Tous les Focus du Mois / All month's focus

A Logical Framework for Modelling Breast Cancer Progression

FOCUS DU MOIS DE : January 2019

Joëlle Despeyroux, Amy Felty, Pietro Lio and Carlos Olarte.
MLCSB 2018
 

Bioinformatic, Linear Logic, Model, Breast Cancer

Data streams for a personalised breast cancer programme could include collections of image data, tumour genome sequencing, likely at the single cell level, and liquid biopsies (DNA and Circulating Tumour Cells (CTCs)). Although they are rich in information, the full power of these datasets will not be realised until we develop methods to model the cancer systems and conduct analyses that transect these streams. In addition  to machine learning approaches, we believe that logical reasoning has the potential to provide help in clinical decision support systems for doctors. The autors develop a logical approach to modelling cancer progression, focusing on mutation analysis and CTCs, which include the appearance of driver mutations, the transformation of normal cells to cancer cells in the breast, their circulation in the blood, and their path to the bone.
Long term goal is to improve the prediction of survival of metastatic breast cancer patients. The autors model the behaviour of the CTCs as a transition system, and we use Linear Logic (LL) to reason about our model. The autors consider several important properties about CTCs and prove them in LL. In addition, The autors formalise our results in the Coq Proof Assistant, thus providing formal proofs of their model. The autors believe that our results provide a promising proof-of-principle and can be generalised to other
cancer types and groups of driver mutations.

Optimization of Network Infrastructures

FOCUS DU MOIS DE : December 2018

A little bit of green in networks and other problems of placement and management of resources.

Frédéric Giroire

algorithmics ; graph ; optimization and probabilities ; networks ; SDN ; NFV ; SFC ; energy efficiency

In this thesis (HDR / habilitation degree), Frédéric Giroire presents a set of solutions to optimize network infrastructures. Pushed by the new sensitivity of the society, politics, and companies to energy costs and global warming, Frédéric investigated the question of how to build green networks. Frédéric first studied some practical scenarios to answer the question: how much energy could be saved for Internet Service Providers by putting into practice energy efficient protocols? It led Frédéric to study fundamental problems of graph theory.
At the core of these energy efficient methods, there is a dynamic adaptation to the changes of demands, which is impossible to do in legacy networks which are mostly manually operated. The emergence of two new paradigms, software defined networking (SDN) and network function virtualization (NFV), leads to a finer control of networks and thus bears the promise to to put energy efficient solutions into practice. Frédéric thus studied how to use SDN to implement dynamic routing.
Frédéric’s approach has been to use theoretical tools to solve problems raised by the introduction of new technologies or new applications. Frédéric’s tools come mainly from combinatorics and in particular from graph theory, algorithmics, optimization and probabilities. When Frédéric was able to propose new methods of resolution, Frédéric then tried to evaluate their practical impact by numerical evaluation, simulation or experimentation with realistic scenarios.
More about this thesis: let's consult the manuscript and the slides of Frédéric’s defense

A Survey of Active Object Languages

FOCUS DU MOIS DE : November 2018

Frank De Boer, Vlad Serbanescu, Reiner Hähnle, Ludovic Henrio, Justine Rochas, et al.. A Survey of Active Object Languages. ACM Computing Surveys, Association for Computing Machinery, 2017, 50 (5), pp.1 - 39.

Concurrent programming structures; Programming languages ; active objects ; actors ; concurrency ; distributed ; systems

To program parallel systems efficiently and easily, a wide range of programming models have been proposed, each with different choices concerning synchronization and communication between parallel entities. Among them, the actor model is based on loosely coupled parallel entities that communicate by means of asynchronous messages and mailboxes. Some actor languages provide a strong integration with object-oriented concepts; these are often called active object languages. This paper reviews four major actor and active object languages and compares them according to carefully chosen dimensions that cover central aspects of the programming paradigms and their implementation.