Person in charge: Philippe Schnoebelen

The “Initiation to Research” course (3 ECTS) embeds you in a working group (called “workshop”) tackling some research problem under the guidance of a senior superviser. The group meets once a week in order to assess progress, fix/update its short and long-term goals, assign tasks to participants. Research work is done between these meetings, working either alone or in some subgroup. Between the weekly meetings, communication with the group is often necessary and use ad-hoc means from email to impromtu discussions.

The pedagogical objectives of these workshops is to develop some specific skills by practicing them in a resarch-oriented setting. These skills are (list not exhaustive):

- Assessing the state of the art on some question/problem: specifying the scope of the question, assessing what are the main questions and why they are important or difficult or .., round up the relevant litterature, organize the existing contributions historically.

- Formulating a problem formally: choosing definitions, stating hypotheses to be proven/disproven, identifying subproblems or special cases, finalize proven results by either expanding/generalizing them or proving impossibility of extensions, find connections with problems in other contexts.

- Presenting/explaining a research result to your colleagues: highlighting what is easy and what is tricky, what is original and what is standard. Also, explaining what remains unclear and why.

- Understanding why a research problem is important: Identifying the underlying stakes, the implicit motivations, the potential applications, the future perspectives.

- Understanding the rules of research as a profession/career: how to write a curriculum vitae, how to find a position, where to publish a research paper and how to write it, what is plagiarism really, where and how to get funding for one's research, etc.

Description: Students will be enrolled in either one long workshop spanning the whole semester, or two short workshops over the two halves of the semester. Joining a long workshop allows investigating a research topic in more depth. Joining two short workshops allows for more diversity in research topics, style of supervision, sets of colleagues with whom to collaborate.

Planning: Each workshop has a scheduled group meeting on Tuesday afternoons during the semester (half semester for short workshops). Other interactions outside this time slot can be organized on a call-by-need basis, as the superviser deems necessary.

Language: Workshops will be in English (unless everyone prefers French or another language).

Evaluation: Each workshop has its own guidelines/rules/.. for evaluation (see details below).

In this first class we describe the objectives and of the course, present the list of workshops on offer for the academic year 2024-25, and explain how students will be assigned to workshops based (partly) on their preferences.

To-Do after the presentation: Submit your preferences by email to phs@lmf.cnrs.fr by Friday 20th, 12h00 AM so that I can organize the groups Friday afternoon. Make sure that your mail includes a full name and lists not only preferred but also backup choices.

The workshops actually start on Sept. 24th.

Superviser: Stefan Haar

Room: 1-M-07

Participants (7): CAUQUIL Diane; YANG Chen; BARON Rémi; LEBLANC Travis; FOURCIN Emile; CHARAF ZADAH Azammat; GIRAUD Raphaël

Description: In this module the students will study the state of the art in the interdisciplinary field of epigenetic prediction using discrete models. The problem is: derive, from available knowledge about a cell's regulatory network, what are the accessible phenotypes, and potentially what are the factors that decide between those. Based on selected authoritative articles - complemented by their own literature search where appropriate - from systems biology and from formal methods informatics (boolean networks, Petri nets), they are expected to cooperate for preparing a sound and comprehensive in-class presentation of the topic.

Expected workload: a few hours weekly.

Grading: will reflect involvement and quality of contributions.

Superviser: Vladimir Zamdzhiev.

Room: 2-E-35

Participants (8): SAADI Lyes; BOUZID Youcef; SASSUS-BOURDA Félix; HOUYET Nathan; GOUI Tem; LEAL Fernando; TANGUY-BOMPARD Ulysse; DEFRANSURE Valentin

Keywords: Programming Languages, Type Systems, Logic.

Description: The goal of this workshop is to study and identify interesting features in programming languages and related type systems. Modern research in programming languages and type systems has produced some interesting new programming features and abstractions that have not yet been introduced into mainstream languages. Students will have the opportunity to dive into modern programming language research and identify specific topics that are of interest to them. Examples can include studying programming abstractions (e.g., monads, dependent types, higher-order polymorphism), more specialised programming languages (e.g., probabilistic programming languages, quantum programming languages), static analysis tools/frameworks, etc. Students are expected to learn about a specific topic and do a presentation during the class during which they introduce the concept. They should also be able to answer questions about it. During the class we can also discuss other aspects of programming language/logic/type system research and/or discuss a possibility of a group project.

Expected Workload: About 5 hours per week.

Planning:

Grading: Details to be discussed, but it will be determined by class participation, contribution and presentation.

Superviser: Philippe Schnoebelen.

Room: 2-X-42

Participants (10): CATHERINOT Noémie; CORNELY Maëlle; DURIEUX Pierre; LOZAC’H Titouan; MATTEI Alban; SCHLOSSER Basile; VALENTIN Thomas; VERY Sébastien; MAISTRE Raphaëlle; TIANWEN Gu

Keywords: Scientific writing.

Description: This workshop is aimed at students who plan to submit an extended abstract to the JITA 2025 conference on Theoretical and Applied Computer Science, to be held in Jan 23rd 2025 on the plateau.

The task for these students is to transform their L3 internship report into a scientific publication. The distance between the two may be rather small (that depends on the actual report) but the workshop will be a good opportunity to learn about some fundamental principles of scientific writing and practice them in a real-life situation. We expect that collective feedback from peers (and from superviser) will help improve the quality of the submissions.

Other aspects that will be explored or discovered are the issues of authorship, the purposes of citations and bibliography, the business of publishers, the ranking of journals and other publication venues, etc.

Workload: The workload will depend in part on how far your internship report is from a submission. It is expected that you provide feedback to your peers. Finally the expected workload includes attending the conference in January and presenting your paper there.

Grading: Each participant will receive a mark made of the superviser's assessment of their contributions to the group efforts and of the quality of his/her oral presentations and written material.

Superviser: Stéphane Demri.

Room: 1-M-07

Participants (9): BOUZID Youcef; CATHERINOT Noémie; LOZAC’H Titouan; MATTEI Alban; SCHLOSSER Basile; VERY Sébastien; HOUYET Nathan; TIANWEN Gu; GIRAUD Raphaël

Description: The goal of this workshop is to study articles published in 2024 in the major AI conferences (AAAI'24, IJCAI'24, ECAI'24, etc.) and workshops about logical formalisms dedicated to knowledge reasoning and more specifically dedicated to theory reasoning embedded in temporal/description/modal logics. Knowledge logics form a family of logical formalisms dedicated to represent knowledge and to reason about it. We shall discuss questions related to scientific watch, critical analysis of recently published articles, conference program committees rules, etc.

Pedagogical objectives Based on freshly published articles about theory reasoning in AI, we discuss general questions about scientific watch. Presentation of articles in 10min and presentation in 30 minuts are expected from the students. Any question related to the relevance of the works, to their originality or their correctness shall be also discussed.

Planning: The first session starts on Nov. 12th, 2024. No session on Nov. 26th, 2024.

Grade 50% is based on the general participation to the workshop, 50% is based on two presentations (10min + 30min, details to be discussed).

Superviser: Laurent Fribourg

Room: 2-E-35

Participants (6): DURIEUX Pierre; VALENTIN Thomas; YANG Chen; BARON Rémi; FOURCIN Emile; DEFRANSURE Valentin

Description: The increasing complexity of research objects (energy network, living cell, autonomous vehicles, swarm of drones,...) imposes more and more the collaboration and interaction of theories from two (or even more) different disciplines. These interactions are particularly sensitive in computer science since this discipline is often found at the border of other disciplines, sometimes even leading to the creation of new disciplines (bioinformatics, quantum computing,...). The objective of this workshop is to prepare the student to understand and master the principles and conceptual tools of the other discipline which faces computer science at the frontier where both interact.

Pedagogical objectives:

The aim of the course is to:

• identify an object of cross-disciplinary research, and a scientific frontier where computer science interacts with an external discipline (mechanics, dynamics, biology,...), and
• characterise the traversing flows of information as well as the specific concepts according to which these flows are elaborated on both sides.

One way to start the working group will be to identify and analyse articles dealing with a given interdisciplinary subject. Examples include:

1. Feynman, Richard P. (1986) : Quantum Mechanical Computers
2. Shor Peter (1992) Scheme for reducing decoherence in quantum computer memory
3. Shulman MJ, Steinberg CM, Westmoreland N (February 1981). “The coding function of nucleotide sequences can be discerned by statistical analysis”. Journal of Theoretical Biology. 88 (3): 409–20.
4. Soinov, L. Bioinformatics and Pattern Recognition Come Together Journal of Pattern Recognition Research (JPRR), Vol 1 (1) 2006 p. 37–41

This experience will help the participants when, later in their career, they will have to present their chosen research area.

Schedule (tentative): Weekly meeting every Tuesday 14h30-16h30, starting Sep. 24th, 2024.

• meeting 1 : the superviser presents the scientific context of the article.
• meeting 2 : the article is presented by two participants working as a pair, and discussed by the group.
• meetings 3-4-5 : some following paers are identified and presented by more pairs.
• meeting 6 : a synthetic survey is written collectively.

Expected workload: a few hours weekly.

Grading: will reflect involvement and quality of contributions.

Superviser: Philippe Schnoebelen.

Room: 2-X-42

Participants (9): SAADI Lyes; CORNELY Maëlle; SASSUS-BOURDA Félix; CAUQUIL Diane; GOUI Tem; LEAL Fernando; TANGUY-BOMPARD Ulysse; LEBLANC Travis; CHARAF ZADAH Azammat

Keywords: Cellular automata, dynamical systems, natural computation, computational models for physics.

Description: The sandpile automaton is a computational model used to describe and analyze, among others, some physical processes like the stability and collapsings of sand piles and dunes. It already has a rich theory, spanning mathematics, theoretical physics, and computer science.

The goal of this workshop is to survey this topic and understand what are the current challenges and research directions. We are particularly interested with identifying open problems that are related to computer science, including questions like the computational power of sandpiles, the connections to cellular automata and complexity theory, or the algorithms for simulating sandpiles.

This workshop aims to produce a useful summary of its findings. The work will therefore consists in bibliographical research, evaluation of papers, organization of ideas, scientific writing. It will be a collective task with the benefits (brain-power, motivation, work-sharing, ..) and challenges (communication, work-sharing, ..) that come with such an organization.

The group will meet weekly and rely on the usual tools (emails, git, discord, ..) for exchanges between two meetings.

Expectations: It is expected that each participant will contribute his/her ideas, time & energy, ensuring group success. The group will be successful if we produce an interesting survey.

Workload: Approximately 5 hours per week (including the weekly meetings).

Grading: Each participant will receive a mark made of (50%) the superviser's assessment of their contributions to the common project, and (50%) the superviser's assessment of the quality of their oral presentations and written material.

References: See wikipedia for sandpile model.

Supervisors: Matthias Függer and Thomas Nowak.

Room: 2-X-47

Participants (5): SOTIRIOU Zacharoula; CUINGNET Martin; WUTTKE Angel; DUFOUR Ewen; ZAREDEHABADI Mohammadhossein

Keywords: Microbiology; Synthetic biology; Circuit design; Distributed systems

Description: The course is organized as a short research project. It starts with a brief introduction into synthetic biology - with a focus on bacteria. We will then study such systems from a circuit design and distributed computing point of view in small groups. Previous knowledge in microbiology, circuit design, or distributed computing is not obligatory. Methods used will be from mathematical analysis, simulations, algorithm and circuit design - with the focus depending on the group's interests.

Pedagogical objectives: The objective is to learn to work within a scientific team. The team will choose a currently open research question, investigate the state-of-the-art and try to tackle the question. Work includes: organization of research meetings on existing work, creative work on new ideas, and writing them down in a short research paper.

Expected workload: Approximately 5h/week (2h/week in class). Be aware that work besides in-class-time is expected (on average 3h/week)

Planning: Team meetings are announced here. Check this page regularly for updates. Updates will also be sent via mail, once you are subscribed. Typically meetings are on Tuesday 2:30 PM - 4:30 PM.

Literature

• If you cannot access a paper let us know.
• From class (lac operon)
  • Díaz-Hernández and Santillán “Bistable behavior of the lac operon in E. coli when induced with a mixture of lactose and TMG”, Frontiers in Physiology, 2010
• Components & tutorials on design:
  • iGEM http://parts.igem.org/Catalog
• Single cell:
  • Brophy and Voigt “Principles of Genetic Circuit Design”, Nature Methods, 2014
  • Nielsen et al. “Genetic circuit design automation” Science, 2016
  • Cello compiler http://cellocad.org/about.html
  • Siuti et al. “Synthetic circuits integrating logic and memory in living cells”, Nature Biotechnology, 2013
  • Guiziou et al. “Hierarchical composition of reliable recombinase logic devices”, Nature Communications, 2019
• Robustness:
  • Sleight et al. “Designing and engineering evolutionary robust genetic circuits”, Journal of Biological Engineering, 2010. http://www.jbioleng.org/content/4/1/12
• Debugging/Characterization:
  • Gorochowski et al. “Genetic circuit characterization and debugging using RNA‐seq”, Mol Syst Biol., 2017
  • Borujeni et al. “Genetic circuit characterization by inferring RNA polymerase movement and ribosome usage”, Nature Communications, 2020. https://doi.org/10.1038/s41467-020-18630-2
• Homologous recombination
  • Fujitani et al. “Dependence of Frequency of Homologous Recombination on the Homology Length”, Genetics, 1995.

• Distributed:
• Liao et al. “Rock-paper-scissors: Engineered population dynamics increase genetic stability”, Science, 2019
• Omar Din et al. “Synchronized cycles of bacterial lysis for in vivo delivery”, Nature, 2017 & Chowdhury et al. “Programmable bacteria induce durable tumor regression and systemic antitumor immunity”, Nature Medicine, 2019
• Regot et al. “Distributed biological computation with multicellular engineered networks”, Nature, 2011
• Sardanyés et al. “Computational implementation of a tunable multicellular memory circuit for engineered eukaryotic consortia”, Frontiers in physiology, 2015
• Cummings et al. “Probability 1 computation with chemical reaction networks”, International Workshop on DNA-Based Computers, 2014
• Esvelt et al. “A system for the continuous directed evolution of biomolecules” Nature, 2011

Grading: Students will be evaluated based on their involvement during team meetings (50%), and final writeup (50%).