Computer Algebra Applications in the Life Sciences

ACA 2025 Special Session

14-18 July 2025, Heraklion (Crete), Greece

Aims and Scope

It is well-known that to answer a question, one must first state and formulate it properly. Many questions, from the effect of a drug on cancer cells to the spread of an epidemic, require mathematical modeling. Every project in the life sciences involves chemical materials, cells, or animals, with the ultimate goal of understanding how changes in the quantity of one element affect the others. While some questions can be addressed using basic methods, most require more sophisticated techniques. For instance, when measuring all relevant quantities is impossible, one encounters the issue of identifiability: is it possible to estimate the model's parameters using data from only the observable variables?

Computer Algebra, as the name suggests, is the field focused on developing algorithms for symbolic computations involving variables and parameters. While life scientists have a wealth of mathematically interesting questions, computer algebra researchers possess a wealth of algorithms and methods capable of addressing complex problems. Our session aims to bring these two groups together and facilitate the matching of questions with solutions. In addition to speakers from previous editions of CASinLife, who will report on collaborations sparked earlier, we are also seeking new participants with fresh challenges and ideas to join our ongoing journey of discovery.

This will be the fourth edition of CASinLife. The first three editions were held as special sessions of ACA 2022 (in Turkey), ACA 2023 (in Poland), and ICMS 2024 (in the UK). Topics of interests include, but are not limited to the following:

• Mathematical modelling for biological/chemical/ecological questions

• Chemical reaction network theory

• Combinatorial optimizations and machine learning tools for mathematical biology

• Cylindrical algebraic decomposition

• Quantifier elimination theory

• Computer algebra packages for real algebraic geometry

• Parameter identifiability analysis

• Phylogenetics

Schedule

Our session is scheduled for the first two days of ACA, 14th-15th July. The detailed schedule is displayed in a table below. Times would be in Greece time zone GMT+02:00. We will have CASinLife group photos in each day of the session a few minutes before the start of the session. Make sure to be in the session's room on time to not miss being in the photos.

Below you can see the abstract of each talk by clicking on its title. The talks are ordered alphabetically by the last name of the speaker. All talks are in-person. Some of the speakers also shared their slides which you can access by clicking on "slides" in front of their talks' titles below.

• Marcus Aichmayr. Reaction networks with (generalized) mass-action kinetics: Sign vector conditions for the existence of a unique general equilibrium. <slides>

• Dr Richard Golnik. Symbolic bifurcation analysis of reaction networks with Python. Part II: Implementation. <slides>

• Dr Bryan Hernandez. Analyzing the dynamics and structure of biochemical reaction networks via network decomposition.

• Dr Jack Jansma. Bayesian inference of interaction rates in a metabolite-bacteria network using time-series counts. <slides>

• Prof. Robert Lewis. New Results about Bricard's Flexible Octahedra. <slides>

• Dr Andrzej Mizera. Graph Neural Network-Based Reinforcement Learning for Controlling Biological Networks - the GATTACA framework. <slides>

• Prof. Atsushi Mochizuki. Biological functions and functional modules originated in the structure of chemical reaction network. <slides>

• Prof. Ovidiu Radulescu. Graph-Theoretic Algorithms for Reducing Chemical Reaction Networks. <slides>

• Dr Fabrice Rouillier. On solving parametric systems.

• Dr Amirhosein Sadeghimanesh. Using ML tools to predict number of solutions of parametric system of polynomial equations with the help of CRNs. <slides>

• Dr Sofia Triantafillou. Learning treatment effects from multiple data. <slides>

• Dr Nicola Vassena. Symbolic bifurcation analysis of reaction networks with Python. Part I: Theory. <slides>

Call for Contributions

If you are interested in presenting your recent work in this session, please send your title and abstract to one of the session organizers, no later than May 25, 2025.

Links:

ACA 2025 Home - CASinLife 2024 Home - CASinLife 2023 Home - CASinLife 2022 Home

Images at the top of the page: The photo in the middle is taken by AmirHosein Sadeghimanesh, the two other images are created by AmirHosein Sadeghimanesh.
For permission to use these images out of this page, contact the corresponding creator.