Now, more than ever, pharmaceutical companies are relying on mathematical modeling & simulation to inform drug discovery and development decisions. In many cases, particularly for novel compounds, targets, and/or combinations, modelers must rely on incomplete data and/or extrapolation beyond existing data to address key questions, such as dose and dose regimen selection for clinical trials. In this talk, I will present a few case studies and related mathematical challenges that my team has faced and discuss why developing a better understanding of these problems is important in the context of drug discovery & development.

# Methods for Biological Modeling Subgroup (MFBM)

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# Sub-group minisymposia

##### MS01-MFBM:

Mathematical Modeling Applied to Pharmaceutical Sciences Problems

**Organized by:** Carl Panetta (St. Jude Children's Research Hospital, US), Helen Moore (Laboratory for Systems Medicine, University of Florida, US)

**C.J. Musante***(Pfizer, US)*

"A Few Open Mathematical Modeling Problems in Drug Discovery & Development"**Jane Bai***(FDA, US)*

"Conducting sensitivity analysis and uncertainty analysis for QSP needs more than mathematical computation"**Freya Bachmann***(Department of Mathematics and Statistics, University of Konstanz, Germany)*

"Computing the Individualized Optimal Drug Dosing Regimen Using Optimal Control"**Tongli Zhang***(Department of Pharmacology & Systems Physiology, College of Medicine, University of Cincinnati, US)*

"Coping with the Challenge of Heterogeneity with Integrated Modeling, Machine Learning, and Dynamical Analysis"

##### MS02-MFBM:

Generalized Boolean network models and the concept of canalization

**Organized by:** Claus Kadelka (Iowa State University, United States)

Note: this minisymposia has multiple sessions. The second session is **MS03-MFBM**.

**Gleb Pogudin***(LIX, CNRS, Ecole Polytechnique, Institute Polytechnique de Paris, France)*

"Attractor stucture of Boolean networks of small canalizing depth"**S. S. Ravi***(Biocomplexity Institute & Initiative, University of Virginia, and Department of Computer Science, University at Albany, United States)*

"Efficient Algorithms for Boolean Nested Canalyzing Functions"**Daniel Rosenkrantz***(Biocomplexity Institute & Initiative, University of Virginia, and Department of Computer Science, University at Albany, United States)*

"Testing Phase Space Properties of Synchronous Dynamical Systems with Nested Canalyzing Local Functions: Complexity Results and Algorithms"**Matthew Wheeler***(Department of Medicine, University of Florida, United States)*

"Reducibility of Boolean Networks: Toward a Theory of Modularity"

##### MS03-MFBM:

Generalized Boolean network models and the concept of canalization

**Organized by:** Claus Kadelka (Iowa State University, United States)

Note: this minisymposia has multiple sessions. The second session is **MS02-MFBM**.

**Claus Kadelka***(Iowa State University, United States)*

"Collective canalization"**Elena Dimitrova***(California Polytechnic State University, United States)*

"Revealing the canalizing structure of Boolean functions — algorithms and applications"**Matthew Macauley***(Clemson University, United States)*

"Toggling independent sets as an asynchronous Boolean network"**Alan Veliz-Cuba***(University of Dayton, Ohio, United States)*

"Identification of control targets in Boolean networks via computational algebra"

##### MS06-MFBM:

Mathematical and computational methods to augment the reliability of biological models for better decision-making

**Organized by:** Vincent Lemaire (Genentech, CA, USA, United States), Khamir Mehta (Amgen, Inc, United States), Malidi Ahamadi (Amgen, CA, United States)

**Chris Rackauckas***(MIT and Pumas AI, MA, USA, United States)*

"Accelerating Quantitative Systems Pharmacology with Machine Learning"**Oleg Demin Jr***(InSysBio, Russia)*

"Implementation of variability or uncertainty in parameter values to validate QSP models."**Gianluca Selvaggio***(Fondazione The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Italy)*

"Parameter free approaches in QSP: modelling the cytokine release following bispecific T-cell engager therapy"**Sietse Braakman***(AbbVie Inc., Quantitative Translational Modeling Group, United States)*

"A framework for the evaluation of QSP models, with a focus on verification, validation and uncertainty quantification (VVUQ) methods"

##### MS07-MFBM:

From Machine Learning to Deep Learning Methods in Biology

**Organized by:** Erica Rutter (University of California, Merced, United States), Suzanne Sindi (University of California, Merced, United States)

Note: this minisymposia has multiple sessions. The second session is **MS08-MFBM**.

**Emilia Kozlowska***(Departement of Systems Biology and Engineering, Silesian University of Technology, Poland)*

"Application of mechanistic and machine learning modeling to predict long-term response to treatment for cancer patients"**Sara Ranjbar***(Mathematical NeuroOncology Lab, Precision Neurotherapeutics Program, Mayo Clinic, Arizona, United States)*

"MRI-based estimation of the abundance of immunohistochemistry markers in GBM brain using deep learning"**Joan Ponce***(UCLA, United States)*

"An integrated framework for building trustworthy data-driven epidemiological models: Application to the COVID-19 outbreak in New York City"**Emily Zhang***(North Carolina State University, USA)*

"Deep Learning and Regression Approaches to Forecasting Blood Glucose Levels for Type 1 Diabetes"

##### MS08-MFBM:

From Machine Learning to Deep Learning Methods in Biology

**Organized by:** Erica Rutter (University of California, Merced, United States), Suzanne Sindi (University of California, Merced, United States)

Note: this minisymposia has multiple sessions. The second session is **MS07-MFBM**.

**Ali Heydari***((i) UC Merced Department of Applied Mathematics and (ii) Health Sciences Research Institute at UC Merced, USA)*

"Deep Generative Models for Realistic Single-Cell RNA-Seq Data Augmentation"**Mohammad Jafari***(Postdoctoral Scholar, Department of Applied Mathematics Jack Baskin School of Engineering University of California, Santa Cruz, USA)*

"Machine Learning-based Feedback Controller for Directing Stem Cell Membrane Potential"**Thomas de Mondesir***(Université Claude Bernard Lyon 1 & UC Merced, France)*

"Generating biological images to train deep-learning-based segmentation models"**Jordan Collignon***(University of California, Merced, USA)*

"A High-throughput Pipeline for Analyzing Experimental Images of Sectored Yeast Colonies"

##### MS09-MFBM:

Emergent behavior across scales: locomotion, mixing, and collective motion in active swimmers

**Organized by:** Robert Guy (University of California Davis, United States), Arvind Gopinath (University of California Merced, United States)

Note: this minisymposia has multiple sessions. The second session is **MS15-MFBM**.

**Henry Fu***(University of Utah, United States)*

"Symmetry breaking propulsion of magnetically rotated spheres in nonlinearly viscoelastic fluids"**Kathryn Link***(University of California Davis, United States)*

"Emergent Properties of Flagellar Waveforms in Viscoelastic Fluids"**Rudi Schuech***(Tulane University, United States)*

"Viscoelastic Network Remodeling by Microswimmers"**Sookkyung Lim***(University of Cincinnati, United States)*

"Simulations of microswimmers propelled by multiple flagella"

##### MS11-MFBM:

Stochastic Systems Biology: Theory and Simulation

**Organized by:** Jae Kyoung Kim (Department of Mathematical Sciences, KAIST, Republic of Korea), Ramon Grima (University of Edinburgh, United Kingdom)

Note: this minisymposia has multiple sessions. The second session is **MS12-MFBM**.

**Zhixing Gao***(Key Laboratory of Advanced Control and Optimization for Chemical Processes, Ministry of Education, East China University of Science and Technology, China)*

"Neural network aided approximation and parameter inference of stochastic models of gene expression"**Abhyudai Singh***(University of Delaware, USA)*

"Modeling stochasticity in timing of intracellular events: A first-passage time approach"**Thomas Prescott***(Alan Turing Institute, United Kingdom)*

"Learning a multifidelity simulation strategy for likelihood-free Bayesian inference."**Ruben Perez-Carrasco***( Imperial College London, United Kingdom)*

"Should we care about cell cycle variability when studying stochastic gene expression?"

##### MS12-MFBM:

Stochastic Systems Biology: Theory and Simulation

**Organized by:** Jae Kyoung Kim (Department of Mathematical Sciences, KAIST, Republic of Korea), Ramon Grima (University of Edinburgh, United Kingdom)

Note: this minisymposia has multiple sessions. The second session is **MS11-MFBM**.

**Hyukpyo Hong***(Department of Mathematical Sciences, KAIST, Republic of Korea)*

"Inference of stochastic dynamics in biochemical reaction networks by exploiting deterministic dynamics"**Zhou Fang***(ETH Zurich, Switzerland)*

" Stochastic filtering for multiscale stochastic reaction networks based on hybrid approximations"**Samuel Isaacson***(Boston University, Department of Mathematics and Statistics, USA)*

"Stochastic Reaction-Drift-Diffusion Methods for Studying Cell Signaling"**Brian Munsky***(Colorado State University, USA)*

"Designing Optimal Microscopy Experiments to Harvest Single-Cell Fluctuation Information while Rejecting Image Distortion Effects"

##### MS13-MFBM:

Data-driven methods for biological modeling in industry

**Organized by:** Kevin Flores (North Carolina State University, USA)

Note: this minisymposia has multiple sessions. The second session is **MS14-MFBM**.

**Anna Sher***(Pfizer, USA)*

"Quantitative Systems Pharmacology (QSP) in cardiovascular disease: Preclinical case studies with real-world data"**Doris Fuertinger***(Fresenius Medical Care, Germany)*

"1 year of precision therapy: Experiences in optimal drug administration based on an individualized biomathematical anemia model"**Alhaji Cherif***(Renal Research Institute, USA)*

"Bone and mineral disturbances in uremic patients"**Malidi Ahamadi***(Amgen, USA)*

"Disease progression platform for Leucine-Rich Repeat Kinase 2 in Parkinson's Disease to Inform Clinical Trial Designs"

##### MS14-MFBM:

Data-driven methods for biological modeling in industry

**Organized by:** Kevin Flores (North Carolina State University, USA)

Note: this minisymposia has multiple sessions. The second session is **MS13-MFBM**.

**Richard Allen***(Quantitative Systems Pharmacology, Early Clinical Development, Pfizer Worldwide Research Development and Medical, USA)*

"Analyzing and Predicting Clinical Trial Data with Systems Modeling"**Florencio Serrano Castillo***(Clinical Pharmacology, Modelling and Simulations, Amgen Inc., USA)*

"Dosing guidance optimization, leveraging real world heterogeneity to forecast clinical biomarker response"**Zackary Kenz***(DILIsym Services, a Simulations Plus Company, USA)*

"Quantitative Systems Pharmacology Modeling of Fibrotic Diseases"**Anna Neely***(TigerRisk Partners, USA)*

"Estimating the growing risk of severe thunderstorms"

##### MS15-MFBM:

Emergent behavior across scales: locomotion, mixing, and collective motion in active swimmers

**Organized by:** Robert Guy (University of California Davis, United States), Arvind Gopinath (University of California Merced, United States)

Note: this minisymposia has multiple sessions. The second session is **MS09-MFBM**.

**Maxime Theillard***(University of California Merced, United States)*

"Multi-scale multi-species modeling of emergent flows and active mixing in confined bacterial swarms"**Paulo Arratia***(University of Pennsylvania, United States)*

"Bacteria hinder stretching and large-scale transport in time-periodic flows"**Bin Liu***(University of California Merced, United States)*

"Anomalous size-dependent active transport in structured environments"**Nick Cogan***(Florida State University, United States)*

"Modeling the Origin of Life Reaction in Microfluidic Chambers"

##### MS18-MFBM:

Mechanical Models of Complex Diseases

**Organized by:** Fabian Spill (University of Birmingham, USA)

**Vijay Rajagopal***(University of Melbourne, Australia)*

"Surface area-to-volume ratio, not cellular viscoelasticity is the major determinant of red blood cell traversal through small channels."**Bindi Brook***(University of Nottingham, UK)*

"Inflammation driven mechanical model of asthmatic airway remodelling"**Herbert Levine***(Northeastern University, USA)*

"The role of extracellular matrix in motility and metastasis"**Stephanie Fraley***(University of California San Diego, USA)*

"A spatial model of YAP/TAZ mechanotransduction reveals new insights into how cells sense ECM dimensionality"

##### MS19-MFBM:

Algebra, Combinatorics, and Topology in Modern Biology

**Organized by:** Daniel Cruz (Georgia Institute of Technology, U.S.), Margherita Maria Ferrari (University of South Florida, U.S.)

Note: this minisymposia has multiple sessions. The second session is **MS20-MFBM**.

**Margherita Maria Ferrari***(University of South Florida, U.S.)*

"Formal grammar modeling three-stranded DNA:RNA braids"**Svetlana Poznanovic***(Clemson University, U.S.)*

"Using Polytopes to Improve RNA Branching Predictions"**Chad Giusti***(University of Delaware, U.S.)*

"Comparing Topological Feature Coding Across Neural Populations"**Abdulmelik Mohammed***(University of South Florida, U.S.)*

"Topological Eulerian Circuits for the Design of DNA Nanostructures"

##### MS20-MFBM:

Algebra, Combinatorics, and Topology in Modern Biology

**Organized by:** Daniel Cruz (Georgia Institute of Technology, U.S.), Margherita Maria Ferrari (University of South Florida, U.S.)

Note: this minisymposia has multiple sessions. The second session is **MS19-MFBM**.

**Mustafa Hajij***(Santa Clara University, U.S.)*

"TDA-Net: Fusion of Persistent Homology and Deep Learning Features for COVID-19 Detection in Chest X-Ray Images"**Hector Banos***(Dalhousie University, Canada)*

"Identifiability of Species Network Topologies from Genomic Sequences"**Nida Obatake***(Texas A&M University, U.S.)*

"Mixed Volume of Chemical Reaction Networks"**Raina Robeva***(Randolph-Macon College, U.S.)*

"Algebraic Biology in the Curriculum"

# Sub-group contributed talks

##### CT01-MFBM:

MFBM Subgroup Contributed Talks

**Wayne Hayes***UC Irvine*

"The One True Way to use GO terms to evaluate Network Alignments"**Giulia Palermo***UCR*

"Harnessing graph theory to decrypt the allosteric mecahnism in CRISPR-Cas9"**Dennis Manjaly Joshy***UC Santa Barbara*

"A Koopman Operator Approach for Genetic Circuit Design"**Ying Zhang***Brandeis University*

"Immersed Boundary Simulations of Red Blood Cells Near Vessel Walls"

##### CT02-MFBM:

MFBM Subgroup Contributed Talks

**Yifei Li***Queensland University of Technology*

"Travelling waves in nonlinear reaction-diffusion equations"**Juan Carlo Flores Mallari***Ateneo de Manila University, Nara Institute of Science and Technology*

"Modeling Collective Behavior of Passengers Boarding and Disembarking from Public Transport in the Philippines"**Leo Diaz***University of Melbourne*

"Hypergraphs as a tool for automated and reproducible modelling of biochemical systems"**Shawn Means***Massey University*

"A Permutation Method to Assemble Networks"

##### CT03-MFBM:

MFBM Subgroup Contributed Talks

**Gregory Szep***King's College London*

"Parameter Inference with Bifurcation Diagrams"**Sta Léa***University of Leeds, United Kingdom*

" IL-7R mathematical modelling: algebraic expressions for amplitude and EC50"**Johannes Borgqvist***Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford*

"Symmetry methods for model-construction and analysis in the context of collective cell migration"**Remus Stana***University of Leeds*

"Diffusion in a domain with inclusion"

##### CT04-MFBM:

MFBM Subgroup Contributed Talks

**Elizabeth Trofimenkoff***University of Lethbridge*

"An algorithm for obtaining parametric conditions for the validity of the steady-state approximation"**Alexander D. Kaiser***Stanford University*

"Design-based models of heart valves and bicuspid aortic valve flows"**Jay Stotsky***University of Minnesota*

"The Impact of Cell-Level Details on Tissue-Scale Properties"**Fawaz K Alalhareth***The University of Texas at Arlington*

"Higher-Order Modified Nonstandard FiniteDifference Methods for Dynamical Systems in Biology"

##### CT05-MFBM:

MFBM Subgroup Contributed Talks

**Fatemeh Sadat Fatemi Nasrollahi***Pennsylvania State University*

"Attractor identification method based on generalized positive feedback loops and their functional relationships"**Megan Coomer***Melbourne University*

"Shaping the Epigenetic Landscape: Complexities and Consequences"**Kumar Saurabh***National Taiwan University*

"MATHEMATICAL MODELING OF ION CHANNEL FLOW WITHIN CONTINUUM FRAMEWORK"**Nayana Wanasingha***Department of Mathematical Sciences, University of Cincinnati*

"Molecular mechanisms regulating frequecy demultiplication of circadian rhythms in Neurospora Crassa"

##### CT06-MFBM:

MFBM Subgroup Contributed Talks

**Miroslav Phan***ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland*

"A Rejection Based Gillespie Algorithm for non-Markovian Stochastic Processes with Individual Reactant Properties"**Elba Raimundez***University of Bonn*

"Efficient sampling by marginalization of scaling parameters for mechanistic models with relative data"**Aden Forrow***Mathematical Institute, University of Oxford*

"Learning stochastic dynamics with measurement noise"**Marco Berghoff***Karlsruhe Institute of Technology*

"Cells In Sillico â€“ Parallel Tissue Development Simulation"

##### CT07-MFBM:

MFBM Subgroup Contributed Talks

**Eli Newby***The Pennsylvania State University*

" Identifying Driver Nodes in Biological Networks using Subsets of the Feedback Vertex Set"**Xiaoyu Duan***University of Pittsburgh*

"Parameter identification of linear-in-parameters systems from a single trajectory"**Katherine Pearce***Department of Mathematics, North Carolina State University*

"Modeling and parameter subset selection for fibrin polymerization kinetics with applications to wound healing"**Yue Liu***University of Oxford*

"Organisation of diffusion-driven stripe formation in expanding domains"

##### CT09-MFBM:

MFBM Subgroup Contributed Talks

**Ivan Borisov***INSYSBIO LLC*

"Constrained Optimization Approach to Predictability Analysis in Bio-Mathematical Modeling"**Anna Molyavko***ICM SB RAS, Krasnoyarsk Mathematical Center*

"Novel alignment-free highly parallel method to compare symbol sequences of an arbitrary length"**Dimitrios Patsatzis***National Technical University of Athens*

"Towards extending the arsenal of cancer immunology modeling with algorithmic asymptotic analysis"**Viktoriia Fedotovskaia***Siberian federal university, Institute of fundamental biology and biotechnology*

"The prevalence of function over taxonomy for triplet composition of mitochondrial and chloroplast plant genes"

# Sub-group poster presentations

##### MFBM Posters

MFBM-1 (Session: PS02)
**Paulina Wodarz**
*University High School, Irvine*

"Analyzing Text Corpora to Determine the Emotional State of Humans"

MFBM-2 (Session: PS02)
**Samarth Kadaba**
*University of California, Santa Barbara*

"Discovering Sequence-Activity Relationships using Machine Learning: Convolutional Neural Networks (CNNs) and Gaussian Process Regressions (GPRs)."

MFBM-3 (Session: PS02)
**Emilee Carson**
*University of Waterloo*

"A machine learning approach for analyzing bistable systems in biology"

MFBM-4 (Session: PS02)
**Alex John Quijano**
*University of California Merced*

"Evolving Contextual Semantics"

MFBM-10 (Session: PS05)
**Yuki Takahashi**
*Akita prefectural University*

"Chromatin dynamics by polymer models and Brownian dynamics with collisions"

MFBM-11 (Session: PS05)
**Eun Han Goo**
*Korea Advanced Institute of Science and Technology(KAIST)*

"Development of a Mathematical Model for Predicting Accurate Hepatic Clearance of Drug"

MFBM-12 (Session: PS05)
**Peerdeman GY**
*University of Applied Sciences Leiden*

"Standardizing the exchange of model states between cellular models using MultiCellDS"

MFBM-13 (Session: PS05)
**Yifei Li**
*Queensland University of Technology*

"Dimensionality affects extinction of bistable populations"

MFBM-5 (Session: PS05)
**Hyundong Kim**
*Korea University*

"Numerical simulation of the pattern formation in reaction-diffusion equations on time-stepped moving curved surfaces"

MFBM-6 (Session: PS05)
**Galina Kolesova**
*InSysBio, Moscow, Russia*

"Application of different approaches to generate virtual patient populations for QSP model of Erythropoiesis"

MFBM-7 (Session: PS05)
**Veronika Musatova**
*INSYSBIO*

"Unified approach for in vitro data based parameters estimation"

MFBM-8 (Session: PS05)
**Dmitry Shchelokov**
*InSysBio, Moscow, Russia*

"Specific lysis modeling and parameter extraction from experimental data"

MFBM-9 (Session: PS05)
**Yun Min Song**
*Korea Advanced Institute of Science and Technology*

"Universally valid reduction of multiscale stochastic biochemical systems with simple non-elementary propensities"