Summer 2020: Congratulations to MASc student, Fadwa Darwaish, and the entire IEEE WIE executive team for winning the 2020 WIE Affinity Group of the Year Award!. Congratulations to MASc student, Daniel Kyrollos, for being awarded a Vector AI Scholarship to support his research in neonatal patient monitoring! Congratulations to MASc student, Samreen Aziz, for winning "Best Student Paper" at the 2020 IEEE MeMeA conference! Jim Green was interviewed on CBC Radio 1 regarding our lab's research to fight COVID19 through peptide research.
Fall 2019: Congratulations to MASc graduate Mohsen Sheikh Hassani for publishing three journal papers in 2019!! Yasmina Souley Dosso has been invited to speak at the upcoming "Women in Data Science" (WiDS) conference to be held in spring 2020 in Ottawa. Our CIMVHR project was featured in the Fall 2019 issue of the Canadian Military Family Magazine.
Spring 2019: Congratulations to PhD students who received major scholarships: Francois Charih (NSERC PGS-D) and Yasmina (OGS). Data Day 6.0 Congratulations to Shermeen Nizami, Yasmina Souley Dosso, Joe Samuel, and Naman Sethi for winning first prize for their poster describing our neonatal patient monitoring project at Data Day 6 here at Carleton. Congratulations also to Aishwarya Purohit and Kevin Dick for winning third prize for their poster describing improvements to PIPE-Sites, a method of predicting the site of protein-protein interactions, and to Joe Samuel and Mohamed Hozayen for winning two awards (1st and 2nd) for their poster describing their 4th year project (under the supervision of Prof. Mohamed Ibnkahla). A big day for CUBIC!
Congratulations to CUBIC alumnus Mohamed Hozayen for being named a 2019 Provost Scholar, in recognition of his undergraduate research excellence and his community engagement.
Winter 2019: Congratulations to PhD student Kevin Dick for placing among the top 100 of 488 finalists (from the original ~4K participants) in the 2019 Bioinformatics Challenge. This year’s competition contained questions covering topics such as graph decomposition, pattern recognition, evolutionary chronological reconstruction, finding minimum super-strings, and greedy matching algorithms. His code is available on GitHub. Undergraduate lab member, Naman Sethi, has had his been written up by the Carleton Newsroom. The article describes his work towards developing an integrated data viewer to simultaneously visualize and analyze RGB-D video, pressure-sensitive mat, physiologic, and event data streams for our ongoing neonatal patient monitoring project with CHEO.
Fall 2018: Congratulations to graduate students Mohsen Sheikh Hassani, Amente Bekele, Roger Selzler, and Francois Charih for successfully defending their theses this term. Francois and Roger have been nominated for Senate Medals for their thesis research! Congratulations to Yasmina Souley Dosso and Kevin Dick for being awarded Queen Elizabeth II scholarships in 2018-2019!
Summer 2018:Yasmina Souley Dosso has won the "Women in Engineering Best Paper" award at MeMeA2018 for her paper entitled "Eulerian Magnification of Multi-Modal RGB-D Video for Heart Rate Estimation"! Congratulations Yasmina!
CUBIC: Carleton University Biomedical Informatics Co-laboratory
At the Carleton University Biomedical Informatics Co-laboratory (CUBIC), we apply machine learning and data science to solve problems in biomedical informatics. Current projects requiring additional students include an exploration of the use of RGB-D video and pressure-sensitive mats for real-time patient monitoring in the NICU at CHEO (data collection ongoing), automated analysis of audiograms for telemedicine applications in under-served communities (with an industry partner), development of a wireless system to monitor neonates during emergency ground and air transport to the NICU at CHEO (collaboration already in place), and development of novel machine learning methods for analyzing protein structure, function, interaction, and chemical modification. Interested students should have strong software and communication skills proven through academic performance and/or industry experience. Hands-on experience with deep learning, artificial intelligence, web development, and statistics is highly valued.
Non-contact Neonatal Patient Monitoring We are working with CHEO to investigate novel patient monitoring technologies in the NICU. We are examining the use of pressure-sensitive mats (PSM) to provide continuous, unobtrusive, and non-contact monitoring of critically ill babies in the neonatal intensive care unit (NICU) at CHEO. We are working with IBM's Centre for Advanced Studies (IBM-CAS), Dr. JoAnn Harrold (Neonatologist @ CHEO), and Mr. Kim Greenwood (Director of Clinical Engineering @ CHEO). In addition to PSM, we are also using multispectral cameras (colour, near-infrared, and depth) to record video of patients from above. From the PSM and video data, we are developing deep learning computer vision approaches for physiological monitoring (HR, RR, etc), characterizing patient movement, and detecting clinical interventions with an eye on semi-automated charting. We have developed a tablet app, such that bedside researchers can annotate all events of interest for up to 6 hours per patient. These gold-standard annotations will be used to develop and validate machine learning approaches to semi-automated non-contact patient monitoring in the NICU.
Estimation of Patient Stress during VR-Therapy Together with Prof. Adrian Chan and clinicians from the Canadian Forces and the Ottawa Hospital Rehabilitation Centre, we are developing novel methods for estimating patients' stress levels (sympathetic activation of the autonomic nervous system) during virtual reality therapy for PTSD, mild traumatic brain injury, and complex pain. Such monitoring will enable clinicians to tailor the intensity of therapy to induce brain plasticity and healing, while avoiding over-stimulating the recovering brain. We are using both gait information, from a VICON motion-capture system, and physiologic signals from a wearable sensor. Deep learning models will be used to analyze these data to generate estimators of stress in real-time, thereby providing an important tool to rehabilitation clinicians.
Quantifying Patient Vibrations During Emergency Transport Each year, thousands of newborns in Canada are transported by air or ground ambulance to receive specialized medical care. These infants are often premature and especially vulnerable during transport. Vibration exposure during transport may contribute risk of serious long-term consequences including brain injury. To decease risk during transport, specialized equipment is used. However, vibration levels experienced by infants and contributing factors are not well understood. This lack of knowledge affects the ability to transport newborn patients in the safest manner possible. With Rob Langlois (MAE), Adrian Chan (SCE), and Stephanie Redpath (CHEO), we are seeking to increase the safety of infant transport by reducing vibration exposure. We propose a research program which seeks to understand how vibrations caused by the road and air environments are transferred to the infant. This will allow us to propose novel methods to reduce vibration exposure and improve the equipment for transporting fragile infants. We will measure vibrations in many transport scenarios including within hospitals as well as in ground ambulances, helicopters, and airplanes. The results will be used to develop test equipment and procedures for evaluating the transport equipment. This research will enable better understanding of the problem and provide a reliable way to test the transport equipment and procedures. It will lead to new tools for planning routes that minimize vibration and for monitoring patient vibration.
Semi-Supervised and Species-Specific Prediction of microRNA. microRNA are short RNA molecules that play an important role in post-transcriptional gene regulation. Our collaborators are continuously sequencing new species and wish to identify novel microRNA within these new genomes. However, most widely-used microRNA prediction tools are only effective on human data. We have developed SMIRP, a framework for the creation of species-specific predictors of microRNA from genomic sequence. We have achieved up to 500% increases in sensitivity at precisions of up to 90% when compared with existing methods. SMIRP has been applied to study numerous genomes including turtles, slime moulds, and a snail. We are now developing methods to leverage transcriptomic RNA-Seq data as this continues to becomes more accessible to experimental researchers.
Post-translational modification. While progress continues to be made on the prediction of structure from sequence, knowledge of a protein's structure may not be sufficient to discern its function. For example, most proteins undergo some form of post-translational modification (PTM) following initial synthesis which may have a profound impact on protein function. Our lab is therefore working to develop intelligent predictors of important PTM's such as sumoylation and phosphorylation. Iterative prediction of protein function and structure is a long term goal as well.
Bioinformatics web services. Please click here for a partial list of web services developed by our lab.
Areas of Research Interest
My research focus has been in the following areas:
Real-time patient monitoring, using pressure-sensitive mats, multi-modal video, and other sensors.
Machine learning, pattern classification, data mining
Bioinformatics, proteomics, and prediction of protein structure, function, interaction, and post-translational modification
Development of novel assistive technology and devices
Current projects include:
Neonatal patient monitoring using pressure sensitive mats (collaboration with IBM-CAS)
Classification of audiograms for tele-medicine applications (collaboration with Clearwater Clinical)
Real-time monitoring for vibration/acceleration, sound, air pressure, and temperature during emergency patient transport to the NICU (collaboration with the CHEO patient transport team)
Semi-supervised and species-specific prediction of microRNA from genomic sequence or transcriptomics data
Prediction of protein-protein interactions from sequence
Development of various novel assistive devices for persons who are disabled and the elderly
Identification of post-translational modifications in proteins, including methylation, sumoylation, glycosylation, and hydroxylation.