Elisa Ficarra

Publication Activity (10 Years)

Years Active: 2002-2024
Publications (10 Years): 45

Top Topics

Convolutional Neural Network

Colorectal Cancer

Gene Expression

Top Venues

Comput. Methods Programs Biomed.

Publications

Gianpaolo Bontempo, Federico Bolelli, Angelo Porrello, Simone Calderara, Elisa Ficarra
A Graph-Based Multi-Scale Approach With Knowledge Distillation for WSI Classification. IEEE Trans. Medical Imaging 43 (4) (2024)
Giacomo Capitani, Federico Bolelli, Angelo Porrello, Simone Calderara, Elisa Ficarra
ClusterFix: A Cluster-Based Debiasing Approach without Protected-Group Supervision. WACV (2024)
Luca Lumetti, Vittorio Pipoli, Federico Bolelli, Elisa Ficarra, Costantino Grana
Enhancing Patch-Based Learning for the Segmentation of the Mandibular Canal. IEEE Access 12 (2024)
Gianpaolo Bontempo, Luca Lumetti, Angelo Porrello, Federico Bolelli, Simone Calderara, Elisa Ficarra
Buffer-MIL: Robust Multi-instance Learning with a Buffer-Based Approach. ICIAP (2) (2023)
Emanuele Marconato, Gianpaolo Bontempo, Elisa Ficarra, Simone Calderara, Andrea Passerini, Stefano Teso
Neuro Symbolic Continual Learning: Knowledge, Reasoning Shortcuts and Concept Rehearsal. CoRR (2023)
Gianpaolo Bontempo, Angelo Porrello, Federico Bolelli, Simone Calderara, Elisa Ficarra
DAS-MIL: Distilling Across Scales for MIL Classification of Histological WSIs. MICCAI (1) (2023)
Elena Pianfetti, Marta Lovino, Elisa Ficarra, Loredana Martignetti
MiREx: mRNA levels prediction from gene sequence and miRNA target knowledge. BMC Bioinform. 24 (1) (2023)
Matteo Stefanini, Marta Lovino, Rita Cucchiara, Elisa Ficarra
Predicting gene and protein expression levels from DNA and protein sequences with Perceiver. Comput. Methods Programs Biomed. 234 (2023)
Emanuele Marconato, Gianpaolo Bontempo, Elisa Ficarra, Simone Calderara, Andrea Passerini, Stefano Teso
Neuro-Symbolic Continual Learning: Knowledge, Reasoning Shortcuts and Concept Rehearsal. ICML (2023)
Francesco Ponzio, Enrico Macii, Elisa Ficarra, Santa Di Cataldo
W2WNet: A two-module probabilistic Convolutional Neural Network with embedded data cleansing functionality. Expert Syst. Appl. 214 (2023)
Gianpaolo Bontempo, Nicola Bartolini, Marta Lovino, Federico Bolelli, Anni Virtanen, Elisa Ficarra
Enhancing PFI Prediction with GDS-MIL: A Graph-Based Dual Stream MIL Approach. ICIAP (1) (2023)
Emanuele Marconato, Gianpaolo Bontempo, Stefano Teso, Elisa Ficarra, Simone Calderara, Andrea Passerini
Catastrophic Forgetting in Continual Concept Bottleneck Models. ICIAP Workshops (2022)
Marta Lovino, Marilisa Montemurro, Venere S. Barrese, Elisa Ficarra
Identifying the oncogenic potential of gene fusions exploiting miRNAs. J. Biomed. Informatics 129 (2022)
Alessio Mascolini, Dario Cardamone, Francesco Ponzio, Santa Di Cataldo, Elisa Ficarra
Exploiting generative self-supervised learning for the assessment of biological images with lack of annotations. BMC Bioinform. 23 (1) (2022)
Alessio Mascolini, Francesco Ponzio, Enrico Macii, Elisa Ficarra, Santa Di Cataldo
High Resolution Explanation Maps for CNNs using Segmentation Networks. VL/HCC (2022)
Marta Lovino, Vincenzo Randazzo, Gabriele Ciravegna, Pietro Barbiero, Elisa Ficarra, Giansalvo Cirrincione
A survey on data integration for multi-omics sample clustering. Neurocomputing 488 (2022)
Jörg Winkler, Gianvito Urgese, Elisa Ficarra, Knut Reinert
LaRA 2: parallel and vectorized program for sequence-structure alignment of RNA sequences. BMC Bioinform. 23 (1) (2022)
Vittorio Pipoli, Mattia Cappelli, Alessandro Palladini, Carlo Peluso, Marta Lovino, Elisa Ficarra
Predicting gene expression levels from DNA sequences and post-transcriptional information with transformers. Comput. Methods Programs Biomed. 225 (2022)
Federica Citarrella, Gianpaolo Bontempo, Marta Lovino, Elisa Ficarra
FusionFlow: An Integrated System Workflow for Gene Fusion Detection in Genomic Samples. ADBIS (Short Papers) (2022)
Francesco Barchi, Emanuele Parisi, Gianvito Urgese, Elisa Ficarra, Andrea Acquaviva
Exploration of Convolutional Neural Network models for source code classification. Eng. Appl. Artif. Intell. 97 (2021)
Alessio Mascolini, Dario Cardamone, Francesco Ponzio, Santa Di Cataldo, Elisa Ficarra
Exploiting generative self-supervised learning for the assessment of biological images with lack of annotations: a COVID-19 case-study. CoRR (2021)
Valerio Mieuli, Francesco Ponzio, Alessio Mascolini, Enrico Macii, Elisa Ficarra, Santa Di Cataldo
A Bayesian approach to Expert Gate Incremental Learning. IJCNN (2021)
Francesco Ponzio, Enrico Macii, Elisa Ficarra, Santa Di Cataldo
W2WNet: a two-module probabilistic Convolutional Neural Network with embedded data cleansing functionality. CoRR (2021)
Marilisa Montemurro, Elena Grassi, Carmelo Gabriele Pizzino, Andrea Bertotti, Elisa Ficarra, Gianvito Urgese
PhyliCS: a Python library to explore scCNA data and quantify spatial tumor heterogeneity. BMC Bioinform. 22 (1) (2021)
Santa Di Cataldo, Sara Vinco, Gianvito Urgese, Flaviana Calignano, Elisa Ficarra, Alberto Macii, Enrico Macii
Optimizing Quality Inspection and Control in Powder Bed Metal Additive Manufacturing: Challenges and Research Directions. Proc. IEEE 109 (4) (2021)
Alejandra Cervera, Heidi Rausio, Tiia Kähkönen, Noora Andersson, Gabriele Partel, Ville Rantanen, Giulia Paciello, Elisa Ficarra, Johanna Hynninen, Sakari Hietanen, Olli Carpén, Rainer Lehtonen, Sampsa Hautaniemi, Kaisa Huhtinen
FUNGI: FUsioN Gene Integration toolset. Bioinform. 37 (19) (2021)
Marta Lovino, Gianpaolo Bontempo, Giansalvo Cirrincione, Elisa Ficarra
Multi-omics Classification on Kidney Samples Exploiting Uncertainty-Aware Models. ICIC (2) (2020)
Thomas Desvignes, Phillipe Loher, Karen Eilbeck, Jeffery Ma, Gianvito Urgese, Bastian Fromm, Jason Sydes, Ernesto Aparicio-Puerta, Víctor Barrera, Roderic Espín, Florian Thibord, Xavier Bofill-De Ros, Eric Londin, Aristeidis G. Telonis, Elisa Ficarra, Marc R. Friedländer, John H. Postlethwait, Isidore Rigoutsos, Michael Hackenberg, Ioannis S. Vlachos, Marc K. Halushka, Lorena Pantano
Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API. Bioinform. 36 (3) (2020)
Marta Lovino, Maria Serena Ciaburri, Gianvito Urgese, Santa Di Cataldo, Elisa Ficarra
DEEPrior: a deep learning tool for the prioritization of gene fusions. Bioinform. 36 (10) (2020)
Marilisa Montemurro, Gianvito Urgese, Elena Grassi, Carmelo Gabriele Pizzino, Andrea Bertotti, Elisa Ficarra
Effective Evaluation of Clustering Algorithms on Single-Cell CNA data. ICBBE (2020)
Pietro Barbiero, Marta Lovino, Mattia Siviero, Gabriele Ciravegna, Vincenzo Randazzo, Elisa Ficarra, Giansalvo Cirrincione
Unsupervised Multi-omic Data Fusion: The Neural Graph Learning Network. ICIC (1) (2020)
Gianvito Urgese, Emanuele Parisi, Orazio M. Scicolone, Santa Di Cataldo, Elisa Ficarra
BioSeqZip: a collapser of NGS redundant reads for the optimization of sequence analysis. Bioinform. 36 (9) (2020)
Francesco Ponzio, Giacomo Deodato, Enrico Macii, Santa Di Cataldo, Elisa Ficarra
Exploiting "Uncertain" Deep Networks for Data Cleaning in Digital Pathology. ISBI (2020)
Francesco Ponzio, Enrico Macii, Elisa Ficarra, Santa Di Cataldo
Going Deeper into Colorectal Cancer Histopathology. BIOSTEC (Selected Papers) (2018)
Orazio M. Scicolone, Giulia Paciello, Elisa Ficarra
geneEx - A Novel Tool to Assess Differential Expression from Gene and Exon Sequencing Data. BIOINFORMATICS (2018)
Marta Lovino, Gianvito Urgese, Enrico Macii, Santa Di Cataldo, Elisa Ficarra
Predicting the Oncogenic Potential of Gene Fusions Using Convolutional Neural Networks. CIBB (2018)
Francesco Ponzio, Enrico Macii, Elisa Ficarra, Santa Di Cataldo
Colorectal Cancer Classification using Deep Convolutional Networks - An Experimental Study. BIOIMAGING (2018)
Alessio Mascolini, S. Puzzo, G. Incatasciato, Francesco Ponzio, Elisa Ficarra, Santa Di Cataldo
A Novel Proof-of-concept Framework for the Exploitation of ConvNets on Whole Slide Images. IIH-MSP (1) (2017)
Francesco Ponzio, Enrico Macii, Elisa Ficarra, Santa Di Cataldo
A Multi-modal Brain Image Registration Framework for US-guided Neuronavigation Systems - Integrating MR and US for Minimally Invasive Neuroimaging. BIOIMAGING (2017)
Giulia Paciello, Elisa Ficarra
FuGePrior: A novel gene fusion prioritization algorithm based on accurate fusion structure analysis in cancer RNA-seq samples. BMC Bioinform. 18 (1) (2017)
Santa Di Cataldo, Simone Tonti, Andrea Bottino, Elisa Ficarra
ANAlyte: A modular image analysis tool for ANA testing with indirect immunofluorescence. Comput. Methods Programs Biomed. 128 (2016)
Santa Di Cataldo, Simone Tonti, Elisa Ciglieri, Francesco Ferrini, Enrico Macii, Elisa Ficarra, Chiara Salio
Automated 3D immunofluorescence analysis of Dorsal Root Ganglia for the investigation of neural circuit alterations: a preliminary study. FedCSIS (Position Papers) (2016)
Gianvito Urgese, Giulia Paciello, Andrea Acquaviva, Elisa Ficarra
isomiR-SEA: an RNA-Seq analysis tool for miRNAs/isomiRs expression level profiling and miRNA-mRNA interaction sites evaluation. BMC Bioinform. 17 (2016)
Simone Tonti, Santa Di Cataldo, Enrico Macii, Elisa Ficarra
Unsupervised HEp-2 mitosis recognition in indirect immunofluorescence imaging. EMBC (2015)
Simone Tonti, Santa Di Cataldo, Andrea Bottino, Elisa Ficarra
An automated approach to the segmentation of HEp-2 cells for the indirect immunofluorescence ANA test. Comput. Medical Imaging Graph. 40 (2015)
Francesco Abate, Sakellarios Zairis, Elisa Ficarra, Andrea Acquaviva, Chris H. Wiggins, Veronique Frattini, Anna Lasorella, Antonio Iavarone, Giorgio Inghirami, Raul Rabadan
Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer. BMC Syst. Biol. 8 (2014)
Gianvito Urgese, Giulia Paciello, Claudio Isella, Enzo Medico, Enrico Macii, Elisa Ficarra, Andrea Acquaviva
miR-SEA: miRNA Seed Extension based Aligner Pipeline for NGS Expression Level Extraction. IWBBIO (2014)
Massimo Natale, Alfredo Benso, Stefano Di Carlo, Elisa Ficarra
FunMod: A Cytoscape Plugin for Identifying Functional Modules in Undirected Protein-Protein Networks. Genom. Proteom. Bioinform. 12 (4) (2014)
Gianvito Urgese, Giulia Paciello, Andrea Acquaviva, Elisa Ficarra, Mariagrazia Graziano, Maurizio Zamboni
Dynamic Gap Selector: A Smith Waterman Sequence Alignment Algorithm with Affine Gap Model Optimization. IWBBIO (2014)
Santa Di Cataldo, Andrea Bottino, Ihtesham Ul Islam, Tiago Figueiredo Vieira, Elisa Ficarra
Subclass Discriminant Analysis of morphological and textural features for HEp-2 staining pattern classification. Pattern Recognit. 47 (7) (2014)
Giulia Paciello, Andrea Acquaviva, Consalvo Petti, Claudio Isella, Enzo Medico, Elisa Ficarra
A Novel Pipeline for Identification and Prioritization of Gene Fusions in Patient-derived Xenografts of Metastatic Colorectal Cancer. BIOINFORMATICS (2014)
Massimo Natale, Alfredo Benso, Stefano Di Carlo, Elisa Ficarra
Identifying Sub-Network Functional Modules in Protein Undirected Networks. BIOINFORMATICS (2014)
Giulia Paciello, Elisa Ficarra, Alberto Zamò, Chiara Pighi, Carmelo Foti, Francesco Abate, Enrico Macii, Andrea Acquaviva
A Novel Pipeline for V(D)J Junction Identification using RNA-Seq Paired-end Reads. BIOINFORMATICS (2013)
Francesco Abate, Andrea Acquaviva, Elisa Ficarra, Roberto Piva, Enrico Macii
Gelsius: A Literature-Based Workflow for Determining Quantitative Associations between Genes and Biological Processes. IEEE ACM Trans. Comput. Biol. Bioinform. 10 (3) (2013)
Ihtesham Ul Islam, Santa Di Cataldo, Andrea Bottino, Elisa Ficarra, Enrico Macii
Classification of HEp-2 Staining Patterns in ImmunoFluorescence Images - Comparison of Support Vector Machines and Subclass Discriminant Analysis Strategies. BIOINFORMATICS (2013)
Ardita Shkurti, Mario Orsi, Enrico Macii, Elisa Ficarra, Andrea Acquaviva
Acceleration of coarse grain molecular dynamics on GPU architectures. J. Comput. Chem. 34 (10) (2013)
Francesco Abate, Andrea Acquaviva, Elisa Ficarra, Enrico Macii
Integration of Literature with Heterogeneous Information for Genes Correlation Scoring. ACM J. Emerg. Technol. Comput. Syst. 9 (4) (2013)
Ihtesham Ul Islam, Santa Di Cataldo, Andrea Bottino, Enrico Macii, Elisa Ficarra
A Preliminary Analysis on HEp-2 Pattern Classification: Evaluating Strategies Based on Support Vector Machines and Subclass Discriminant Analysis. BIOSTEC (Selected Papers) (2013)
Santa Di Cataldo, Elisa Ficarra, Enrico Macii
Computer-aided techniques for chromogenic immunohistochemistry: Status and directions. Comput. Biol. Medicine 42 (10) (2012)
Santa Di Cataldo, Andrea Bottino, Elisa Ficarra, Enrico Macii
Applying textural features to the classification of HEp-2 cell patterns in IIF images. ICPR (2012)
Ardita Shkurti, Andrea Acquaviva, Elisa Ficarra, Mario Orsi, Enrico Macii
Characterization of Coarse Grain Molecular Dynamic Simulation Performance on Graphic Processing Unit Architectures. BIOINFORMATICS (2012)
Francesco Abate, Giulia Paciello, Andrea Acquaviva, Elisa Ficarra, Alberto Ferrarini, Massimo Delledonne, Enrico Macii
A Novel Analysis Flow for Fused Transcripts Discovery from Paired-end RNA-Seq Data. BIOINFORMATICS (2012)
Paula Helena Reyes-Herrera, Elisa Ficarra
One Decade of Development and Evolution of MicroRNA Target Prediction Algorithms. Genom. Proteom. Bioinform. 10 (5) (2012)
Massimo Natale, Alfonso Caiazzo, Enrico M. Bucci, Elisa Ficarra
A Novel Gaussian Extrapolation Approach for 2D Gel Electrophoresis Saturated Protein Spots. Genom. Proteom. Bioinform. 10 (6) (2012)
Francesco Abate, Andrea Acquaviva, Giulia Paciello, Carmelo Foti, Elisa Ficarra, Alberto Ferrarini, Massimo Delledonne, Ilaria Iacobucci, Simona Soverini, Giovanni Martinelli, Enrico Macii
Bellerophontes: an RNA-Seq data analysis framework for chimeric transcripts discovery based on accurate fusion model. Bioinform. 28 (16) (2012)
Massimo Natale, Alfonso Caiazzo, Enrico M. Bucci, Elisa Ficarra
A Novel Gaussian Fitting Approach for 2D Gel Electrophoresis Saturated Protein Spots. BIOINFORMATICS (2012)
Giulia Paciello, Andrea Acquaviva, Elisa Ficarra, M. A. Deriu, A. Grosso, Enrico Macii
Binding Free Energy Calculation via Molecular Dynamics Simulations for a miRNA: mRNA Interaction. BIOINFORMATICS (2011)
Francesco Abate, Andrea Acquaviva, Elisa Ficarra, Giulia Paciello, Enrico Macii, Alberto Ferrarini, Massimo Delledonne, Simona Soverini, Giovanni Martinelli
A novel framework for chimeric transcript detection based on accurate gene fusion model. BIBM Workshops (2011)
Santa Di Cataldo, Elisa Ficarra, Andrea Acquaviva, Enrico Macii
Motion Artifact Correction in ASL images: An Improved Automated Procedure. BIBM (2011)
Paula Helena Reyes-Herrera, Elisa Ficarra, Andrea Acquaviva, Enrico Macii
miREE: miRNA Recognition Elements Ensemble. BMC Bioinform. 12 (2011)
Elisa Ficarra, Santa Di Cataldo, Andrea Acquaviva, Enrico Macii
Automated Segmentation of Cells With IHC Membrane Staining. IEEE Trans. Biomed. Eng. 58 (5) (2011)
Francesco Abate, Elisa Ficarra, Andrea Acquaviva, Enrico Macii
Improving Latent Semantic Analysis of Biomedical Literature Integrating UMLS Metathesaurus and Biomedical Pathways Databases. BIOSTEC (Selected Papers) (2011)
Massimo Mazzillo, Pier Giorgio Fallica, Elisa Ficarra, A. Messina, Mario Francesco Romeo, Roberto Zafalon
Solid state photodetectors for nuclear medical imaging applications. DATE (2011)
Francesco Abate, Andrea Acquaviva, Elisa Ficarra, Enrico Macii
A New Latent Semantic Analysis based Methodology for Knowledge Extraction from Biomedical Literature and Biological Pathways Databases. BIOINFORMATICS (2011)
Ardita Shkurti, Andrea Acquaviva, Elisa Ficarra, Enrico Macii, Mario Orsi, Martino Ruggiero
GPU acceleration of simulation tool for lipid-bilayers. BIBM Workshops (2010)
Santa Di Cataldo, Elisa Ficarra, Andrea Acquaviva, Enrico Macii
Automated segmentation of tissue images for computerized IHC analysis. Comput. Methods Programs Biomed. 100 (1) (2010)
Santa Di Cataldo, Elisa Ficarra, Andrea Acquaviva, Enrico Macii
Achieving the way for automated segmentation of nuclei in cancer tissue images through morphology-based approach: A quantitative evaluation. Comput. Medical Imaging Graph. 34 (6) (2010)
Francesco Abate, Elisa Ficarra, Andrea Acquaviva, Enrico Macii
An Automated Tool for Scoring Biomedical Terms Correlation Based on Semantic Analysis. CISIS (2010)
Paula Helena Reyes-Herrera, Andrea Acquaviva, Elisa Ficarra, Enrico Macii
MicroRNA Target Prediction and Exploration through Candidate Binding Sites Generation. CISIS (2010)
Santa Di Cataldo, Elisa Ficarra, Enrico Macii
Fully-Automated Segmentation of Tumor Areas in Tissue Confocal Images - Comparison between a Custom Unsupervised and a Supervised SVM Approach. BIOSIGNALS (1) (2008)
Elisa Ficarra, Giovanni De Micheli, Sungroh Yoon, Luca Benini, Enrico Macii
Joint co-clustering: Co-clustering of genomic and clinical bioimaging data. Comput. Math. Appl. 55 (5) (2008)
Santa Di Cataldo, Elisa Ficarra, Enrico Macii
Automated Discrimination of Pathological Regions in Tissue Images: Unsupervised Clustering vs. Supervised SVM Classification. BIOSTEC (Selected Papers) (2008)
Santa Di Cataldo, Elisa Ficarra, Andrea Acquaviva, Enrico Macii
Segmentation of nuclei in cancer tissue images: Contrasting active contours with morphology-based approach. BIBE (2008)
Santa Di Cataldo, Elisa Ficarra, Enrico Macii
Selection of Tumor Areas and Segmentation of Nuclear Membranes in Tissue Confocal Images: A Fully Automated Approach. BIBM (2007)
Elena Baralis, Elisa Ficarra, Alessandro Fiori, Enrico Macii
Gene-Markers Representation for Microarray Data Integration. BIBE (2007)
Elisa Ficarra, Enrico Macii, Giovanni De Micheli, Luca Benini
Computer-Aided Evaluation of Protein Expression in Pathological Tissue Images. CBMS (2006)
Daniele Apiletti, Giulia Bruno, Elisa Ficarra, Elena Baralis
Data Cleaning and Semantic Improvement in Biological Databases. J. Integr. Bioinform. 3 (2) (2006)
Daniele Masotti, Elisa Ficarra, Enrico Macii, Luca Benini
Optimized Technique for Dna Structural Properties Discovering. Int. J. Artif. Intell. Tools 15 (5) (2006)
Elisa Ficarra, Luca Benini, Enrico Macii, Giampaolo Zuccheri
Automated DNA fragments recognition and sizing through AFM image processing. IEEE Trans. Inf. Technol. Biomed. 9 (4) (2005)
Elisa Ficarra, Daniele Masotti, Enrico Macii, Luca Benini, Giampaolo Zuccheri, Bruno Samorì
Automatic intrinsic DNA curvature computation from AFM images. IEEE Trans. Biomed. Eng. 52 (12) (2005)
Daniele Masotti, Elisa Ficarra, Enrico Macii, Luca Benini
Techniques for Enhancing Computation of DNA Curvature Molecules. BIBE (2004)
Elisa Ficarra, Luca Benini, Bruno Riccò, Giampaolo Zuccheri
Automated DNA sizing in atomic force microscope images. ISBI (2002)