Using Transactional Information to Predict Link Strength in Online Social Networks. - Indika Kahanda; Jennifer Neville (ICWSM, 2009)

Evaluating a variety of text-mined features for automatic protein function prediction with GOstruct. - Christopher S. Funk; Indika Kahanda; Asa Ben-Hur; Karin M. Verspoor (J. Biomed. Semant., 2015)

GOstruct 2.0: Automated Protein Function Prediction for Annotated Proteins. - Indika Kahanda; Asa Ben-Hur (BCB, 2017)

Quality Assurance of Bioinformatics Software: A Case Study of Testing a Biomedical Text Processing Tool Using Metamorphic Testing. - Madhusudan Srinivasan; Morteza Pourreza Shahri; Indika Kahanda; Upulee Kanewala (MET@ICSE, 2018)

Overview of the BioCreative VI text-mining services for Kinome Curation Track. - Julien Gobeill; Pascale Gaudet; Daniel Dopp; Adam Morrone; Indika Kahanda; Yi-Yu Hsu; Chih-Hsuan Wei; Zhiyong Lu; Patrick Ruch (Database J. Biol. Databases Curation, 2018)

A look back at the quality of Protein Function Prediction tools in CAFA. - Morteza Pourreza Shahri; Madhusudan Srinivasan; Diane Bimczok; Upulee Kanewala; Indika Kahanda (PeerJ Prepr., 2018)

Metamorphic Testing for Quality Assurance of Protein Function Prediction Tools. - Morteza Pourreza Shahri; Madhusudan Srinivasan; Gillian Reynolds; Diane Bimczok; Indika Kahanda; Upulee Kanewala (AITest, 2019)

Poster: Pangenome-Wide Association Studies with Frequented Regions. - Buwani Manuweera; Joann Mudge; Indika Kahanda; Brendan Mumey; Thiruvarangan Ramaraj; Alan M. Cleary (BCB, 2019)

Pangenome-Wide Association Studies with Frequented Regions. - Buwani Manuweera; Joann Mudge; Indika Kahanda; Brendan Mumey; Thiruvarangan Ramaraj; Alan M. Cleary (BCB, 2019)

PPPred: Classifying Protein-phenotype Co-mentions Extracted from Biomedical Literature. - Morteza Pourreza Shahri; Gillian Reynolds; Mandi Marie Roe; Indika Kahanda (BCB, 2019)

RDoC Task at BioNLP-OST 2019. - Mohammad Anani; Nazmul Kazi; Matthew Kuntz; Indika Kahanda (BioNLP-OST@EMNLP-IJNCLP, 2019)

Computational methods for the ab initio identification of novel microRNA in plants: a systematic review. - Buwani Manuweera; Gillian Reynolds; Indika Kahanda (PeerJ Comput. Sci., 2019)

Automatically generating psychiatric case notes from digital transcripts of doctor-patient conversations using text mining. - Nazmul Kazi; Indika Kahanda (PeerJ Prepr., 2019)

ProPheno: An online dataset for completely characterizing the human protein-phenotype landscape in biomedical literature. - Morteza Pourreza Shahri; Indika Kahanda (PeerJ Prepr., 2019)

Exploring Frequented Regions in Pan-Genomic Graphs. - Alan M. Cleary; Thiruvarangan Ramaraj; Indika Kahanda; Joann Mudge; Brendan Mumey (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

miRNAFinder: A pre-microRNA classifier for plants and analysis of feature impact. - Puwasuru Ihalagedara; Sandali Lokuge; Shyaman Jayasundara; Damayanthi Herath; Indika Kahanda (CIBCB, 2020)

MRpredT: Using Text Mining for Metamorphic Relation Prediction. - Karishma Rahman; Indika Kahanda; Upulee Kanewala (ICSE (Workshops), 2020)

DeepACPpred: A Novel Hybrid CNN-RNN Architecture for Predicting Anti-Cancer Peptides. - Nathaniel Lane; Indika Kahanda (PACBB, 2020)

RDoCer: Information Retrieval and Sentence Extraction for Mental Health using Research Domain Criteria. - Daniel Laden; Shyaman Jayasundara; Indika Kahanda (ICSC, 2020)

ProPheno 1.0: An Online Dataset for Accelerating the Complete Characterization of the Human Protein-Phenotype Landscape in Biomedical Literature. - Morteza Pourreza Shahri; Indika Kahanda (ICSC, 2020)

DeepPPPred: Deep Ensemble Learning with Transformers, Recurrent and Convolutional Neural Networks for Human Protein-Phenotype Co-mention Classification. - Morteza Pourreza Shahri; Katrina Lyon; Julia Schearer; Indika Kahanda (BIBM, 2021)

BioSGAN: Protein-Phenotype Co-mention Classification Using Semi-Supervised Generative Adversarial Networks. - Francis Anokye; Indika Kahanda (CBMS, 2021)

Automatically Cataloging Scholarly Articles using Library of Congress Subject Headings. - Nazmul Kazi; Nathaniel Lane; Indika Kahanda (EACL (Student Research Workshop), 2021)

Vegetation Coverage in Marsh Grass Photography Using Convolutional Neural Networks. - Lucas Welch; Xudong Liu 003; Indika Kahanda; Sandeep Reddivari; Karthikeyan Umapathy (FLAIRS, 2021)

Deep semi-supervised learning ensemble framework for classifying co-mentions of human proteins and phenotypes. - Morteza Pourreza Shahri; Indika Kahanda (BMC Bioinform., 2021)

Impact of Concatenation of Digital Craniocaudal Mammography Images on a Deep-Learning Breast-Density Classifier Using Inception-V3 and ViT. - Conrad Testagrose; Vikash Gupta; Barbaros S. Erdal; Richard D. White; Robert W. Maxwell; Xudong Liu 003; Indika Kahanda; Sherif Elfayoumy; William Klostermeyer; Mutlu Demirer (BIBM, 2022)

miRNAFinder: A comprehensive web resource for plant Pre-microRNA classification. - Sandali Lokuge; Shyaman Jayasundara; Puwasuru Ihalagedara; Indika Kahanda; Damayanthi Herath (Biosyst., 2022)

Breast-Density Semantic Segmentation with Probability Scaling for BI-RADS Assessment using DeepLabV3. - Conrad T. Testagrose; Vikash Gupta; Barbaros S. Erdal; Richard D. White; Robert W. Maxwell; Xudong Liu 003; Indika Kahanda; Sherif Elfayoumy; William Klostermeyer; Mutlu Demirer (BCB, 2023)

Genotype-to-Phenotype Associations with Frequented Region Variants. - Indika Kahanda; Buwani Manuweera; Brendan Mumey; Thiruvarangan Ramaraj; Alan M. Cleary; Joann Mudge (BIBM, 2023)

Poster: BioFactCheck: Exploring the Feasibility of Explainable Automated Inconsistency Detection in Biomedical and Health Literature. - Prajwol Lamichhane; Indika Kahanda; Xudong Liu 003; Karthikeyan Umapathy; Sandeep Reddivari; Catherine Christie; Andrea Arikawa; Jenifer Ross (CHASE, 2023)

UNF-IDT: Automated Irony Detection in English Tweets. - Guna Sekaran Jaganathan; Grentina Kilungeja; Indika Kahanda (ICMLA, 2023)

Enhancing Transfer Learning of LLMs through Fine- Tuning on Task - Related Corpora for Automated Short-Answer Grading. - Nazmul Kazi; Indika Kahanda (ICMLA, 2023)

Zero-Shot Information Extraction with Community-Fine-Tuned Large Language Models From Open-Ended Interview Transcripts. - Nazmul Kazi; Indika Kahanda; S. Indu Rupassara; John W. Kindt (ICMLA, 2023)

Enhancing Health Information Retrieval with Large Language Models: A Study on MedQuAD Dataset. - Prajwol Lamichhane; Indika Kahanda (ICMLA, 2023)

Patronizing and Condescending Language Detection. - Conrad Testagrose; Athlene V. Jones; Indika Kahanda (ICMLA, 2023)

Poster: Towards Understanding Root Causes of Real Failures in Healthcare Machine Learning Applications. - Guna Sekaran Jaganathan; Nazmul Kazi; Indika Kahanda; Upulee Kanewala (ICST, 2024)

MLHCBugs: A Framework to Reproduce Real Faults in Healthcare Machine Learning Applications. - Guna Sekaran Jaganathan; Nazmul Kazi; Indika Kahanda; Upulee Kanewala (ICST, 2024)