Computer Algebra Applications in the Life Sciences

ACA 2023 Special Session

17-21 July 2023, Warsaw, Poland

Aims and Scope

In recent years, the use of computer algebra to tackle questions in biology and ecology has become more popular. This is thanks to an increase in awareness about the applications of computational algebra tools such as Gröbner bases, resultants, and cylindrical algebraic decomposition to study systems of equations and inequalities; and the advantages of symbolic algorithms to treat parameters as free variables instead of fixed numbers. Many conjectures of experimentalists have been proven or rejected using such tools. But still, there are many algorithms and ideas from computer algebra that have strong potential of being used in the study of biological problems which have not been touched and are waiting for exploration. Even the algorithms that are currently being employed still need further optimization. Other than the theoretical optimization, there is a huge potential of using machine learning tools in speeding up these algorithms which only very recently has started to be investigated.

The goal of this session is to bring biologists, mathematicians, and computer scientists with a common interest together. This will help applied mathematicians to hear new questions in biology that need development of new mathematical tools; computer scientists to hear about new algorithms and try to improve them to have lower complexity; and biologists to hear about new tools and packages that may benefit their research.

After a fruitful edition of CASinLife at ACA 2022 in Turkey, we are aiming to hold a similarly themed session at ACA 2023 in Poland: to follow up on the discussions of the previous year, and to start new discussions. We hope that our session can attract more participants from diverse backgrounds and receive a wider range of ideas and questions. Topics of interests include, but are not limited to the following:

• Modelling biological/chemical/ecological questions using algebra

• Chemical reaction network theory

• Machine learning tools for mathematical biology

• Cylindrical algebraic decomposition

• Quantifier elimination theory

•  Computer algebra packages for real algebraic geometry

•  Parameter identifiability analysis

Schedule

Our session is scheduled for Tuesday and Thursday, 18th and 20th July. The detailed schedule is displayed below. Times would be in Poland 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. Some of the speakers gave permission to share their slides which you can access by clicking on "<slides>" in front of title of their talks. 

Below you can see which talk is in-person and which is online plus the title of the talks. 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.

• Marcus Aichmayr, in-person. Computing sign vector conditions for existence and uniqueness of equilibria of chemical reaction networks. <slides>

• Oskar Henriksson, in-person. Generic dimension of varieties arising in reaction network theory and 3D genome reconstruction. <slides>

• Dr Alexandru Iosif, in-person. Duality in mass-action networks.

• Jiayue Qi, in-person. Five equivalent representations of a phylogenetic tree.

• Dr Adam L. MacLean, online. Gene regulatory network inference with joint multi-omic single-cell data to learn dynamic cell state transitions.

• Dr Andrzej Mizera, in-person. Divide & Control: An Efficient Decomposition-based Approach Towards the Control of Asynchronous Boolean Networks. <slides>

• Professor Ovidiu Radulescu, in-person. Inferring stochastic models of gene transcription from initiation events by computer algebra.

• Professor Valery Romanovski, in-person. Hopf bifurcations in some biochemical models.

• Dr Adam Strzebonski, in-person. CAD Adjacency Computation Using Validated Numerics. <slides>

• Dr Angélica Torres, in-person. Phylogenetic invariants for time-reversible models.

• Dr Nicola Vassena, in-person. How to find or exclude bifurcations in biochemical systems?

* Additionally there is a talk given by AmirHosein Sadeghimanesh in another session on Wednesday 19th at 17:30-18:00 in case you are interested. Title of the talk is "Semi-algebraic representations for the multistationarity region of reaction networks". <slides>

Photos of the session

For the photos of the session click on "Photo gallery" at top right side of the page.

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 21, 2023. Please use the LaTeX template  for your submission.

Links:

ACA 2023 Home - CASinLife 2022 Home

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