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Mattia Prosperi
Mattia C. F. Prosperi
Person information
- affiliation: University of Florida, Gainesville, FL, USA
- affiliation: University of Manchester, UK
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2020 – today
- 2024
- [j39]Simone Rancati, Giovanna Nicora, Mattia Prosperi, Riccardo Bellazzi, Marco Salemi, Simone Marini:
Forecasting dominance of SARS-CoV-2 lineages by anomaly detection using deep AutoEncoders. Briefings Bioinform. 25(6) (2024) - [c45]Chaoyue Sun, Yiyang Liu, Christina Parisi, Rebecca Fisk-Hoffman, Marco Salemi, Ruogu Fang, Brandi Danforth, Mattia Prosperi, Simone Marini:
Learning on Forecasting HIV Epidemic Based on Individuals' Contact Networks. BIOSTEC (2) 2024: 103-111 - [c44]Mattia Prosperi, Simone Marini, Christina Boucher:
An Average-Case Efficient Two-Stage Algorithm for Enumerating All Longest Common Substrings of Minimum Length $k$ Between Genome Pairs. ICHI 2024: 93-102 - [c43]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 Prosperi, Jiang Bian, Ragnhildur I. Bjarnadottir, Yonghui Wu:
Identifying Symptoms of Delirium from Clinical Narratives Using Natural Language Processing. ICHI 2024: 305-311 - [c42]Michael Aaron G. Sy, Mattia Prosperi, Mohammadali Serajian, Christina Boucher, Panayotis Takis Benos, Simone Marini:
Prediction of A. Baumannii Amikacin Resistance in Clinical Metagenomics. MIE 2024: 212-213 - 2023
- [j38]Zhaoyi Chen, Hansi Zhang, Xi Yang, Songzi Wu, Xing He, Jie Xu, Jingchuan Guo
, Mattia 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: 104973 (2023) - [j37]Piaopiao Li
The role of health system penetration rate in estimating the prevalence of type 1 diabetes in children and adolescents using electronic health records. J. Am. Medical Informatics Assoc. 31(1): 165-173 (2023) - [j36]Urszula Alina Snigurska
Application of a practice-based approach in variable selection for a prediction model development study of hospital-induced delirium. BMC Medical Informatics Decis. Mak. 23(1): 181 (2023) - [j35]Nathalie Bonin
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): 744-752 (2023) - [c41]Inyoung Jun, Sarah E. S. Leary, Jie Xu, Jiang Bian, Mattia Prosperi:
Quantification of Racial Disparity on Urinary Tract Infection Recurrence and Treatment Resistance in Florida using Algorithmic Fairness Methods. ICHI 2023: 261-267 - [c40]Thuc Duy Le, Jiuyong Li, Robert Ness, Sofia Triantafillou, Shohei Shimizu, Peng Cui, Kun Kuang, Jian Pei, Fei Wang, Mattia Prosperi:
Preface: The 2023 ACM SIGKDD Workshop on Causal Discovery, Prediction and Decision. CDPD 2023: 1-2 - [c39]Inyoung Jun, Scott A. Cohen, Sarah E. Ser, Simone Marini, Robert J. Lucero, Jiang Bian, Mattia Prosperi:
Optimizing Dynamic Antibiotic Treatment Strategies against Invasive Methicillin-Resistant Staphylococcus Aureus Infections using Causal Survival Forests and G-Formula on Statewide Electronic Health Record Data. CDPD 2023: 98-115 - [c38]Zheng Feng, Zhaoyi Chen, Yi Guo, Mattia Prosperi, Hiren J. Mehta, Dejana Braithwaite, Yonghui Wu, Jiang Bian:
Real-World Effectiveness of Lung Cancer Screening Using Deep Learning-Based Counterfactual Prediction. MedInfo 2023: 419-423 - [e1]Thuc Duy Le, Jiuyong Li, Robert Ness, Sofia Triantafillou, Shohei Shimizu, Peng Cui, Kun Kuang, Jian Pei, Fei Wang, Mattia Prosperi:
The KDD'23 Workshop on Causal Discovery, Prediction and Decision, 07 August 2023, Long Beach, CA, USA. Proceedings of Machine Learning Research 218, PMLR 2023 [contents] - [i8]Shantanu Ghosh, Zheng Feng, Jiang Bian, Kevin Butler, Mattia Prosperi:
DR-VIDAL - Doubly Robust Variational Information-theoretic Deep Adversarial Learning for Counterfactual Prediction and Treatment Effect Estimation on Real World Data. CoRR abs/2303.04201 (2023) - [i7]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 Prosperi, Jiang Bian, Ragnhildur I. Bjarnadottir
Identifying Symptoms of Delirium from Clinical Narratives Using Natural Language Processing. CoRR abs/2304.00111 (2023) - 2022
- [j34]Mattia 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: 102326 (2022) - [j33]Simone Marini
Towards routine employment of computational tools for antimicrobial resistance determination via high-throughput sequencing. Briefings Bioinform. 23(2) (2022) - [j32]Simone Marini
Optimizing viral genome subsampling by genetic diversity and temporal distribution (TARDiS) for phylogenetics. Bioinform. 38(3): 856-860 (2022) - [j31]Yunpeng Zhao, Xing He, Zheng Feng, Sarah Bost, Mattia 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: 104804 (2022) - [j30]Hansi Zhang, Tianchen Lyu, Pengfei Yin, Sarah Bost, Xing He, Yi Guo, Mattia Prosperi, William R. Hogan, Jiang Bian:
A scoping review of semantic integration of health data and information. Int. J. Medical Informatics 165: 104834 (2022) - [j29]Kingshuk Mukherjee
Finding Overlapping Rmaps via Clustering. IEEE ACM Trans. Comput. Biol. Bioinform. 19(6): 3114-3123 (2022) - [c37]Shantanu Ghosh, Zheng Feng, Jiang Bian, Kevin Butler, Mattia Prosperi:
DR-VIDAL - Doubly Robust Variational Information-theoretic Deep Adversarial Learning for Counterfactual Prediction and Treatment Effect Estimation. AMIA 2022 - [c36]Urszula Alina Snigurska, Sarah E. Ser, Mattia 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 - [c35]Franco Milicchio, Marco Oliva, Mattia Prosperi:
An interleaved hardware-accelerated k-mer parser. BIBM 2022: 2929-2933 - [c34]Mattia Prosperi, Jie Xu, Jingchuan Serena Guo
Identification of Social and Racial Disparities in Risk of HIV Infection in Florida using Causal AI Methods. BIBM 2022: 2934-2939 - [c33]Mattia Prosperi, Brittany Rife Magalis, Simone Marini, Marco Salemi:
Transmission cluster characteristics of global, regional, and lineage-specific SARS-CoV-2 phylogenies. BIBM 2022: 2940-2944 - [c32]Patrizia Vizza
Annotations of Virus Data for Knowledge Enrichment. ICHI 2022: 492-494 - [i6]Inyoung Jun, Simone Marini, Christina Boucher, J. Glenn Morris, Jiang Bian, Mattia 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 abs/2207.07458 (2022) - [i5]Zheng Feng, Mattia Prosperi, Jiang Bian:
Variational Temporal Deconfounder for Individualized Treatment Effect Estimation from Longitudinal Observational Data. CoRR abs/2207.11251 (2022) - 2021
- [j28]Mattia Prosperi
Fast and exact quantification of motif occurrences in biological sequences. BMC Bioinform. 22(1): 445 (2021) - [j27]Inyoung Jun
Challenges in replicating secondary analysis of electronic health records data with multiple computable phenotypes: A case study on methicillin-resistant Staphylococcus aureus bacteremia infections. Int. J. Medical Informatics 153: 104531 (2021) - [j26]Shantanu Ghosh
Deep propensity network using a sparse autoencoder for estimation of treatment effects. J. Am. Medical Informatics Assoc. 28(6): 1197-1206 (2021) - [j25]Yi Guo
The application of artificial intelligence and data integration in COVID-19 studies: a scoping review. J. Am. Medical Informatics Assoc. 28(9): 2050-2067 (2021) - [j24]Mattia Prosperi, Yi Guo, Jiang Bian:
Bagged random causal networks for interventional queries on observational biomedical datasets. J. Biomed. Informatics 115: 103689 (2021) - [j23]Zhaoyi Chen
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) - [c31]Yunpeng Zhao, Pengfei Yin, Yongqiu Li, Xing He, Jingcheng Du, Cui Tao, Yi Guo, Mattia 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 - [c30]Mattia Prosperi, Simone Marini:
KARGA: Multi-platform Toolkit for k-mer-based Antibiotic Resistance Gene Analysis of High-throughput Sequencing Data. BHI 2021: 1-4 - [c29]Franco Milicchio, Mattia Prosperi:
Experimental Survey on Power Dissipation of k-mer-Handling Data Structures for Mobile Bioinformatics. BIBM 2021: 3201-3206 - [c28]Mattia Prosperi, Shantanu Ghosh
Causal AI with Real World Data: Do Statins Protect from Alzheimer's Disease Onset? ICMHI 2021: 296-303 - [i4]Mattia 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 abs/2107.03383 (2021) - 2020
- [j22]Marco Oliva, Franco Milicchio
Portable nanopore analytics: are we there yet? Bioinform. 36(16): 4399-4405 (2020) - [j21]Yi Guo, Jiang Bian
Assessing the effect of data integration on predictive ability of cancer survival models. Health Informatics J. 26(1) (2020) - [j20]Yunpeng Zhao
Assessing mental health signals among sexual and gender minorities using Twitter data. Health Informatics J. 26(2): 765-786 (2020) - [j19]David S. Lindberg, Mattia Prosperi, Ragnhildur I. Bjarnadottir
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: 104272 (2020) - [j18]Hansi Zhang, Christopher Wheldon
Mining Twitter to assess the determinants of health behavior toward human papillomavirus vaccination in the United States. J. Am. Medical Informatics Assoc. 27(2): 225-235 (2020) - [j17]Jiang Bian
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): 1999-2010 (2020) - [j16]Hansi Zhang, Yi Guo, Mattia Prosperi, Jiang Bian
An ontology-based documentation of data discovery and integration process in cancer outcomes research. BMC Medical Informatics Decis. Mak. 20-S(4): 292 (2020) - [j15]Mattia Prosperi
Causal inference and counterfactual prediction in machine learning for actionable healthcare. Nat. Mach. Intell. 2(7): 369-375 (2020) - [c27]Mattia Prosperi, Jiang Bian, Mo Wang
Multivariate Independence Set Search via Progressive Addition for Conditional Markov Acyclic Networks. BIBM 2020: 1477-1481 - [c26]Giuseppe Tradigo, Patrizia Vizza
On the use of clinical based infection data for pandemic case studies. BIBM 2020: 2313-2317 - [c25]Yunpeng Zhao, Mattia 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: 333-344 - [i3]Yunpeng Zhao, Mattia Prosperi, Tianchen Lyu, Yi Guo, Jiang Bian:
Integrating Crowdsourcing and Active Learning for Classification of Work-Life Events from Tweets. CoRR abs/2003.12139 (2020)
2010 – 2019
- 2019
- [j14]Rebecca Rose, Olga Golosova, Dmitrii Sukhomlinov, Aleksey Tiunov, Mattia Prosperi:
Flexible design of multiple metagenomics classification pipelines with UGENE. Bioinform. 35(11): 1963-1965 (2019) - [j13]Robert James Lucero
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: 63-69 (2019) - [j12]Xing He
ALOHA: developing an interactive graph-based visualization for dietary supplement knowledge graph through user-centered design. BMC Medical Informatics Decis. Mak. 19-S(4): 150:1-150:18 (2019) - [j11]Mattia Prosperi, Jiang Bian:
Is it time to rethink institutional review boards for the era of big data? Nat. Mach. Intell. 1(6): 260 (2019) - [c24]Mattia 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: 259-268 - [c23]Massimiliano S. Tagliamonte, Sheldon G. Waugh, Mattia Prosperi, Volker Mai
An Integrated Approach for Efficient Multi-Omics Joint Analysis. BCB 2019: 619-625 - [c22]François Modave, Yunpeng Zhao, Janice L. Krieger, Zhe He
Understanding Perceptions and Attitudes in Breast Cancer Discussions on Twitter. MedInfo 2019: 1293-1297 - [c21]Yunpeng Zhao, Jinhai Huo, Mattia Prosperi, Yi Guo, Yongqiu Li, Jiang Bian:
Exploring Lung Cancer Screening Discussions on Twitter. MedInfo 2019: 2011-2012 - [i2]François Modave, Yunpeng Zhao, Janice L. Krieger, Zhe He, Yi Guo, Jinhai Huo, Mattia Prosperi, Jiang Bian:
Understanding Perceptions and Attitudes in Breast Cancer Discussions on Twitter. CoRR abs/1905.12469 (2019) - [i1]Hansi Zhang, Christopher Wheldon, Adam G. Dunn, Cui Tao, Jinhai Huo, Rui Zhang, Mattia Prosperi, Yi Guo, Jiang Bian:
Mining Twitter to Assess the Determinants of Health Behavior towards Human Papillomavirus Vaccination in the United States. CoRR abs/1907.11624 (2019) - 2018
- [j10]Zhaoyi Chen
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): 72:1-72:14 (2018) - [j9]Mattia Prosperi
Big data hurdles in precision medicine and precision public health. BMC Medical Informatics Decis. Mak. 18(1): 139:1-139:15 (2018) - [c20]Hansi Zhang, Zhe He, Xing He, Yi Guo, David R. Nelson, François Modave, Yonghui Wu, William R. Hogan, Mattia Prosperi, Jiang Bian:
Computable Eligibility Criteria through Ontology-driven Data Access: A Case Study of Hepatitis C Virus Trials. AMIA 2018 - [c19]Xing He
Prototyping an Interactive Visualization of Dietary Supplement Knowledge Graph. BIBM 2018: 1649-1652 - [c18]Franco Milicchio, Marco Oliva, Christina Boucher, Mattia Prosperi:
Third-generation sequencing data analytics on mobile devices: cache oblivious and out-of-core approaches as a proof-of-concept. FNC/MobiSPC 2018: 219-226 - [c17]Xinsong Du
An Operational Deep Learning Pipeline for Classifying Life Events from Individual Tweets. SIMBig 2018: 54-66 - 2017
- [c16]Franco Milicchio, Mattia Prosperi:
Efficient data structures for mobile de novo genome assembly by third-generation sequencing. FNC/MobiSPC 2017: 440-447 - [c15]Giuseppe Tradigo, Raffaele Vacca
A new approach to disentangle genetic and epigenetic components on disease comorbidities: studying correlation between genotypic and phenotypic disease networks. FNC/MobiSPC 2017: 453-458 - [c14]Tianyao Huo, Thomas J. George Jr.
Explore Care Pathways of Colorectal Cancer Patients with Social Network Analysis. MedInfo 2017: 1270 - 2016
- [j8]Franco Milicchio
Visual programming for next-generation sequencing data analytics. BioData Min. 9: 16 (2016) - [c13]Mattia 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: 611-615 - [c12]Franco Milicchio
High-performance data structures for de novo assembly of genomes: cache oblivious generic programming. BCB 2016: 657-662 - [c11]Giuseppe Tradigo, Francesca Cristiano, Stefano Alcaro, Sergio Greco
G-quadruplex Structure Prediction and integration in the GenData2020 data model. BCB 2016: 663-670 - [c10]Francesca Cristiano, Pierangelo Veltri
On the identification of long non-coding RNAs from RNA-seq. BIBM 2016: 1103-1106 - [c9]Franco Milicchio
A* fast and scalable high-throughput sequencing data error correction via oligomers. CIBCB 2016: 1-9 - [c8]Franco Milicchio
Accessible Tourism for the Deaf via Mobile Apps. PETRA 2016: 23 - 2015
- [c7]Paolo Fraccaro
Development and preliminary validation of a dynamic, patient-tailored method to detect abnormal laboratory test results. MedInfo 2015: 701-705 - 2014
- [j7]Mattia C. F. Prosperi, Sarah L. Ingham, Anthony Howell
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: 87 (2014) - [j6]Melissa M. Norström, Nazle M. Veras, Wei Huang, Mattia C. F. Prosperi, Jennifer Cook, Wendy Hartogensis, Frederick M. Hecht
Baseline CD4+ 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) - [c6]Richard Williams, Iain E. Buchan, Mattia Prosperi, John D. Ainsworth:
Using String Metrics to Identify Patient Journeys through Care Pathways. AMIA 2014 - [c5]Franco Milicchio
HErCoOl: High-Throughput Error Correction by Oligomers. CBMS 2014: 227-232 - 2012
- [j5]Mattia C. F. Prosperi, Marco Salemi:
QuRe: software for viral quasispecies reconstruction from next-generation sequencing data. Bioinform. 28(1): 132-133 (2012) - 2011
- [j4]Mattia C. F. Prosperi, Luciano Prosperi, Alessandro Bruselles
Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing. BMC Bioinform. 12: 5 (2011) - [j3]Mattia C. F. Prosperi, Simona Di Giambenedetto, Iuri Fanti, Genny Meini, Bianca Bruzzone, Annapaola Callegaro, Giovanni Penco, Patrizia Bagnarelli, Valeria Micheli
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: 40 (2011)
2000 – 2009
- 2009
- [j2]Mattia C. F. Prosperi, Roberto D'Autilia
Stochastic modelling of genotypic drug-resistance for human immunodeficiency virus towards long-term combination therapy optimization. Bioinform. 25(8): 1040-1047 (2009) - 2008
- [j1]Andrea Gasparri
A bacterial colony growth algorithm for mobile robot localization. Auton. Robots 24(4): 349-364 (2008) - [c4]Andrea Gasparri
A bacterial colony growth framework for collaborative multi-robot localization. ICRA 2008: 2806-2811 - [c3]Michal Rosen-Zvi
Selecting anti-HIV therapies based on a variety of genomic and clinical factors. ISMB 2008: 399-406 - [p1]Mattia Prosperi, Giovanni Ulivi:
Evolutionary Fuzzy Modelling for Drug Resistant HIV-1 Treatment Optimization. Engineering Evolutionary Intelligent Systems 2008: 251-287 - 2007
- [c2]Mattia C. F. Prosperi, Giovanni Ulivi, Maurizio Zazzi
Statistical Comparison of Machine Learning Techniques for Treatment Optimisation of Drug-Resistant HIV-1. CBMS 2007: 427-432 - [c1]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: 465-470
Coauthor Index
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