Mattia C. F. Prosperi

Publication Activity (10 Years)

Years Active: 2007-2023
Publications (10 Years): 67

Top Topics

Natural Language Processing

Causal Inference

Hepatitis C Virus

Top Venues

Int. J. Medical Informatics

Publications

Zhaoyi Chen, Hansi Zhang, Xi Yang, Songzi Wu, Xing He, Jie Xu, Jingchuan Guo, Mattia C. F. Prosperi, Fei Wang, Hua Xu, Yong Chen, Hui Hu, Steven DeKosky, Matthew Farrer, Yi Guo, Yonghui Wu, Jiang Bian
Assess the documentation of cognitive tests and biomarkers in electronic health records via natural language processing for Alzheimer's disease and related dementias. Int. J. Medical Informatics 170 (2023)
Shantanu Ghosh, Zheng Feng, Jiang Bian, Kevin Butler, Mattia C. F. Prosperi
DR-VIDAL - Doubly Robust Variational Information-theoretic Deep Adversarial Learning for Counterfactual Prediction and Treatment Effect Estimation on Real World Data. CoRR (2023)
Nathalie Bonin, Enrique Doster, Hannah Worley, Lee J. Pinnell, Jonathan E. Bravo, Peter Ferm, Simone Marini, Mattia C. F. Prosperi, Noelle R. Noyes, Paul S. Morley, Christina Boucher
MEGARes and AMR++, v3.0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing. Nucleic Acids Res. 51 (D1) (2023)
Aokun Chen, Daniel Paredes, Zehao Yu, Xiwei Lou, Roberta Brunson, Jamie N. Thomas, Kimberly A. Martinez, Robert J. Lucero, Tanja Magoc, Laurence M. Solberg, Urszula Alina Snigurska, Sarah E. Ser, Mattia C. F. Prosperi, Jiang Bian, Ragnhildur I. Bjarnadottir, Yonghui Wu
Identifying Symptoms of Delirium from Clinical Narratives Using Natural Language Processing. CoRR (2023)
Yunpeng Zhao, Xing He, Zheng Feng, Sarah Bost, Mattia C. F. Prosperi, Yonghui Wu, Yi Guo, Jiang Bian
Biases in using social media data for public health surveillance: A scoping review. Int. J. Medical Informatics 164 (2022)
Patrizia Vizza, Giuseppe Tradigo, Pietro H. Guzzi, Barbara Puccio, Mattia C. F. Prosperi, Carlo Torti, Pierangelo Veltri
Annotations of Virus Data for Knowledge Enrichment. ICHI (2022)
Mattia C. F. Prosperi, Brittany Rife Magalis, Simone Marini, Marco Salemi
Transmission cluster characteristics of global, regional, and lineage-specific SARS-CoV-2 phylogenies. BIBM (2022)
Shantanu Ghosh, Zheng Feng, Jiang Bian, Kevin Butler, Mattia C. F. Prosperi
DR-VIDAL - Doubly Robust Variational Information-theoretic Deep Adversarial Learning for Counterfactual Prediction and Treatment Effect Estimation. AMIA (2022)
Simone Marini, Rodrigo A. Mora, Christina Boucher, Noelle Robertson Noyes, Mattia C. F. Prosperi
Towards routine employment of computational tools for antimicrobial resistance determination via high-throughput sequencing. Briefings Bioinform. 23 (2) (2022)
Hansi Zhang, Tianchen Lyu, Pengfei Yin, Sarah Bost, Xing He, Yi Guo, Mattia C. F. Prosperi, Willian R. Hogan, Jiang Bian
A scoping review of semantic integration of health data and information. Int. J. Medical Informatics 165 (2022)
Mattia C. F. Prosperi, Christina Boucher, Jiang Bian, Simone Marini
Assessing putative bias in prediction of anti-microbial resistance from real-world genotyping data under explicit causal assumptions. Artif. Intell. Medicine 130 (2022)
Franco Milicchio, Marco Oliva, Mattia C. F. Prosperi
An interleaved hardware-accelerated k-mer parser. BIBM (2022)
Urszula Alina Snigurska, Sarah Ser, Mattia C. F. Prosperi, Ragnhildur I. Bjarnadottir, Robert Lucero
Complementing ICD Codes with Nurses' Assessment Data Can Improve the Identification of Patients with Hearing and Visual Impairments. AMIA (2022)
Inyoung Jun, Simone Marini, Christina Boucher, J. Glenn Morris, Jiang Bian, Mattia C. F. Prosperi
Joint Application of the Target Trial Causal Framework and Machine Learning Modeling to Optimize Antibiotic Therapy: Use Case on Acute Bacterial Skin and Skin Structure Infections due to Methicillin-resistant Staphylococcus aureus. CoRR (2022)
Kingshuk Mukherjee, Daniel Dole-Muinos, Massimiliano Rossi, Ayomide Ajayi, Mattia C. F. Prosperi, Christina Boucher
Finding Overlapping Rmaps via Clustering. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (6) (2022)
Mattia C. F. Prosperi, Jie Xu, Jingchuan Serena Guo, Jiang Bian, Wei-Han William Chen, Shantrel Canidate, Simone Marini, Mo Wang
Identification of Social and Racial Disparities in Risk of HIV Infection in Florida using Causal AI Methods. BIBM (2022)
Simone Marini, Carla Mavian, Alberto Riva, Mattia C. F. Prosperi, Marco Salemi, Brittany Rife Magalis
Optimizing viral genome subsampling by genetic diversity and temporal distribution (TARDiS) for phylogenetics. Bioinform. 38 (3) (2022)
Zheng Feng, Mattia C. F. Prosperi, Jiang Bian
Variational Temporal Deconfounder for Individualized Treatment Effect Estimation from Longitudinal Observational Data. CoRR (2022)
Mattia C. F. Prosperi, Simone Marini, Christina Boucher
Fast and exact quantification of motif occurrences in biological sequences. BMC Bioinform. 22 (1) (2021)
Shantanu Ghosh, Jiang Bian, Yi Guo, Mattia C. F. Prosperi
Deep propensity network using a sparse autoencoder for estimation of treatment effects. J. Am. Medical Informatics Assoc. 28 (6) (2021)
Mattia C. F. Prosperi, Shantanu Ghosh, Zhaoyi Chen, Marco Salemi, Tianchen Lyu, Jinying Zhao, Jiang Bian
Causal AI with Real World Data: Do Statins Protect from Alzheimer's Disease Onset? ICMHI (2021)
Yi Guo, Yahan Zhang, Tianchen Lyu, Mattia C. F. Prosperi, Fei Wang, Hua Xu, Jiang Bian
The application of artificial intelligence and data integration in COVID-19 studies: a scoping review. J. Am. Medical Informatics Assoc. 28 (9) (2021)
Zhaoyi Chen, Hansi Zhang, Yi Guo, Thomas J. George, Mattia C. F. Prosperi, William R. Hogan, Zhe He, Elizabeth A. Shenkman, Fei Wang, Jiang Bian
Exploring the feasibility of using real-world data from a large clinical data research network to simulate clinical trials of Alzheimer's disease. npj Digit. Medicine 4 (2021)
Mattia C. F. Prosperi, Simone Marini
KARGA: Multi-platform Toolkit for k-mer-based Antibiotic Resistance Gene Analysis of High-throughput Sequencing Data. BHI (2021)
Mattia C. F. Prosperi, Yi Guo, Jiang Bian
Bagged random causal networks for interventional queries on observational biomedical datasets. J. Biomed. Informatics 115 (2021)
Yunpeng Zhao, Pengfei Yin, Yongqiu Li, Xing He, Jingcheng Du, Cui Tao, Yi Guo, Mattia C. F. Prosperi, Pierangelo Veltri, Xi Yang, Yonghui Wu, Jiang Bian
Data and Model Biases in Social Media Analyses: A Case Study of COVID-19 Tweets. AMIA (2021)
Franco Milicchio, Mattia C. F. Prosperi
Experimental Survey on Power Dissipation of k-mer-Handling Data Structures for Mobile Bioinformatics. BIBM (2021)
Mattia C. F. Prosperi, Simone Marini, Christina Boucher, Jiang Bian
Assessing putative bias in prediction of anti-microbial resistance from real-world genotyping data under explicit causal assumptions. CoRR (2021)
Inyoung Jun, Shannan N. Rich, Zhaoyi Chen, Jiang Bian, Mattia C. F. Prosperi
bacteremia infections. Int. J. Medical Informatics 153 (2021)
Hansi Zhang, Christopher Wheldon, Adam G. Dunn, Cui Tao, Jinhai Huo, Rui Zhang, Mattia C. F. Prosperi, Yi Guo, Jiang Bian
Mining Twitter to assess the determinants of health behavior toward human papillomavirus vaccination in the United States. J. Am. Medical Informatics Assoc. 27 (2) (2020)
Yi Guo, Jiang Bian, François Modave, Qian Li, Thomas J. George, Mattia C. F. Prosperi, Elizabeth Shenkman
Assessing the effect of data integration on predictive ability of cancer survival models. Health Informatics J. 26 (1) (2020)
David S. Lindberg, Mattia C. F. Prosperi, Ragnhildur I. Bjarnadottir, Jaime Thomas, Marsha Crane, Zhaoyi Chen, Kristen Shear, Laurence M. Solberg, Urszula Alina Snigurska, Yonghui Wu, Yunpeng Xia, Robert J. Lucero
Identification of important factors in an inpatient fall risk prediction model to improve the quality of care using EHR and electronic administrative data: A machine-learning approach. Int. J. Medical Informatics 143 (2020)
Hansi Zhang, Yi Guo, Mattia C. F. Prosperi, Jiang Bian
An ontology-based documentation of data discovery and integration process in cancer outcomes research. BMC Medical Informatics Decis. Mak. (4) (2020)
Mattia C. F. Prosperi, Jiang Bian, Mo Wang
Multivariate Independence Set Search via Progressive Addition for Conditional Markov Acyclic Networks. BIBM (2020)
Yunpeng Zhao, Mattia C. F. Prosperi, Tianchen Lyu, Yi Guo, Jiang Bian
Integrating Crowdsourcing and Active Learning for Classification of Work-Life Events from Tweets. CoRR (2020)
Yunpeng Zhao, Yi Guo, Xing He, Yonghui Wu, Xi Yang, Mattia C. F. Prosperi, Yanghua Jin, Jiang Bian
Assessing mental health signals among sexual and gender minorities using Twitter data. Health Informatics J. 26 (2) (2020)
Yunpeng Zhao, Mattia C. F. Prosperi, Tianchen Lyu, Yi Guo, Le Zhou, Jiang Bian
Integrating Crowdsourcing and Active Learning for Classification of Work-Life Events from Tweets. IEA/AIE (2020)
Marco Oliva, Franco Milicchio, Kaden King, Grace Benson, Christina Boucher, Mattia C. F. Prosperi, Inanç Birol
Portable nanopore analytics: are we there yet? Bioinform. 36 (16) (2020)
Jiang Bian, Tianchen Lyu, Alexander Loiacono, Tonatiuh Mendoza Viramontes, Gloria P. Lipori, Yi Guo, Yonghui Wu, Mattia C. F. Prosperi, Thomas J. George, Christopher A. Harle, Elizabeth A. Shenkman, William R. Hogan
Assessing the practice of data quality evaluation in a national clinical data research network through a systematic scoping review in the era of real-world data. J. Am. Medical Informatics Assoc. 27 (12) (2020)
Mattia C. F. Prosperi, Yi Guo, Matthew Sperrin, James S. Koopman, Jae S. Min, Xing He, Shannan N. Rich, Mo Wang, Iain E. Buchan, Jiang Bian
Causal inference and counterfactual prediction in machine learning for actionable healthcare. Nat. Mach. Intell. 2 (7) (2020)
Giuseppe Tradigo, Patrizia Vizza, Gabriel Gabriele, Maria Mazzitelli, Carlo Torti, Mattia C. F. Prosperi, Pietro Hiram Guzzi, Pierangelo Veltri
On the use of clinical based infection data for pandemic case studies. BIBM (2020)
Xing He, Rui Zhang, Rubina F. Rizvi, Jake Vasilakes, Xi Yang, Yi Guo, Zhe He, Mattia C. F. Prosperi, Jinhai Huo, Jordan Alpert, Jiang Bian
ALOHA: developing an interactive graph-based visualization for dietary supplement knowledge graph through user-centered design. BMC Medical Informatics Decis. Mak. (4) (2019)
Yunpeng Zhao, Jinhai Huo, Mattia C. F. Prosperi, Yi Guo, Yongqiu Li, Jiang Bian
Exploring Lung Cancer Screening Discussions on Twitter. MedInfo (2019)
François Modave, Yunpeng Zhao, Janice L. Krieger, Zhe He, Yi Guo, Jinhai Huo, Mattia C. F. Prosperi, Jiang Bian
Understanding Perceptions and Attitudes in Breast Cancer Discussions on Twitter. CoRR (2019)
François Modave, Yunpeng Zhao, Janice L. Krieger, Zhe He, Yi Guo, Jinhai Huo, Mattia C. F. Prosperi, Jiang Bian
Understanding Perceptions and Attitudes in Breast Cancer Discussions on Twitter. MedInfo (2019)
Rebecca Rose, Olga Golosova, Dmitrii Sukhomlinov, Aleksey Tiunov, Mattia C. F. Prosperi
Flexible design of multiple metagenomics classification pipelines with UGENE. Bioinform. 35 (11) (2019)
Hansi Zhang, Christopher Wheldon, Adam G. Dunn, Cui Tao, Jinhai Huo, Rui Zhang, Mattia C. F. Prosperi, Yi Guo, Jiang Bian
Mining Twitter to Assess the Determinants of Health Behavior towards Human Papillomavirus Vaccination in the United States. CoRR (2019)
Mattia C. F. Prosperi, Jiang Bian
Is it time to rethink institutional review boards for the era of big data? Nat. Mach. Intell. 1 (6) (2019)
Robert James Lucero, David S. Lindberg, Elizabeth Fehlberg, Ragnhildur I. Bjarnadottir, Yin Li, Jeannie P. Cimiotti, Marsha Crane, Mattia C. F. Prosperi
A data-driven and practice-based approach to identify risk factors associated with hospital-acquired falls: Applying manual and semi- and fully-automated methods. Int. J. Medical Informatics 122 (2019)
Mattia C. F. Prosperi, Taj Azarian, Judith A. Johnson, Marco Salemi, Franco Milicchio, Marco Oliva
Unexpected Predictors of Antibiotic Resistance in Housekeeping Genes of Staphylococcus Aureus. BCB (2019)
Massimiliano S. Tagliamonte, Sheldon G. Waugh, Mattia C. F. Prosperi, Volker Mai
An Integrated Approach for Efficient Multi-Omics Joint Analysis. BCB (2019)
Mattia C. F. Prosperi, Jae Min, Jiang Bian, François Modave
Big data hurdles in precision medicine and precision public health. BMC Medical Informatics Decis. Mak. 18 (1) (2018)
Zhaoyi Chen, Victoria Y. Bird, Rupam Ruchi, Mark S. Segal, Jiang Bian, Saeed R. Khan, Marie-Carmelle Elie, Mattia C. F. Prosperi
Development of a personalized diagnostic model for kidney stone disease tailored to acute care by integrating large clinical, demographics and laboratory data: the diagnostic acute care algorithm - kidney stones (DACA-KS). BMC Medical Informatics Decis. Mak. 18 (1) (2018)
Franco Milicchio, Marco Oliva, Christina Boucher, Mattia C. F. Prosperi
Third-generation sequencing data analytics on mobile devices: cache oblivious and out-of-core approaches as a proof-of-concept. FNC/MobiSPC (2018)
Xing He, Rui Zhang, Rubina F. Rizvi, Jake Vasilakes, Xi Yang, Yi Guo, Zhe He, Mattia C. F. Prosperi, Jiang Bian
Prototyping an Interactive Visualization of Dietary Supplement Knowledge Graph. BIBM (2018)
Xinsong Du, Jiang Bian, Mattia C. F. Prosperi
An Operational Deep Learning Pipeline for Classifying Life Events from Individual Tweets. SIMBig (2018)
Hansi Zhang, Zhe He, Xing He, Yi Guo, David R. Nelson, François Modave, Yonghui Wu, William R. Hogan, Mattia C. F. Prosperi, Jiang Bian
Computable Eligibility Criteria through Ontology-driven Data Access: A Case Study of Hepatitis C Virus Trials. AMIA (2018)
Franco Milicchio, Mattia C. F. Prosperi
Efficient data structures for mobile de novo genome assembly by third-generation sequencing. FNC/MobiSPC (2017)
Tianyao Huo, Thomas J. George Jr., Yi Guo, Zhe He, Mattia C. F. Prosperi, François Modave, Jiang Bian
Explore Care Pathways of Colorectal Cancer Patients with Social Network Analysis. MedInfo (2017)
Giuseppe Tradigo, Raffaele Vacca, T. Manini, Victoria Y. Bird, Travis A. Gerke, Pierangelo Veltri, Mattia C. F. Prosperi
A new approach to disentangle genetic and epigenetic components on disease comorbidities: studying correlation between genotypic and phenotypic disease networks. FNC/MobiSPC (2017)
Franco Milicchio, Rebecca Rose, Jiang Bian, Jae Min, Mattia C. F. Prosperi
Visual programming for next-generation sequencing data analytics. BioData Min. 9 (2016)
Giuseppe Tradigo, Francesca Cristiano, Stefano Alcaro, Sergio Greco, Gianluca Pollastri, Pierangelo Veltri, Mattia C. F. Prosperi
G-quadruplex Structure Prediction and integration in the GenData2020 data model. BCB (2016)
Francesca Cristiano, Pierangelo Veltri, Mattia C. F. Prosperi, Giuseppe Tradigo
On the identification of long non-coding RNAs from RNA-seq. BIBM (2016)
Franco Milicchio, Iain E. Buchan, Mattia C. F. Prosperi
A* fast and scalable high-throughput sequencing data error correction via oligomers. CIBCB (2016)
Franco Milicchio, Mattia C. F. Prosperi
Accessible Tourism for the Deaf via Mobile Apps. PETRA (2016)
Franco Milicchio, Giuseppe Tradigo, Pierangelo Veltri, Mattia C. F. Prosperi
High-performance data structures for de novo assembly of genomes: cache oblivious generic programming. BCB (2016)
Mattia C. F. Prosperi, Alejandro Pironti, Francesca Incardona, Giuseppe Tradigo, Maurizio Zazzi
Predicting human-immunodeficiency virus rebound after therapy initiation/switch using genetic, laboratory, and clinical data. BCB (2016)
Paolo Fraccaro, Benjamin Brown, Mattia C. F. Prosperi, Matthew Sperrin, Iain E. Buchan, Niels Peek
Development and preliminary validation of a dynamic, patient-tailored method to detect abnormal laboratory test results. MedInfo (2015)
Mattia C. F. Prosperi, Sarah L. Ingham, Anthony Howell, Fiona Lalloo, Iain E. Buchan, Dafydd Gareth Evans
Can multiple SNP testing in BRCA2 and BRCA1 female carriers be used to improve risk prediction models in conjunction with clinical assessment? BMC Medical Informatics Decis. Mak. 14 (2014)
Melissa M. Norström, Nazle M. Veras, Wei Huang, Mattia C. F. Prosperi, Jennifer Cook, Wendy Hartogensis, Frederick M. Hecht, Annika C. Karlsoon, Marco Salemi
T Cell Counts Correlates with HIV-1 Synonymous Rate in HLA-B*5701 Subjects with Different Risk of Disease Progression. PLoS Comput. Biol. 10 (9) (2014)
Richard Williams, Iain E. Buchan, Mattia C. F. Prosperi, John D. Ainsworth
Using String Metrics to Identify Patient Journeys through Care Pathways. AMIA (2014)
Franco Milicchio, Mattia C. F. Prosperi
HErCoOl: High-Throughput Error Correction by Oligomers. CBMS (2014)
Mattia C. F. Prosperi, Marco Salemi
QuRe: software for viral quasispecies reconstruction from next-generation sequencing data. Bioinform. 28 (1) (2012)
Mattia C. F. Prosperi, Simona Di Giambenedetto, Iuri Fanti, Genny Meini, Bianca Bruzzone, Annapaola Callegaro, Giovanni Penco, Patrizia Bagnarelli, Valeria Micheli, Elisabetta Paolini, Antonio Di Biagio, Valeria Ghisetti, Massimo Di Pietro, Maurizio Zazzi, Andrea De Luca, et al.
A Prognostic Model for Estimating the Time to Virologic Failure in HIV-1 Infected Patients Undergoing a New Combination Antiretroviral Therapy Regimen. BMC Medical Informatics Decis. Mak. 11 (2011)
Mattia C. F. Prosperi, Luciano Prosperi, Alessandro Bruselles, Isabella Abbate, Gabriella Rozera, Donatella Vincenti, Maria Carmela Solmone, Maria Rosaria Capobianchi, Giovanni Ulivi
Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing. BMC Bioinform. 12 (2011)
Mattia C. F. Prosperi, Roberto D'Autilia, Francesca Incardona, Andrea De Luca, Maurizio Zazzi, Giovanni Ulivi
Stochastic modelling of genotypic drug-resistance for human immunodeficiency virus towards long-term combination therapy optimization. Bioinform. 25 (8) (2009)
Andrea Gasparri, Mattia C. F. Prosperi
A bacterial colony growth framework for collaborative multi-robot localization. ICRA (2008)
Andrea Gasparri, Mattia C. F. Prosperi
A bacterial colony growth algorithm for mobile robot localization. Auton. Robots 24 (4) (2008)
Michal Rosen-Zvi, André Altmann, Mattia C. F. Prosperi, Ehud Aharoni, Hani Neuvirth, Anders Sönnerborg, Eugen Schülter, Daniel Struck, Yardena Peres, Francesca Incardona, Rolf Kaiser, Maurizio Zazzi, Thomas Lengauer
Selecting anti-HIV therapies based on a variety of genomic and clinical factors. ISMB (2008)
Iuri Fanti, Mattia C. F. Prosperi, Giovanni Ulivi, Alessandro Micarelli
HIV-1 Coreceptor Usage Prediction via Indexed Local Kernel Smoothing Methods and Grid-Based Multiple Statistical Validation. CBMS (2007)
Mattia C. F. Prosperi, Giovanni Ulivi, Maurizio Zazzi
Statistical Comparison of Machine Learning Techniques for Treatment Optimisation of Drug-Resistant HIV-1. CBMS (2007)