[hpc-announce] [Call for Participation] HiCOMB 2025 @IPDPS (4th June)

[Vinod Rebello]

*HiCOMB 2025*
24th IEEE International Workshop on High Performance Computational Biology
In conjunction with the IEEE International Parallel and Distributed
Processing Symposium (IPDPS'25)
Milan, Italy

June 4, 2025
11:00am - 4:00pm CEST (GMT+2)

*Conference Venue*: The conference will be held at *Politecnico di
Milano – *located at Piazza Leonardo da Vinci 32, Milan 20133
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The HiCOMB 2025 Workshop is on Wednesday, June 4th, in Building 3.

*Keynote Speakers*

Professor Srinivas Aluru
Department of Computer Science
Georgia Institute of Technology, USA

Title: Genome Graphs: Opportunities and Challenges for High Performance
Computing

Abstract:  The rapid advancement of cost-effective high-throughput
sequencing technologies has enabled extensive intra-species sequencing and
the systematic cataloging of genetic diversity, leading to the rise of
pangenomics. A frequently used data structure in pangenomics is the genome
graph, which is a compact graph representation of multiple reference
genomes. Genome graphs capture genetic diversity by incorporating variants
from multiple genomes, thereby reducing single-reference bias. This
framework gives rise to two broad classes of problems: selecting which
genetic variants to incorporate into the graph, and efficiently mapping
sequencing reads to graph-based references. As a young and rapidly
expanding field, pangenomics offers largely untapped opportunities for
designing parallel algorithms and the application of high-performance
computing. In this talk, I will present key concepts and recent advances in
variant selection and sequence-to-graph mapping, and my group’s early
forays into developing high-performance computing approaches to these
problems.

Bio:  Srinivas Aluru is a Regents’ Professor and Senior Associate Dean in
the College of Computing at the Georgia Institute of Technology. His
research areas include high-performance computing, parallel algorithms,
data science, bioinformatics, systems biology, combinatorial scientific
computing, and applied algorithms. He has made pioneering contributions to
the field of parallel computational biology, spanning both fundamental
algorithms and compelling applications, including the assembly and analysis
of genomes, next-generation sequencing data analysis, inference and
analysis of genome-scale networks, and the emerging fields of pangenomics
and single-cell biology. Aluru is a recipient of several prestigious
awards, including the NSF CAREER award, IBM faculty award, Swarnajayanti
Fellowship from the Government of India, and the John. V. Atanasoff
Discovery Award from Iowa State University. At Georgia Tech, he received
the Outstanding Senior Faculty Research and Leadership awards in the
College of Computing, the Dean’s Award for faculty excellence, and the
Outstanding Research Program Development Award at the institute level. He
has also been honoured with the IEEE Computer Society Meritorious Service
and Golden Core awards, is a Fellow of the AAAS, ACM, IEEE, and SIAM, and
is the 2025 recipient of the IEEE Computer Society Charles Babbage Award.


Professor Marco Aldinucci
Department of Computer Science
University of Torino, Italy

Title:  Streaming Workflows: From Scientific Applications to AI and Back

Abstract:  Within the Italian National Center in HPC and Quantum Computing
(ISCS), the University of Turin and Pisa have co-developed two cloud-HPC
development tools. The first is StreamFlow, an implementation of the open
standard CWL (Common Workflow Language) that makes it possible to design
scientific workflows (aka pipelines) that can be seamlessly ported to
different platforms. StreamFlow fosters declarative workflows that can be
executed on HPC platforms (e.g., based on SLURM), cloud platforms (e.g.,
based on K8S, AWS), and hybrid platforms without code modification. The
second tool is CAPIO (Cross-Application Programmable I/O), which transforms
files exchanged between parallel applications into streams, introducing
further parallelism and helping to avoid the I/O bottleneck.
StreamFlow+CAPIO has many applications, from genomics pipelines to
astrophysics and materials science workflows to AI for science pipelines.

Bio:  Marco Aldinucci is a full professor and the head of the Parallel
Computing research group at the University of Torino. He has authored over
200 scientific articles and has received several prestigious awards. These
include the HPC Advisory Council University Award in 2011, the NVidia
Research Award in 2013, the IBM Faculty Award in 2015, and the Autodesk
Award in 2021. He served as the Italian delegate on the Governing Board of
the EuroHPC Joint Undertaking from 2018 to 2021, and he is currently a
member of its Research and Innovation Advisory Board (RIAG). Marco has
participated in over 20 EU-funded research projects that have focused on
parallel, cloud, and high-performance computing (HPC), securing more than
€15 million in research funds for the University of Torino. He has
co-designed and contributed to several programming frameworks and libraries
for parallel computing, such as Fastflow, Streamflow, and CAPIO. In 2017,
Marco led the design of the HPC4AI laboratory, and in 2020, he became the
founding director of the CINI HPC Key Technologies and Tools national
laboratory, which brings together researchers from 38 Italian universities.
This experience was further applied to FutureHPC, the technological spoke
of the Italian National Centre on HPC, Big Data, and Quantum Computing,
where he initiated the Software & Integration national laboratory in 2023.


*Program Schedule*
10:30 – 11:00am Coffee Break
  Plenary Session I (11am - 12:30pm)
11:00 – 11:10 Opening Remarks
Workshop Chairs
11:10 – 12:05 *Keynote address from Professor Marco Aldinucci*, University
of Torino, Italy
Title: *Streaming Workflows: From Scientific Applications to AI and Back*

*Q&A*
12:10 – 12:30 *Development and Deployment of a Genomic Cancer Data
Extraction Pipeline on the Cloud*
Eleni Adam, Terry Stilwell, Desh Ranjan, and Harold Riethman (Old Dominion
University, USA)
12:30 – 2:00pm Lunch
  *Plenary Session II (2:00 – 4:00pm)*
2:00 – 2:55

*Keynote address from Professor Srinivas Aluru*, Georgia Institute of
Technology, USA
Title: *Genome Graphs: Opportunities and Challenges for High Performance
Computing*

*Q&A*
2:55 – 3:25 *Protein Database Search using Processing-in-Memory
Architecture*
Dominique Lavenier, Charly Airault, Charles Deltel, Florestan De Moor,
Erwan Drezen, and Meven Mognol (IRISA, INRIA, and the Pasteur Institute,
France)
3:25 – 3:55 *Exploring the AMD Deep Learning Processor Unit for
Accelerating Selective Sweep Detection*
Nikolaos Alachiotis and Matthijs Souilljee (University of Twente, The
Netherlands)
3:55 – 4:00

Closing Remarks
4:00 – 4:30pm Coffee Break