Events
Perspective on Deep Imaging
Ge Wang PhD
Mar 05, 2020|12:00 PM – 1:00 PM
130 University Health Services Building (Pizza & drinks served at 11:50) Please RSVP to BMI@uky.edu
Artificial intelligence is now recognized as an on-going paradigm shift, with an emphasis on machine learning especially deep learning. Computer vision and image analysis are two major applications of deep learning. While computer vision and image analysis deal with existing images and produce features of these images (images to features), tomographic imaging produces images of multi-dimensional structures from experimentally measured data (line integrals, harmonic components, and so on, of underlying images) which are tomographic features (features to images). Since 2016, deep learning is being actively developed worldwide for tomographic imaging, forming a new area of imaging research. In this presentation, we present a perspective on deep imaging involving data processing, image reconstruction, radiomics, and beyond. We show deeptomographic results and also explore network innovations.
Slides from presentations:
Accelerating Bioinformatics Applications using GPUs
Fernanda Foertter PhD
Feb 20, 2020|12:00 PM – 1:00 PM
University Health Services 130 (pizza and drinks at 11:50 - RSVP to BMI@uky.edu)
The biological sciences are currently experiencing an increase in data size and complexity. Traditional methods are now reaching the point they can no longer keep up with the data output. Larger datasets, particularly when combined with other data sources, open opportunities to apply methods like deep learning on these complex data. NVIDIA is contributing to these needs by developing algorithms that can leverage graphics processing units (GPUs). These problems benefit from high memory bandwidth and very high parallelism inherent of the GPU architecture. This talk will explore some of the collaborations we have with industry and academia and share some of what our research team is currently working on.
Promoting Transparency in Biomedical Publications Using Natural Language Processing
Halil Kilicoglu PhD
Feb 06, 2020|12:00 PM – 1:00 PM
130 University Health Services Building, Please RSVP to BMI@uky.edu
Rigor, reproducibility, and transparency of biomedical research has been the topic of much debate in recent years. Some ongoing efforts aim to address the issues in research conduct and dissemination by focusing on standardization and guideline development. As biomedical research output increases exponentially, automated tools are needed to complement such efforts and assist the stakeholders (e.g., scientists, journals, funding organizations) in assessing and improving research output.
Textual artifacts (e.g., grant applications, study protocols, manuscripts, and publications) are central to biomedical communication. With the progress made in in biomedical language processing and text mining (bioNLP) in recent years, it is timely to ask if and how bioNLP techniques can be used to help address some of the rigor and integrity problems manifested in these artifacts. In this talk, I will motivate the use of bioNLP methods toward these goals by providing some use cases, and discuss a couple of tasks that I have recently pursued in this area: a) assessing clinical trial publications for reporting guideline adherence, and b) elucidating contradictory claims in biomedical publications. I will also highlight some of the challenges facing bioNLP research focusing on this area.
Epigenomic insights of environmental disease
Zhibin Wang PhD
Dec 05, 2019|12:30 PM – 1:30 PM
130 University Health Services Building (Pizza & drinks served at 12:20. Please RSVP to BMI@uky.edu)
Clinical Event Mining and Visualization for Chronic Rheumatic Diseases
Sujin Kim PhD
Nov 13, 2019|12:00 PM – 1:00 PM
UHS 130
Understanding the use of pattern mining algorithms and the development of a prototype system to visualize the relationships of frequent clinical events based on mined clinical sequences and associations.
CANCELLED - Deciphering the regulatory code of metabolism in Arabidopsis - CANCELLED
Seung Yon (Sue) Rhee PhD
Nov 07, 2019|12:30 PM – 1:30 PM
Coordinated control of metabolic genes is crucial for plant development and adaptation to various environments. To discover general rules of metabolic regulation, we used omics data, machine learning, and experimental validation. To understand how metabolic genes are controlled by epigenetic marks, we mapped regulatory patterns of 16 epigenetic marks across metabolism in Arabidopsis and found a predominant regulatory pattern for specialized metabolic genes involved in controlling the precise timing of gene expression upon stimuli. To understand how transcription factors regulate metabolism, we constructed condition- and tissue-specific regulatory networks in Arabidopsis and identified patterns of transcriptional regulation at various levels. These studies elucidate metabolism coordination and contribute to developing toolkits for pathway engineering in plants.
Reinforcement Learning for Brain Machine Interfaces
Jihye Bae PhD
Oct 17, 2019|12:30 PM – 1:30 PM
130 University Health Services Building
There have been promising advances in brain machine interfaces. However, many challenges still remain before this technology can become practical. In this talk, we will discuss some of the main issues along with possible approaches to overcome them. In particular, methods to translate neural signals to control external devices using reinforcement learning will be introduced.
Transforming Ontologies into Nested Facet Systems
GQ Zhang PhD
Sep 19, 2019|12:30 PM – 1:30 PM
130 University Health Services Building
Irrespective of data size and complexity, query and exploration tools for accessing data resources remain a central linkage for human-data interaction. A fundamental barrier in making query interfaces easier to use,ultimately as easy as online shopping, is the lack of faceted, interactive capabilities. We propose to repurpose existing ontologies by transforming them into nested facet systems (NFS) to support human-data interaction. Two basic issues need to be addressed for this to happen: one is that the structure and quality of ontologies need to be examined and elevated for the purpose of NFS; the second is that mappings from data-source specific metadata to a corresponding NFS need to be developed to support this new generation of NFS-enabled web-interfaces. The purpose of this presentation is to motivate the concept of NFS, provide a preliminary order-theoretic formulation for NFS, and suggest topics for further investigation.
Bacterial Outer Membranes and Interactions with Membrane Proteins
Wonpil Im PhD
Sep 05, 2019|12:30 PM – 1:30 PM
130 University Health Services Building (Pizza & drinks served at 12:20)
The outer membrane of gram-negative bacteria is a unique asymmetric membrane bilayer that is composed of phospholipids in the inner leaflet and lipopolysaccharides (LPS) in the outer leaflet. Its function as a selective barrier is crucial for the survival of bacteria in many distinct environments, and it also renders gram-negative bacteria more resistant to antibiotics than their gram-positive counterparts. LPS comprises three regions: lipid A, core oligosaccharide, and O-antigen polysaccharide. In this talk, I will present our ongoing efforts to understanding various bacterial outer membranes and their interactions with outer membrane proteins. In addition, I will also present other research projects in my lab, such as the CHARMM-GUI development, a local structure-centric bioinformatics for drug development, and structure.
Mining electronic health records narratives for clinical research: The case of lifestyle modification
Eneida A. Mendonca MD, PhD, FAAP, FACMI
Jan 09, 2019|12:00 PM – 1:00 PM
University Health Services (UHS), room 130
This talk will address the importance of assessing lifestyle modification and behavior, and the challenges of using EHR data to identify lifestyle modifications and behavior in clinical narratives. Registration is required by January 8.
The clinical and research informatics role in promoting a knowledge-drive medicine
Umberto Tachinardi MD, MS, FACMI
Jan 08, 2019| 8:00 AM – 9:00 AM
CT Wethington Building, room 127
Principles and practical examples demonstrating how biomedical informatics enables translational biomedical sciences, precision medicine, and a learning health system. Registration required by January 7.
MS in Data Science at UK
Heather Bush, PhD, Miroslaw Truszczynski, PhD and GQ Zhang, PhD
Dec 12, 2018|12:00 PM – 1:00 PM
University Health Services (UHS) 130
A presentation of the curriculum and requirements of the proposed MS in Data Science degree program to be implemented at the University of Kentucky
Commonwealth Computational Summit 2018
Oct 23, 2018| 8:30 AM – 6:00 PM
Bill Gatton Student Center
Featuring speakers from academia, industry, and government. Hosted by UK's Center for Computational Science. Must register to attend.
Ninth Annual Therapeutics Outcomes Discovery & Delivery (TODD) Symposium: Precision Medicine, Genomics and Big Data
Sep 06, 2018| 8:00 AM – 5:30 PM
Lee T. Todd, Jr. Building, Room 124
Speakers include William Douglas Figg Sr, NIH; Atul Butte, University of California; Jill Kolesar, University of Kentucky; and Tim Tracy, Aprecia Pharmaceuticals.
Standardizing CT images using generative adversarial networks
Jin Chen PhD
Jun 13, 2018|12:00 PM – 1:00 PM
University Health Service, room 130 (beside Employee Health)
Dr. Chen will discuss work to improve the analysis of CT images by developing models that learn to identify features from a set of training images and also generate synthetic images that display these features.
Text mining in precision medicine: Opportunities and challenges
Hongfang Liu PhD
Jun 01, 2018|12:00 PM – 1:00 PM
CT Wethington Building, room 014
Dr. Liu will review how text mining has been applied to precision medicine, and then discuss efforts at the Mayo Clinic.
From Big Data to Bedside (BD2B): Precision oncology in an era of artificial intelligence
Xinghua Lu MD, PhD
May 16, 2018|12:00 PM – 1:00 PM
CT Wethington Building, room 014
Dr. Lu will discuss how artificial intelligence technologies can provide insight to disease mechanism of individual tumors, cancer pathways, the state of signaling machinery in tumor cells, and the efficacy of anti-cancer drugs.
Precision informatics at Cincinnati Children’s
Peter White PhD
Apr 30, 2018|12:00 PM – 1:00 PM
CT Wethington Building, room 014
Dr. White will discuss work at Cincinnati Children’s to educate stakeholders on informatics literacy and integrate biomedical and clinical data across the institution, as well as the social structures needed to support these efforts.
Deep phenotyping on EHR narratives facilitates genetic diagnosis by clinical exomes
Chunhua Weng PhD
Mar 26, 2018|12:00 PM – 1:00 PM
CT Wethington Building, room 014
CCTS Seminar Presentation:
SUDEP (Sudden Death in Epilepsy Patients)
Samden Lhatoo MD, DCRP
Jan 31, 2018|12:00 PM – 12:30 PM
Chandler Hospital, HG 611, Pavilion H 6th Floor
Biomedical ontologies in action
Olivier Bodenrider MD, PhD
Nov 07, 2017|12:00 PM – 1:00 PM
CT Wethington Building, room 014
1st annual Commonwealth Computational Summit
Oct 17, 2017| 8:30 AM – 5:30 PM
WT Young Library Auditorium, University of Kentucky
Similarity analytics in the age of precision medicine
Fei Wang PhD
May 11, 2017|12:00 PM – 1:00 PM
CT Wethington Building, room 014
How computers see people
Nathan Jacobs PhD
May 10, 2017|12:00 PM – 12:50 PM
University Health Service Building, room 130
The questions and answers for biomedical data science
Jong Cheol Jeong PhD
May 09, 2017|12:00 PM – 12:50 PM
CT Wethington Building, room 014
Demonstrating the value of design research in biomedical informatics
Melissa Clarkson PhD, MDes, MA
Apr 27, 2017|12:00 PM – 1:00 PM
CT Wethington Building, room 127
Feature selection and learning on high-dimensional and large-scale data
Qiang Cheng PhD
Apr 24, 2017|12:00 PM – 1:00 PM
CT Wethington Building, room 127
High-throughput biomedical image computing for digital health
Fuyong Xing
Apr 19, 2017|12:00 PM – 1:00 PM
Lee T Todd Building (BioPharm Complex), room 170
Humans, machines and the future of work
Apr 13, 2017| 4:00 PM – 5:00 PM
Chemistry-Physics Building, room 153
Trial prospector
Apr 12, 2017|12:00 PM – 1:00 PM
University Health Service Building, room 130
Toward portable NLP solutions for healthcare — the journey of CLAMP
Hua Xu PhD
Mar 20, 2017|12:00 PM – 1:00 PM
CT Wethington Building, room 014
Deep brain stimulation informatics
Cameron McIntyre PhD
Mar 14, 2017|12:00 PM – 1:00 PM
Lee T Todd Building, room 170