Near-unsupervised computational methods for exploring 'omic' data

Self-Organizing Nebulous Growths for Robust and Incremental Data Visualization

Damith A Senanayake, Wei Wang, Shalin H Naik, Saman Halgamuge

2021-10-01

Nonparametric dimensionality reduction techniques, such as t-distributed Stochastic Neighbor Embedding (t-SNE) and uniform manifol..

IMPARO: inferring microbial interactions through parameter optimisation

Rajith Vidanaarachchi, Marnie Shaw, Sen-Lin Tang, Saman Halgamuge

2020-08-19

BACKGROUND: Microbial Interaction Networks (MINs) provide important information for understanding bacterial communities. MINs can ..

A Physarum-Inspired Algorithm for Minimum-Cost Relay Node Placement in Wireless Sensor Networks

Yahui Sun, Daniel Rehfeldt, Marcus Brazil, Doreen Thomas, Saman Halgamuge

2020-04-01

Relay node placement, which aims to connect pre-deployed sensor nodes to base stations, is essential in minimizing the costs of wi..

Estimating neuronal conductance model parameters using dynamic action potential clamp

Y Deerasooriya, G Berecki, D Kaplan, IC Forster, S Halgamuge, S Petrou

2019-09-01

Parameterization of neuronal membrane conductance models relies on data acquired from current clamp (CC) or voltage clamp (VC) rec..

ENVirT: inference of ecological characteristics of viruses from metagenomic data

Duleepa Jayasundara, Damayanthi Herath, Damith Senanayake, Isaam Saeed, Cheng-Yu Yang, Yuan Sun, Bill C Chang, Sen-Lin Tang, Saman K Halgamuge

2019-02-04

Background: Estimating the parameters that describe the ecology of viruses,particularly those that are novel, can be made possible..

Discovering the pharmacodynamics of conolidine and cannabidiol using a cultured neuronal network based workflow

GDC Mendis, G Berecki, E Morrisroe, S Pachernegg, M Li, M Varney, PB Osborne, CA Reid, S Halgamuge, S Petrou

2019-01-15

Determining the mechanism of action (MOA) of novel or naturally occurring compounds mostly relies on assays tailored for individua..

Improving MMD-GaN training with repulsive loss function

W Wang, Y Sun, S Halgamuge

2019-01-01

Generative adversarial nets (GANs) are widely used to learn the data sampling process and their performance may heavily depend on ..

A two-tiered unsupervised clustering approach for drug repositioning through heterogeneous data integration

Pathima Nusrath Hameed, Karin Verspoor, Snezana Kusljic, Saman Halgamuge

2018-04-11

BACKGROUND: Drug repositioning is the process of identifying new uses for existing drugs. Computational drug repositioning methods..

Assessment of Gait Characteristics in Total Knee Arthroplasty Patients Using a Hierarchical Partial Least Squares Method

Wei Wang, David C Ackland, Jodie A McClelland, Kate E Webster, Saman Halgamuge

2018-01-01

Quantitative gait analysis is an important tool in objective assessment and management of total knee arthroplasty (TKA) patients. ..

The node-weighted Steiner tree approach to identify elements of cancer-related signaling pathways

Yahui Sun, Chenkai Ma, Saman Halgamuge

2017-12-28

BACKGROUND: Cancer constitutes a momentous health burden in our society. Critical information on cancer may be hidden in its signa..

Positive-Unlabeled Learning for inferring drug interactions based on heterogeneous attributes

Pathima Nusrath Hameed, Karin Verspoor, Snezana Kusljic, Saman Halgamuge

2017-03-01

BACKGROUND: Investigating and understanding drug-drug interactions (DDIs) is important in improving the effectiveness of clinical ..

Keynote address: Data engineering meets health

Saman K Halgamuge

2016-04-01

Use of adaptive network burst detection methods for multielectrode array data and the generation of artificial spike patterns for method evaluation

GDC Mendis, E Morrisroe, S Petrou, SK Halgamuge

2016-04-01

OBJECTIVE: Multielectrode arrays are an informative extracellular recording technology that enables the analysis of cultured neuro..

Deep Near Unsupervised Learning for Data Analysis in Metabolomics, Drug-Drug Interaction Discovery and Human Gait Recognition

Saman K Halgamuge

2016-01-01

Fast Algorithms Inspired by Physarum Polycephalum for Node Weighted Steiner Tree Problem with Multiple Terminals

Yahui Sun, Saman Halgamuge

2016-01-01

Recently it has been shown that Physarum-inspired algorithms can solve some network optimization problems. However, it is not yet ..

Mechatronics Fundamentals and Applications Preface

Clarence W de Silva, Farbod Khoshnoud, Maoqing Li, Saman K Halgamuge

2016-01-01

A new peak detection algorithm for MALDI mass spectrometry data based on a modified Asymmetric Pseudo-Voigt model

C Wijetunge, I Saeed, BA BOUGHTON, U Roessner, SK Halgamuge

2015-12-09

Background Mass Spectrometry (MS) is a ubiquitous analytical tool in biological research and is used to measure the mass-to-charge..