In the field of simulation sciences, a popular and effective strategy to address the challenges of high computational and storage costs is to create a simpler statistical/mathematical surrogate, mimicking the original expensive simulation mode. The surrogate is then utilized to perform detailed analysis tasks instead of the expensive simulation model. In this talk, I will describe collaborative research with Prof. Chou in which we designed an interactive visual analysis framework, backed by a neural network-based surrogate model, to assist in analyzing and visualizing a complex yeast cell polarization simulation model. The model simulates the concentration of important protein molecules along the membrane of a yeast cell (single-cell microorganism) during its mating process. The simulation model comprises 35 uncalibrated input parameters and generates a 400-dimensional output. we demonstrate the advantage of using neural networks as surrogate models for visual analysis by incorporating some of the recent advances in the field of uncertainty quantification, interpretability and explainability of neural network-based models. We utilize the trained network to perform interactive parameter sensitivity analysis of the original simulation at multiple levels-of-detail as well as recommend optimal parameter configurations using the activation maximization framework of neural networks. We also facilitate analysis of the trained network to extract useful insights about the simulation model, learned by the network, during the training process.
Thursday, July 20 at 10:30am
MS06-CDEV-1: Computational models for developmental and cell biology: A celebration of the works of Prof. Ching-Shan Chou
Organized by: Wing-Cheong Lo, Weitao Chen, Wenrui Hao, Leili Shahriyari Note: this minisymposia has multiple sessions. The other session is MS07-CDEV-1.
- Han-Wei Shen The Ohio State University (Computer Science and Engineering) "Neural Network Assisted Visual Analysis of yeast simulation data"
- Yutong Sha & Qing Nie University of California, Irvine (Department of Mathematics) "Reconstructing transition dynamics from static single-cell genomic data"
- Weitao Chen University of California, Riverside (Department of Mathematics) "A Mechanochemical Coupled Model to Understand Budding Behavior in Aging Yeast – An extension of Prof. Ching-Shan Chou’s work"
- Xinfeng Liu University of South Carolina (Mathematics) "Data-driven mathematical modeling, computation and experimental investigation of dynamical heterogeneity in breast cancer"
MS06-CDEV-2: Recent Studies on the Biomechanics and Fluid Dynamics of Living Systems: Cellular Biomechanics and Microfluidics
Organized by: Wanda Strychalski, Alexander Hoover Note: this minisymposia has multiple sessions. The other session is MS07-CDEV-2.
- Wanda Strychalski Case Western Reserve University (Mathematics, Applied Mathematics, and Statistics) "Quantifying the role of fluid mechanics during confined cell migration"
- Jared Barber Indiana University-Purdue University Indianapolis (Mathematical Sciences) "A 2D model to assess stresses on flexible osteocytes and the influence of elastic properties"
- Thomas Fai Brandeis University (Mathematics) "Lubricated Immersed Boundary Method with Application to Fiber Bundles"
- Luoding Zhu Indiana University - Purdue Univiersity Indianapolis (Mathematics) "Computational modeling of stress/strain amplification of an osteocyte process interacting with a viscous flow in a 3D canaliculus"
MS06-ECOP-1: Microbial and ecological dynamics across the many natural scales
Organized by: Christopher Heggerud, Tyler Meadows Note: this minisymposia has multiple sessions. The other session is MS07-ECOP-1.
- Alan Hastings University of California - Davis (Environmental Science and Policy) "Transient dynamics: the key to ecological understanding"
- Rebecca Tyson University of British Columbia, Okanogan "Mutualism at the leading edge: Insights into the eco-evolutionary dynamics of host-symbiont communities during range expansion"
- Susmita Sadhu Georgia College & State University (Department of Mathematics) "Methods for analyzing long transient dynamics in a three-dimensional predator-prey model featuring two timescales"
- Tyler Meadows Queen's University (Mathematics and Statistics) "Evolution of persister cells"
MS06-MEPI-1: Recent advances in parameter identifiability of mathematical models in mathematical biology
Organized by: Omar Saucedo, Bren Case, Lauren Childs Note: this minisymposia has multiple sessions. The other session is MS07-MEPI-1.
- Widodo Samyono Jarvis Christian University (Mathematics and Sciences) "Parameters Identifiability for selecting the best model using differential equations optimization"
- Marisa Eisenberg University of Michigan, Ann Arbor (Epidemiology and Complex Systems) "Identifiability and infectious disease interventions: exploring when uncertainty matters"
- All Participants "Open Forum"
MS06-MEPI-2: Disease Dynamics Across Scales
Organized by: Joshua Caleb Macdonald, Hayriye Gulbudak Note: this minisymposia has multiple sessions. The other session is MS07-MEPI-2.
- Anna Jolles Oregon State University (Carlson College of Veterinary Medicine and Department of Integrative Biology) "Mechanisms of persistence of highly transmissible foot-and-mouth viruses in their maintenance host, African buffalo (Syncerus caffer)"
- Simon Gubbins The Pirbright Institute (Transmission Biology) "Cross-scale dynamics of foot-and-mouth disease virus: from within hosts to between farms"
- Jan Medlock Oregon State University (Biomedical Sciences) "The Persistence of Foot-and-Mouth Disease Virus in African Buffalo"
- Cameron Browne University of Louisiana at Lafayette (Mathematics) "Environmental adaptation and seasonality in cholera eco-evolutionary dynamics"
MS06-MFBM-1: Algebra, Combinatorics, and Topology in Modern Biology
Organized by: Daniel A. Cruz,Margherita Maria Ferrari
- Lina Fajardo Gomez University of South Florida (Mathematics) "Homology for Directed Graphs with Applications to DNA Recombination"
- Puttipong Pongtanapaisan Arizona State University (Mathematics and statistics) "On the scarcity of split links spanning a lattice tube"
- Caitlin Lienkaemper Boston University (Department of Mathematics and Statistics) "Combinatorial coexpression in mosquito olfaction"
- Radmila Sazdanovic NC State University (Mathematics) "Categorified chromosome aberration model"
- Margherita Maria Ferrari University of Manitoba (Department of Mathematics) "Graph theory for DNA self-assembly"
MS06-MFBM-2: Data-driven multiscale modeling of cancer
Organized by: Heber Rocha, John Metzcar, Paul Macklin
- Alexander Browning University of Oxford (Mathematical Institute) "Drawing biological insight from non-identifiabile models of tumour growth using simple surrogates"
- Jeanette Johnson Johns Hopkins University (Immunology) "Integrating Omics Data and Agent-Based Models for Comprehensive Digital Biology"
- Adam MacLean University of Southern California (Department of Quantitative and Computational Biology) "Learning gene regulatory networks that control cell state transitions from multi-modal single-cell genomics"
- Matthew Simpson Queensland University of Technology (School of Mathematical Sciences) "A stochastic mathematical model of 4D tumour spheroids with real-time fluorescent cell cycle labelling"
MS06-NEUR-1: Uncovering activity patterns, oscillations and other key dynamics of neuronal (and other) networks
Organized by: Cheng Ly, Janet Best, Pamela Pyzza, Yangyang Wang Note: this minisymposia has multiple sessions. The other session is MS07-NEUR-1.
- Krasimira Tsaneva-Atanasova University of Exeter (Mathematics and Statistics) "Mathematical modelling of GnRH pulse generator frequency modulation through the interaction between kisspeptin and GABA-glutamate in the posterodorsal medial amygdala"
- Andrea K. Barreiro Southern Methodist University (Mathematics) "Fluid dynamics as a driver of retronasal olfaction"
- Madeline Edwards University of Pittsburgh (Department of Neuroscience) "Exploring the Roles of Interneuron Subtypes in Network Dynamics"
- Andrea Welsh University of Pittsburgh (Department of Mathematics) "Modeling Mouse Colon Non-propulsion Dynamics"
MS06-ONCO-1: Integration of cellular processes in cell motility and cancer progression
Organized by: Yangjin Kim, Magdalena Stolarska Note: this minisymposia has multiple sessions. The other session is MS07-ONCO-1.
- Dumitru Trucu University of Dundee (Mathematics) "Multiscale Modelling Glioblastoma Progression within the Fibrous Brain Tissue"
- Junho Lee Konkuk University (Mathematics / Seoul, Republic of Korea) "Role of senescent tumor cell in building a cytokine shield in tumor microenvironment: mathematical models"
- Eunjung Kim Korea Institute of Science and Technology (Natural Product Informatics) "Acquired resistance shapes the treatment outcomes by modulating the distribution of resistance"
MS06-OTHE-1: Modeling sex differences in health and disease
Organized by: Melissa Stadt Note: this minisymposia has multiple sessions. The other session is MS07-OTHE-1.
- Lihong Zhao University of California, Merced (Department of Applied Mathematics) "Mathematical modeling of the menstrual cycle and hormonal contraception"
- Erica Graham Bryn Mawr College (Mathematics) "Functional Variations in the Ovulatory Cycle: Insights from Modeling"
- Carley V. Cook University at Buffalo (Department of Chemical and Biological Engineering) "Mathematical Modeling of Osteoporosis Due to Surgical Menopause"