HPC-BOD 2022
4th International Workshop on High Performance Computing, Big Data Analytics and Integration for Multi-Omics Biomedical Data
In conjunction with IEEE BIBM 2022
Dec. 6-9, 2022, Las Vegas, NV USA
| Schedule for the 4th IEEE Workshop on High Performance Computing, Big Data Analytics, and Integration for Multi-Omics Biomedical Data (HPC-BOD 2022)
Workshop Chairs: Fahad Saeed (FIU), Serdar Bozdag (UNT) |
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| Time | Title | Presenter/Author |
| 2:00 pm – 2:10 pm | Opening Remarks – Fahad Saeed | |
| 2:10 pm – 2:30pm | S08203 – Comprehensive analysis of gene expression profiles to radiation exposure reveals molecular signatures of low-dose radiation response | Xihaier Luo, Sean McCorkle, Gilchan Park, Vanessa Lopez-Marrero, Shinjae Yoo, Edward Dougherty, Xiaoning Qian, Francis Alexander, and Byung-Jun Yoon |
| 2:30 pm – 2:50pm | B600 – Shallow Sparse Autoencoder Based Epileptic Seizure Prediction | Gul Hameed Khan, Nadeem Ahmad Khan, Muhammad Awais Bin Altaf |
| 2:50 pm – 3:10 pm | S08201 – Identification of Cross-feeding Metabolism Reveals Oral-Microbiome Modulated Host Behavior | Suganya Chandrababu and Dhundy Bastola |
| 3:10 pm – 3:30 pm | B834 – Crescent: A GPU-based Targeted Nanopore Sequence Selector | Tong Li, Xueqi Li, Yewen Li, Ruibao Song, and Xun Wang |
| 3:30 pm – 4:00 pm | Coffee Break | |
| 4:00 pm – 4:20 pm | S08205 – Comparison of deep and shallow graph representation learning algorithms for detecting modules in molecular networks | Zhiwei Song, Brittany Baur, and Sushmita Roy |
| 4:20 pm – 4:40 pm | B915 – Personalized Semantic Annotation Recommendations on Biomedical Content through an Expanded Socio-technical Approach | Asim Abbas, Nadeem Iqbal, and Syed Ahmad Chan Bukhari |
| 4:40 pm – 5:00 pm | B506 – PNF: a novel method based on connectivity and similarity for data integration and cancer subtyping | Shihao Zhang, Fenghui Liu, Feng Wang, Lin Qi, and Yun Tie |
| 5:00 pm – 5:20 pm | S08207 – Deep Learning Based MS2 Feature Detection for Data-independent Shotgun Proteomics | Jonathan He, Olivia Liu, and Xuan Guo |
| 5:20 pm – 5:30 pm | Closing Remarks – Serdar Bozdag | |
HPC-BOD 2022 Call For Papers
Enormous amounts of data are being produced using modern technologies such as Next Generation Sequencing machines and high-throughput Mass Spectrometers. The availability of such large and heterogeneous datasets creates challenges in terms of storage, transmission, computation, integration and analysis. In order to process such data in a timely manner, big data analytics techniques and high-performance computing (HPC) is becoming an essential component in systems biology, bioinformatics and computational biology.
The goal of this workshop is to provide a forum for big data analytics and HPC professionals and academics alike to discuss latest research in HPC solutions to these compute-intensive and data-intensive problems. We are especially interested in HPC algorithms, and big data analytic techniques, and machine learning/deep learning algorithms for integration of large-scale high-throughput multi-omics data sets.
The workshop will feature submitted papers as well as invited papers and talks from reputed researchers in the field of big data analytics, HPC and computational biology.
This will be 4th time that we will be arranging this workshop. The previous version of the workshop has appeared in PLOS One Special Collection.
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Important Dates:
Due date for full workshop papers submission: Oct 23rd, 2022
Notification of paper acceptance to authors: Nov 10th 2022
Camera-ready of accepted papers: Nov 17th, 2022
The submission link is: Submit Paper Here
Full papers (8 pages), short-papers (4 pages) and extended abstracts (1 to 2 pages) are welcome.
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Thrust 1: Integration of Big Multi-Omics Data.
Areas of interest within computational life sciences include (but not limited to):
Computational genomics and metagenomics: Genome assembly, long/short read data structures, read mapping, clustering, variant analysis, error correction, genome annotation, and other computational problems in large-scale genomics
Computational proteomics and proteogenomics: Peptide identification from Big Mass Spectrometry data including database search and de novo methods, Genome annotations via mass spectrometry, Identification of post-translational modifications, Structural genomics via mass spectrometry, Protein-protein interactions and other computational problems in large-scale proteomics
Network biology methods for multi-omics integration: Network representation learning (e.g., deep learning on graphs and network embedding), higher-order network analysis (network motifs/graphlets and networks of networks), inference of biological networks (e.g., gene regulatory networks, competing endogenous RNA networks, link prediction), comparison of biological networks (network alignment analysis and alignment-free network comparison), network-based personalized medicine (e.g., drug response prediction and drug target prediction)
Computational Neuroinformatics and Connectomics: Standardization in multiscale and multimodal modeling, Computational infrastructure for neuroscience: automation / pipelines, Machine learning in neuroscience, Reproducible neuroscience + open science
Other Omics and Integration for Systems Biology: Other computational problems in omics including but not limited to Epigenomics, Lipidomics, Glycomics, Foodomics, Transcriptomics, Metabolomics and methods to integrate these omics datasets to get systems biology insights of disease pathophysiology.
Thrust 2: High-Performance Computing for Big Data Omics.
Areas of interest within HPC include (but are not limited to):
Parallel and distributed algorithms for big data Omics: Scalable machine learning, parallel graph/sequence analytics, combinatorial pattern matching, optimization, parallel data structures, compression/decompression, multicore, manycore, CPU/GPU, FPGA, system-on-chip, hardware accelerators, energy-aware architectures, hardware/software co-design
Accessible Scientific workflows for Big Data Omics: Data management, Data wrangling, Automated workflows, Cloud-enabled solutions for computational biology, and Energy-aware High-Performance Biological Applications
Big Data Omics Analytics, Infrastructure, and Management: Novel techniques to deal with big omics data including but not limited to sketching, sampling, streaming, compression/decompression, succinct data-structures and algorithms, novel encoding techniques, efficient methods to integrate multi-omics data and Multimedia and Multi-structured Omics data
Hardware Acceleration for Big Omics Data: FPGA/CGRA/GPU accelerators for Big Data applications, Domain-specific and heterogeneous architectures, and design that can accelerate machine-learning aspects of dealing with big omics data.
Submission guidelines
Papers should be formatted to 8 pages IEEE Computer Society Proceedings Manuscript Formatting Guidelines (https://www.ieee.org/conferences/publishing/templates.html). HPC-BOD technical program committee will review all submissions on the basis of their originality, technical soundness, significance, presentation, and relevance to the conference attendees.
The submission link is: Submit Paper Here
All submissions will be peer-reviewed by members from the program committee using a single-blind review process. At the time of submission, the author list should be final. Any subsequent changes to the author list post-submission needs to be done with the approval of the program chairs.
Acceptance of any of these would mean an oral presentation. However, the authors would have to pay registration for the paper to be included in the IEEE BIBM proceedings.
Important Dates:
Due date for full workshop papers submission: Oct 23rd, 2022
Notification of paper acceptance to authors: Nov 10th 2022
Camera-ready of accepted papers: Nov 17th, 2022
Selected papers will possibly be published in Plos Special Collections (web-link) and in the Journal of Computational Biology and Bioinformatics (JBCB) (web-link).
Workshop Organization
Workshop Chairs:
Fahad Saeed (Florida International University, Miami FL)
Serdar Bozdag (University of North Texas, Denton, Texas)
Program Committee
Vashishath, Yashu (UNT)
Rifat, Jubair Ibn Malik (UNT)
Al Olaimat, Mohammad (UNT)
Ebeid, Islam (UNT)
Kesimoglu, Ziynet Nesibe (UNT)
Chad Myers, University of Minnesota
Brittany Baur, University of Michigan
Ashok Srinivasan, UWF
Umair Muhammad (FIU)
Muhammad Haseeb (FIU)
Usman Tariq (FIU)
Oswaldo Artiles (FIU)
Keynote Speaker(s)
TBA
Previous Workshops