published in the European Journal of Cancer.
2023-07-20: My article "Ten quick tips for bioinformatics analyses using an Apache Spark distributed computing environment" was published in the PLOS Computational Biology journal.
2023-07-06: My article "Ten quick tips for avoiding pitfalls in multi-omics data integration analyses" was published in the PLOS Computational Biology journal.
2023-06-22: My article "A statistical comparison between Matthews correlation coefficient (MCC), prevalence threshold, and Fowlkes–Mallows index" was published in the Journal of Biomedical Informatics.
2023-06-15: The last articles of the CIBB 2021 supplements in BMC Bioinformatics and BMC Medical Informatics and Decision Making, and of the CIBB 2021 proceedings in Springer Lecture Notes in Bioinformatics, for which I served as guest editor, were published online.
2023-06-09: I gave a talk on my geneExpressionFromGEO R package at the R/Medicine 2023 online conference.
2023-03-04: My article "Signature literature review reveals AHCY, DPYSL3, and NME1 as the most recurrent prognostic genes for neuroblastoma" was published in the BioData Mining journal.
2023-02-23: My article "Ten simple rules for providing bioinformatics support within a hospital" was published in the BioData Mining journal.
2023-02-17: My article "The Matthews correlation coefficient (MCC) should replace the ROC AUC as the standard metric for assessing binary classification" was published in the BioData Mining journal.
2023-01-05: My article "Ten quick tips for computational analysis of medical images" was published in the PLOS Computational Biology journal.
2022-12-15: My article "Eleven quick tips for data cleaning and feature engineering" was published in the PLOS Computational Biology journal.
2022-11-21: The first articles of the CMLS 2021 supplements, for which I served as a guest editor, were published in the BMC Bioinformatics volume 23 supplement 11 and in the BMC Medical Informatics and Decision Making volume 22 supplement 4.
2022-11-03: My article "Towards a potential pan-cancer prognostic signature for gene expression based on probesets and ensemble machine learning" was published in the BioData Mining journal.
2022-10-26: My article "A brief survey of tools for genomic regions enrichment analysis" was published in the Frontiers in Bioinformatics journal.
2022-10-04: My article "A survey on publicly available open datasets of electronic health records (EHRs) of patients with neuroblastoma" was published in the Data Science Journal.
2022-09-27: My article "The ABC recommendations for validation of supervised machine learning results in biomedical sciences" was published in the Frontiers in Big Data journal.
2022-08-25: My article "Ten simple rules for organizing a special session at a scientific conference" was published in the PLOS Computational Biology journal.
2022-08-11: My article "Nine quick tips for pathway enrichment analysis" was published in the PLOS Computational Biology journal.
2022-07-14: The first articles of the CIBB 2021 conference supplements, that I coordinated and for which I served as a guest editor, were published in the BMC Bioinformatics volume 23 supplement 6 and in the BMC Medical Informatics and Decision Making volume 22 supplement 6.
2022-03-25: My article "An invitation to greater use of Matthews correlation coefficient in robotics and artificial intelligence" was published in the Frontiers in Robotics and AI journal.
2022-02-07: My article "A machine learning analysis of health records of patients with chronic kidney disease at risk of cardiovascular disease" is featured and explained in the ExplainThisPaper.com website.
2021-12-23: My article "geoCancerPrognosticDatasetsRetriever, a bioinformatics tool to easily identify cancer prognostic datasets on Gene Expression Omnibus (GEO)", written with Abbas Alameer, was published in the Bioinformatics Oxford journal.
2021-12-22: My article "A machine learning analysis of health records of patients with chronic kidney disease at risk of cardiovascular disease" was published in the IEEE Access journal.
2021-12-14: My chapter "geneExpressionFromGEO: an R package to facilitate data reading from Gene Expression Omnibus (GEO)" was published in the Microarray Data Analysis (Methods in Molecular Biology, Springer Protocols) book.
2021-12-02: My R software package easyDifferentialGeneCoexpression was published on CRAN, my R package healthyControlsPresenceChecker was published on Bioconductor, and the Perl software packages geoCancerPrognosticDatasetsRetriever and geoCancerDiagnosticDatasetsRetriever to which I contributed have been published on CPAN.
2021-10-04: The supplement of the 1st International Workshop on Conceptual Modeling for Life Sciences (CMLS 2020), for which I served as a guest editor, was published in the BMC Bioinformatics journal.
2021-07-05: My article "The coefficient of determination R-squared is more informative than SMAPE, MAE, MAPE, MSE and RMSE in regression analysis evaluation" was published in the PeerJ Computer Science journal.
2021-05-27: My article "Arterial disease computational prediction and health record feature ranking among patients diagnosed with inflammatory bowel disease" was published in the IEEE Access journal.
2021-05-26: My article "The Matthews correlation coefficient (MCC) is more informative than Cohen’s Kappa and Brier score in binary classification assessment" was published in the IEEE Access journal.
2021-03-31: My article "The benefits of the Matthews correlation coefficient (MCC) over the diagnostic odds ratio (DOR) in binary classification assessment" was published in the IEEE Access journal.
2021-03-25: I gave a keynote talk entitled "The advantages of the Matthews correlation coefficient (MCC) in binary classification evaluation" at the Symposium on Interdisciplinary Bioinformatics and Biomedical Data Science 2021, organized online at Philipps-Universität Marburg.
2021-03-17: The book chapter "Brief survey on machine learning in epistasis", that I wrote with Trent Faultless, was published in the Epistasis book within the Springer Methods in Molecular Biology series.
2021-03-09: The article "Machine learning compared to conventional statistical models for predicting myocardial infarction readmission and mortality: a systematic review", to which I contributed, was published in the Canadian Journal of Cardiology.
2021-02-05: My article "An ensemble learning approach for enhanced classification of patients with hepatitis and cirrhosis" was published in the IEEE Access journal.
2021-02-04: My article "The Matthews correlation coefficient (MCC) is more reliable than balanced accuracy, bookmaker informedness, and markedness in two-class confusion matrix evaluation" was published in the BioData Mining journal.
2021-02-03: My article "Data analytics and clinical feature ranking of medical records of patients with sepsis" was published in the BioData Mining journal.
2021-01-27: My article "Computational intelligence identifies alkaline phosphatase (ALP), alpha-fetoprotein (AFP), and hemoglobin levels as most predictive survival factors for hepatocellular carcinoma" was published in the Health Informatics Journal.
2020-12-17: Five articles of my CIBB 2019 Special Session on Machine Learning in Healthcare Informatics and Medical Biology have been published in the conference proceedings book.
2020-12-07: My R software package geneExpressionFromGEO has been included in the CRAN package archive.
2020-12-01: My article "An enhanced Random Forests approach to predict heart failure from small imbalanced gene expression data" was published in the IEEE/ACM Transactions on Computational Biology and Bioinformatics journal.
2020-11-17: The article "Machine learning vs. conventional statistical models for predicting heart failure readmission and mortality", of which I am a co-author, was published in the European Society of Cardiology (ESC) Heart Failure journal.
2020-10-13: My article "Survival prediction of patients with sepsis from age, sex, and septic episode number alone" was published in the Scientific Reports journal.
2020-08-31: My chapter "Siamese neural networks: an overview" was published in the Artificial Neural Networks (3rd edition) book edited by Hugh Cartwright and released by Springer within the Springer Methods in Molecular Biology series.
2020-08-20: The supplement "Selected articles from the CIBB 2019 Special Session on Machine Learning in Healthcare Informatics and Medical Biology", for which I served as guest editor, was published in the BMC Medical Informatics and Decision Making journal.
2020-06-23: My preprint entitled "The MCC-F1 curve: a performance evaluation technique for binary classification" has been released on arXiv.org
2020-06-16: My derived dataset about heart failure clinical records was published on the University of California Irvine Machine Learning Repository.
2020-04-09: The Frontiers in Genetics journal published an editorial I wrote with Angelo Facchiano and Dominik Heider about our Research Topic "Artificial intelligence bioinformatics: development and application of tools for omics and inter-omics studies".
2020-04-06: My paper "Ten quick tips for machine learning in computational biology" has been translated into simplified Chinese by some volunteers of the EpiMan.cn forum coordinated by Qiguo Lian (Shanghai Institute of Planned Parenthood Research) and reviewed by Yun Niu (Krembil Research Institute). This Chinese document is available here.
2020-02-03: My paper "Machine learning can predict survival of patients with heart failure from serum creatinine and ejection fraction alone" was published in the BMC Medical Informatics and Decision Making journal.
2020-01-02: My paper "The advantages of the Matthews correlation coefficient (MCC) over F1 score and accuracy in binary classification evaluation" was published in the BMC Genomics journal.
2019-09-05: The special session on "Machine Learning in Health Informatics and Medical Biology" that I organized was held at CIBB 2019 conference in Bergamo (Italy, EU).
2019-07-02: I was appointed co-editor for the Research Topic "Artificial intelligence bioinformatics: development and application of tools for omics and inter-omics studies" for the Frontiers in Genetics journal.
2019-06-24: My paper "Ten quick tips for machine learning in computational biology" has been ranked top 5th most accessed paper on BioData Mining ever.
2019-06-17: The paper "Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen" of which I am a consortium co-author was published on Nature Communications.
2019-05-03: I participated in the Ted Rogers Centre for Hearth Research 2019 Heart Failure Symposium in Toronto.
2019-04-11: I am a member of the program committees of the the 16th International Conference on Computational Intelligence methods for Bioinformatics and Biostatistics (CIBB 2019) and of the 6th International Conference on Information Management and Big Data (SIMBig 2019) - Track on Biomedical Data Science.
2019-02-19: I presented my paper "Computational prediction of diagnosis and feature selection on mesothelioma patient health records" at the Toronto Deep Learning Series. Here's the video recording on YouTube.
2019-01-24: The paper "Stratification of amyotrophic lateral sclerosis patients: a crowdsourcing approach" of which I am a consortium co-author was published on Scientific Reports.
2019-01-15: My preprint "BEHST: genomic set enrichment analysis enhanced through integration of chromatin long-range interactions" has been released on bioRxiv.
2019-01-10: My paper "Computational prediction of diagnosis and feature selection on mesothelioma patient health records" was published in the PLOS One journal, within the Machine Learning for Health and Biomedicine collection.
2019-01-02: My paper "Supervised deep learning embeddings for the prediction of cervical cancer diagnosis" has been ranked 3rd most viewed and downloaded article in the PeerJ Computer Science journal in 2018.
2018-09-08: I am the organizer of the special session entitled "Machine learning in health informatics and biological systems" at the CIBB 2018 conference in Almada, Portugal, EU.
2018-09-06: The book chapter "Biological and medical ontologies: Protein Ontology (PRO)" that I wrote was published in the Elsevier's Encyclopedia of Bioinformatics and Computational Biology.
2018-07-19: I participate as a panelist to the AI in Health event organized by the Toronto AI MeetUp in Toronto, Ontario, Canada.
2018-07-03: The paper "Bioconda: sustainable and comprehensive software distribution for the life sciences" about the Bioconda project was published on Nature Methods, and I am one of the co-authors.
2018-06-17: I participate to the Journey to Conquer Cancer Run Or Walk 2018 for Princess Margaret Cancer Foundation.
2018-05-31: I give a talk entitled "Ten quick tips for machine learning in computational biology" at the Toronto AI MeetUp.
2018-05-14: My paper entitled "Supervised deep learning embeddings for the prediction of cervical cancer diagnosis" was published on the PeerJ Computer Science journal.
2018-04-09: I am a co-author of the preprint entitled "Stratification of amyotrophic lateral sclerosis patients: a crowdsourcing approach", released on bioRxiv by the community of the DREAM Amyotrophic lateral sclerosis (ALS) Stratification Prize4Life Challenge.
2018-03-26: I am a participant in the Kaggle 5-Day Data Cleaning Challenge.
2018-03-20: I am the organizer and one of the teachers of the University Health Network Office for Research Trainees "Translating bioinformatics for everyday biology" workshop at the Princess Margaret Cancer Centre.
2018-03-18: I served as a judge at the Bioinformatics and Computational Biology Hackathon BCB BioHacks2018 at the University of Toronto.
2018-02-26: I gave an invited talk entitled "Ten quick tips for machine learning in computational biology" at the Weekly Research Seminar of the Broad Institute.
2017-12-08: My paper entitled "Ten quick tips for machine learning in computational biology" was published on the BioData Mining journal.
2017-11-19: I presented a poster entitled "BEHST: genomic set enrichment analysis enhanced through integration of chromatin long-range interactions" at the RECOMB/ISCB 2017 Conference on Regulatory & Systems Genomics with DREAM CHALLENGES, at Memorial Sloan Kettering Center, New York City, USA.
2017-11-15: I am a co-author of the preprint entitled "A cancer pharmacogenomic screen powering crowd-sourced advancement of drug combination prediction", released on bioRxiv by the community of the AstraZeneca-Sanger Drug Combination Prediction DREAM Challenge.
2017-10-24: I am a co-author of the preprint entitled "Bioconda: a sustainable and comprehensive software distribution for the life sciences", recently uploaded on bioRxiv by the Bioconda community.
2017-05-02: My paper “Novelty indicator for enhanced prioritization of predicted Gene Ontology annotations“, which I wrote with Fernando Palluzzi and Marco Masseroli, was published in the IEEE/ACM Transactions on Computational Biology and Bioinformatics journal.
2017-01-08: Michael M. Hoffman and I wrote a report about the Genome Informatics 2016 conference, which has been recently published on the Genome Biology journal.
2016-11-23: My lab and I have published a new preprint entitled “Semi-automated genome annotation using epigenomic data and Segway” on bioRxiv You’re welcome to read it and send us your suggestion about it.
2016-09-29: On 3rd October 2016 I’ll present a poster on “Deep siamese neural networks for prediction of long-range interactions in chromatin” Abcam Symposium 2016, at MaRS Auditorium in Toronto.
2016-08-08: Our chapter entitled "Validation pipeline for computational prediction of genomics annotations", written by me and Marco Masseroli, was published in the Springer Lecture Notes in Bioinformatics (LNBI) book of the Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB) 2015 conferenceselected papers.
2016-05-06: From 16th to 19th May 2016, I will be with my lab-mates at the Great Lakes Bioinformatics Conference (GLBIO) 2016 at University of Toronto. I will have an oral presentation about my work, entitled “Distal chromatin loop prediction with deep siamese neural networks“.
2016-04-06: Our paper “Ontology-based prediction and prioritization of gene functional annotations“, which I wrote with Marco Masseroli, was published in the IEEE/ACM Transactions on Computational Biology and Bioinformatics journal.
davide.chicco(AT)gmail.com
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