James Robert Green

Carleton University · Department of Systems and Computer Engineering

The prediction of novel pre-microRNA (miRNA) from genomic sequence has received considerable attention recently. However, the majority of studies have focused on the human genome. Previous studies have demonstrated that sensitivity (correctly detecting true miRNA) is sustained when human-trained methods are applied to other species, however they ha...

All protein-protein interaction (PPI) predictors require the determination of an operational decision threshold when differentiating positive PPIs from negatives. Historically, a single global threshold, typically optimized via cross-validation testing, is applied to all protein pairs. However, we here use data visualization techniques to show that...

Experimental drug development is time-consuming, expensive and limited to a relatively small number of targets. However, recent studies show that repositioning of existing drugs can function more efficiently than de novo experimental drug development to minimize costs and risks. Previous studies have proven that network analysis is a versatile plat...

Many people with hearing loss are unaware of it and do not seek benefit from available interventions such as hearing aids. This is in part due to the limited accessibility to qualified hearing healthcare providers in developing and developed countries alike. Automated audiometry, which has gained in popularity amidst the torrent of advances in tele...

Methods for the de novo identification of microRNA (miRNA) have been developed using a range of sequence-based features. With the increasing availability of next generation sequencing (NGS) transcriptome data, there is a need for miRNA identification that integrates both NGS transcript expression-based patterns as well as advanced genomic sequence-...

Depth cameras can provide an effective, noncontact, and privacy-preserving means to monitor patients in the Neonatal Intensive Care Unit (NICU). Clinical interventions and routine care events can disrupt video-based patient monitoring. Automatically detecting these periods can decrease the time required for hand-annotating recordings, which is need...

Introduction Tacrolimus is an immunosuppressant commonly administered in transplant recipients. Given its narrow therapeutic range and susceptibility to various influencing variables, determining its optimal dosage is challenging. This systematic review seeks to identify effective analytical modelling techniques and methods for optimal tacrolimus d...

In order to receive acute care in a regionalized health care system, many patients require transportation to higher care facilities, exposing them to vibration and noise within the transport environment. Transportation by road ambulance has been analysed with respect to noise and vibration exposure for neonatal patients in previous studies, which m...

Thermal videos provide a privacy-preserving yet information-rich data source for remote health monitoring, especially for respiration rate (RR) estimation. This paper introduces an end-to-end deep learning approach to RR measurement using thermal video data. A detection transformer (DeTr) first finds the subject’s facial region of interest in each...

This study presents an approach to enhance the well-being and safety of aging populations through better understanding their everyday activities. Our approach uses ambient sensor data and analyzes them with multi-modal feature learning and explainable AI through the ImageBind framework. By integrating the SHapley Additive exPlanations (SHAP) method...

Powerline vegetation encroachment detection is pivotal in averting power outages and forest fires, especially in urban areas where a high density of buildings, roads, and other urban structures complicates detection. While prior research has effectively detected encroachments within point clouds, they largely overlooked the challenges posed by urba...

Background Approximately half of all patients with advanced chronic kidney disease (CKD) who progress to kidney failure initiate dialysis in an unplanned fashion which is associated with high morbidity, mortality, and healthcare costs. A novel prediction model designed to identify advanced CKD patients who are at high risk for developing kidney fai...

High-resolution images offer more information about scenes that can improve model accuracy. However, the dominant model architecture in computer vision, the vision transformer (ViT), cannot effectively leverage larger images without finetuning -- ViTs poorly extrapolate to more patches at test time, although transformers offer sequence length flexi...

Exposure to excessive whole-body vibration is linked to health issues and may result in increased rates of mortality and morbidity in infants. Newborn infants requiring specialized treatment at neonatal intensive care units often require transportation by road ambulance to specialized care centers, exposing the infants to potentially harmful vibrat...

The exploration of post-translational modifications (PTMs) within the proteome is pivotal for advancing disease and cancer therapeutics. However, identifying genuine PTM sites amid numerous candidates is challenging. Integrating machine learning (ML) models with high-throughput in vitro peptide synthesis has introduced an ML-hybrid search methodolo...

The soybean cyst nematode (SCN) is a devastating pathogen for economic and food security considerations. Although the SCN genome has recently been sequenced, the presence of any miRNA has not been systematically explored and reported. This paper describes the development of a species-specific SCN miRNA discovery pipeline and its application to the...

The Neonatal Patient Transport System (NPTS) collaborative research team seeks to measure and mitigate vibrations experienced by neonatal patients during ground and air transport. A custom test apparatus was designed for use with an electrodynamic shaker to investigate the effectiveness of transport mattresses and harnesses used inside the isolette...

No. While our experiments ultimately failed, this work was motivated by the seemingly reasonable hypothesis that encoding protein sequences as a fractal-based image in combination with a binary mask identifying those pixels representative of the protein binding interface could effectively be used to fine-tune a semantic segmentation model. We were...

Background Development of a short timeframe (6–12 months) kidney failure risk prediction model may serve to improve transitions from advanced chronic kidney disease (CKD) to kidney failure and reduce rates of unplanned dialysis. The optimal model for short timeframe kidney failure risk prediction remains unknown. Methods This retrospective study i...

The soybean cyst nematode (SCN) [ Heterodera glycines Ichinohe] is a devastating pathogen of soybean [ Glycine max (L.) Merr.] that is rapidly becoming a global economic issue. Two loci conferring SCN resistance have been identified in soybean, Rhg1 and Rhg4; however, they offer declining protection. Therefore, it is imperative that we identify add...

div class="section abstract"> Neonatal Infants (neonates) requiring a higher level of care often require transportation via road ambulance to neonatal intensive care units. The trip in the ambulance exposes these infants to potentially harmful noise and vibration. The aim of this study was to categorize the sound level in and around the Neonatal Pa...

microRNAs (miRNAs) are small non-coding ribonucleic acids that post-transcriptionally regulate gene expression through the targeting of messenger RNA (mRNAs). Most miRNA target predictors have focused on animal species and prediction performance drops substantially when applied to plant species. Several rule-based miRNA target predictors have been...

Infant pose monitoring during sleep has multiple applications in both healthcare and home settings. In a healthcare setting, pose detection can be used for region of interest detection and movement detection for noncontact-based monitoring systems. In a home setting, pose detection can be used to detect sleep positions which has shown to have a str...

Continuously monitoring patient vital signs in the neonatal intensive care unit (NICU) requires wired sensors that can irritate fragile skin, motivating the development of non-contact physiologic signal estimation approaches. Such estimators typically involve a pipeline of multiple data analysis stages, including pre-processing, region of interest...

Monitoring critical infrastructure is of great importance for resilience against current and emerging hazards. In Canada, at the national level, critical infrastructure is strategically classified into the following 10 sectors: energy and utilities, finance, food, transportation, government, information and communication technology, health, water,...

Across many domains, real-world problems can be represented as a network. Nodes represent domain-specific elements and edges capture the relationship between elements. Leveraging high-performance computing and optimized link prediction algorithms, it is increasingly possible to evaluate every possible combination of nodal pairs enabling the generat...

Infant pose monitoring during sleep has multiple applications in both healthcare and home settings. In a healthcare setting, pose detection can be used for region of interest detection and movement detection for noncontact based monitoring systems. In a home setting, pose detection can be used to detect sleep positions which has shown to have a str...

Although the remote sensing (RS) community has begun to pretrain transformers (intended to be fine-tuned on RS tasks), it is unclear how these models perform under distribution shifts. Here, we pretrain a new RS transformer--called SatViT-V2--on 1.3 million satellite-derived RS images, then fine-tune it (along with five other models) to investigate...

A number of private and public insurers compensate workers whose hearing loss can be directly attributed to excessive exposure to noise in the workplace. The claim assessment process is typically lengthy and requires significant effort from human adjudicators who must interpret hand-recorded audiograms, often sent via fax or equivalent. In this wor...

The identification of novel drug-target interactions (DTI) is critical to drug discovery and drug repurposing to address contemporary medical and public health challenges presented by emergent diseases. Historically, computational methods have framed DTI prediction as a binary classification problem (indicating whether or not a drug physically inte...

Engineering peptides to achieve a desired therapeutic effect through the inhibition of a specific target activity or protein interaction is a non-trivial task. Few of the existing in silico peptide design algorithms generate target-specific peptides. Instead, many methods produce peptides that achieve a desired effect through an unknown mechanism....

Antibacterial drugs (AD) change the metabolic status of bacteria, contributing to bacterial death. However, antibiotic resistance and the emergence of multidrug-resistant bacteria increase interest in understanding metabolic network (MN) mutations and the interaction of AD vs MN. In this study, we employed the IFPTML = Information Fusion (IF) + Per...

Neonatal infants in need of advanced care, often require transportation via road ambulance to neonatal intensive care units. The ambulance exposes these vulnerable infants to potentially harmful noise and vibration. To better understand the levels of vibration, this paper maps the magnitude of acceleration due to vibration throughout the cabin of a...

Astroglial cells are key players in the development and maintenance of neurons and neuronal networks. Astroglia express steroid hormone receptors and show rapid responses to hormonal manipulations. However, despite important sex differences in the cortex and hippocampus, few studies have examined sex differences in astroglial cells in telencephalic...

The lived environment, particularly when proximal to roadways, is filled with multi-digit and multi-numbered values corresponding to advertised commodities. The reliable detection of single multi-digit values from natural imagery has been widely studied through the last decade (e.g. Street View House Numbers [SVHN]); however, extraction and assignm...

The development of non-contact patient monitoring applications for the neonatal intensive care unit (NICU) is an active research area, particularly in facial video analysis. Recent studies have used facial video data to estimate vital signs, assess pain from facial expression, differentiate sleep-wake status, detect jaundice, and in face recognitio...

Despite the enormous success of the “pretraining and fine-tuning” paradigm, widespread across machine learning, it has yet to pervade remote sensing (RS). To help rectify this, we pretrain a vision transformer (ViT) on 1.3 million satellite-derived RS images. We pretrain SatViT using a state-of-the-art (SOTA) self-supervised learning (SSL) algorith...

Multiple private and public insurers compensate workers whose hearing loss can be directly attributed to excessive exposure to noise in the workplace. The claim assessment process is typically lengthy and requires significant effort from human adjudicators who must interpret hand-recorded audiograms, often sent via fax or equivalent. In this work,...

Video-based monitoring of patients in the neonatal intensive care unit (NICU) has great potential for improving patient care. Video-based detection of clinical events, such as bottle feeding, would represent a step towards semi-automated charting of clinical events. Recording such events contemporaneously would address the limitations associated wi...

Primary Subject area Neonatal-Perinatal Medicine Background Each year, thousands of newborns are transported by air or ground ambulance to receive specialized medical care. For neurologically immature and physiologically compromised infants, especially preterm infants, the noise and vibration exposure during transport are high despite preventative...

Metabolic Reaction Networks (MRNs) are complex networks produced by thousands of chemical reactions or transformations (links) of metabolites (nodes) in a live organism. An essential goal of chemical biology is to test the connectivity (structure) of these complex MRNs models presented for new microorganisms with promising features. In theory, we c...

Engineering peptides to achieve a desired therapeutic effect through the inhibition of a specific target activity or protein interaction is a non-trivial task. Few of the existing in silico peptide design algorithms generate target-specific peptides. Instead, many methods produce peptides that achieve a desired effect through an unknown mechanism....

The soybean crop, Glycine max (L.) Merr., is consumed by humans, Homo sapiens, worldwide. While the respective bodies of literature and -omics data for each of these organisms are extensive, comparatively few studies investigate the molecular biological processes occurring between the two. We are interested in elucidating the network of protein-pro...

Continuity of care is achieved in the neonatal intensive care unit (NICU) through careful documentation of all events of clinical significance, including clinical interventions and routine care events (e.g., feeding, diaper change, weighing, etc.). As a step towards automating this documentation process, we propose a scene recognition algorithm tha...

Vibration and noise exposure during emergency neonatal ground and air transport are recognized as hazards for the neonate; however, no standardized test environment exists to reliably quantify such exposure with high repeatability. An on-road test was performed to provide a quantitative measurement of on-road vibrations to be used in the deve...

Background Understanding the disease pathogenesis of the novel coronavirus, denoted SARS-CoV-2, is critical to the development of anti-SARS-CoV-2 therapeutics. The global propagation