March 22, 2020

SPOQ: norm ratio sparsity restoration

So SPOQ means, in Swedish, "Svenskt Pediatriskt Ortopediskt Qvalitetsregister(Swedish Pediatric Orthopaedic Quality register)

And Mr SPOQ (at BandCamp, and...) is a german electronic music artist (from Aschaffenburg) as well. In his Cinnamon album, there is a tune called "Distance" (at BandCamp). 

But how does the above relate to our SPOQ (SPOQ Lp-Over-Lq Regularization for Sparse Signal Recovery applied to Mass Spectrometry) algorithm? Later, it is too late. 


Chants des confins : music in times of COVID-19/coronavirus

Chants des confins, or Confines' songs, are a set of tunes, one music for each day of confinement due to COVID-19 coronavirus pandemia. And two lines. Two rhymes. Rarely more. In the mood for now. I listen to this song five times in a row before posting it. People who comment will get the compilation at the end.

In recursive order, so far: The Waterboys, Bloc Party, Hubert-Félix-Thiéfaine, Reis-Demuth-Wiltgen, Genesis, Paul Simon and Art Garfunkel, Paul Robeson, Ernest Melton, Didier Squiban, Connan Mockasin, Nina Simone, Merja Sonia, Chet Baker, Laïs, Joan Baez, Nils Frahm, Kate Bush, Megadeth, Radiohead. And counting.

Now he rode East and he rode West, He rode North and South also
Until he came to a wide open plain, It was there that he spied his lady-o
We promised the world we'd tame it, what were we hoping for?
A sense of purpose and a sense of skill, a sense of function but a disregard
Dans les ruines de l'école où brûle un tableau noir
Une craie s'est brisée en écrivant : espoir. Kill the kid
[Instrumental. Title from an Greek legend about someone who buried a treasure after being defeated. The Oracle of Delphi advised researchers to look under every stone]
"(Toilet) Paper late!" cried a voice in the crowd
"Old man dies!" The note he left was signed 'Old Father Thames'
April, come she will, May, she will stay.
June, she'll changed her tune,  July, she will fly.
Yes ready for sorrow
And ready to suffer
Yes ready to fight 'til death

[Instrumental. Comment from Ernest Melton: "But it’s really a message to myself that, at the end of the day, I don’t have to be a slave to trivial stuff in my life. That’s all it is."]
(version instrumentale)
Neventi vad d'ar Vretoned! [Heureuse nouvelle aux Bretons !]
Ha malloz-ru d'ar C'hallaoued! [Et malédiction rouge aux Français !]
From Big West
That never change
Yes, I love the ground on where he goes
And still I hope

Aamulla varhain kun aurinko nousi (Early in the morning when the sun rose)
Yö oli kaunis ja äänesi hellä (The night was beautiful and your voice so tender)
Everyday that I awake, I must be mindful
That everyday is all I have to call my own
Il est perdu dans la nuit, La lune, la lune
houd uw kanneke proper Dianneke, houd uw kanneke vaste (x2)
But the cardboard-filled windows and old men on the benches
Tell you now that the whole town is empty
#plik #clank
I wake up crying
You're making rain
But now I'm safe in the eye of the tornado
I can't replace the lies, that let a 1000 days go
I'd be crazy not to follow
Follow where you lead your eyes

May 25, 2019

Un vrai air de vie : Adolfo Kaminsky, une vie de faussaire et de photographe

Adolfo Kaminsky fut un faussaire honnête et je crois un honnête faussaire.

Aucun ne s'imaginait que le faussaire n'était qu'un enfant
(none of them could have suspected the forger was just a kid).
J'ai appris son existence grâce à P., qui m'offrit sa biographie dédicacée personnalisée. Le livre, intitulé "Adolfo Kaminsky, une vie de faussaire", a paru en 2009, écrit par Sarah Kaminsky, sa fille. Une version anglaise de 2016 porte le titre de "Adolfo Kaminsky: A Forger’s Life". J'aime le mot "forger" en anglais pour "faussaire". Comme l'idée de frapper une réalité brûlante au rouge sur le coin de l'enclume, pour lui donner une autre forme. Des formes, Adolfo en occupa : chimiste praticien, teinturier, photographe de l'art cinétique et de décors de cinéma, et grand résistant, offrant des faux papiers à des centaines de victimes du nazisme, et engagé dans quantités de combats de libération, qui l'ont déçu à chaque fois. Sans l'empêcher de s'engager à nouveau à chaque fois.


Jeudi 22 mai se tenait du MahJ, musée d'art et d'histoire du judaïsme à Paris, le vernissage d'une exposition de photographies d'Adolfo Kaminsky. Exposition que j'ai partagée avec Yvette, dont le père a disparu dans un camp d'extermination, et qui éprouve que tous les horribles souvenirs qu'elle avait mis (dit-elle) "à la cave", resurgissent. Un film d'animation complète l'histoire. Un couple de photos très touchant : des amoureux sur un banc, à côté  le banc, vide.


Le vernissage s'est conclu par un entretien, où Adolfo Kaminsky raconte avec simplicité et modestie (malgré le sur-jeu de l'animateur) ses exploits, sous le regard pétillant de celui qu'il était plus jeune.


Parmi les anecdotes, il s'engagea dans la fabrication de faux billets, non pour les utiliser, mais comme "outil de pression", vis-à-vis du pouvoir. A la signature des accords d'Evian, cette monnaie d'échange devenait caduque. Il brûla donc tous les faux billets, sans même imaginer les utiliser. Quand Sarah, sa fille, apprit l'histoire, et sachant qu'il avait toujours vécu fauché, lui demanda : "ce n'était pas trop dur de brûler tout cet argent ?", il répondit que oui  en effet, les billets brûlent très mal, à cause des encres...

Pour les amateurs de radio et de podcasts, voici les émissions lui étant consacrées:

October 6, 2018

A Monty Python space Odyssey

After 2001, a space odyssey, the second best movie ever could be Monty Python, the holy grail:
Mønti Pythøn ik den Hølie Gräilen Røtern nik Akten Di Wik Alsø wik Alsø alsø wik Wi nøt trei a høliday in Sweden this yër? See the løveli lakes The wøndërful telephøne system And mäni interesting furry animals

A Pink Floyd odyssey: Jupiter and beyond the infinite


September 27, 2018

BRANE power: Gene network inference with graph optimization

And the IPFEN 2018 Yves Chauvin PhD prize is awarded to Aurélie Pirayre, for IFPEN first thesis on bioinformatics with graph optimization for gene networks. In French, you can now read ‘‘BRANE Power’’ : gènes et algorithmes, une alliance pour la chimie verte.

Aurélie Pirayre, Grégoire Allaire, Didier Houssin, Pierre-Henri Bigeard, Eric Heintzé

PhD manuscript and slides for her thesis:
  • Reconstruction and clustering with graph optimization and priors on gene networks and images (manuscript)
    • Abstract: The discovery of novel gene regulatory processes improves the understanding of cell phenotypic responses to external stimuli for many biological applications, such as medicine, environment or biotechnologies. To this purpose, transcriptomic data are generated and analyzed from DNA microarrays or more recently RNAseq experiments. They consist in genetic expression level sequences obtained for all genes of a studied organism placed in different living conditions. From these data, gene regulation mechanisms can be recovered by revealing topological links encoded in graphs. In regulatory graphs, nodes correspond to genes. A link between two nodes is identified if a regulation relationship exists between the two corresponding genes. Such networks are called Gene Regulatory Networks (GRNs). Their construction as well as their analysis remain challenging despite the large number of available inference methods. In this thesis, we propose to address this network inference problem with recently developed techniques pertaining to graph optimization. Given all the pairwise gene regulation information available, we propose to determine the presence of edges in the final GRN by adopting an energy optimization formulation integrating additional constraints. Either biological (information about gene interactions) or structural (information about node connectivity) a priori have been considered to restrict the space of possible solutions. Different priors lead to different properties of the global cost function, for which various optimization strategies, either discrete and continuous, can be applied. The post-processing network refinements we designed led to computational approaches named BRANE for \Biologically-Related A priori for Network Enhancement". For each of the proposed methods --- BRANE Cut, BRANE Relax and BRANE Clust --- our contributions are threefold: a priori-based formulation, design of the optimization strategy and validation (numerical and/or biological) on benchmark datasets from DREAM4 and DREAM5 challenges showing numerical improvement reaching 20%. In a ramification of this thesis, we slide from graph inference to more generic data processing such as inverse problems. We notably invest in HOGMep, a Bayesian-based approach using a Variational Bayesian Approximation framework for its resolution. This approach allows to jointly perform reconstruction and clustering/segmentation tasks on multi-component data (for instance signals or images). Its performance in a color image deconvolution context demonstrates both quality of reconstruction and segmentation. A preliminary study in a medical data classification context linking genotype and phenotype yields promising results for forthcoming bioinformatics adaptations.
  • Slides (PhD defense on July 3rd, 2017)
are finally online (check the EURASIP Library of Ph.D. Theses). The work was ruled by the concept of BRANE power; a methodology for gene regulatory network inference and clustering based on graph optimization and biological priors. BRANE stands for Biologically Related Apriori Network Enhancement. It rhymes with cell membrane (and brain, for who it's worth).

Gene regulatory network inference with BRANE Cut

State-of-the-art results are obtained on synthetic and real transcriptomic data (DREAM-4, DREAM-5 for DREAM consortium challenges, Escherichia coli dataset). Derived methods are BRANE Cut (with graph cuts), BRANE Relax (with proximal optimization) and BRANE Clust (with graph Laplacian). 

Gene network joint inference and clustering with BRANE Clust



Used concepts include:
  • data science, optimization on graphs: maximal flow, minimum cut, random walker algorithm, variational and Bayes variational formalism, convex relaxation, alternating optimization, combinatorial Dirichlet problem, hard-clustering and soft-clustering
  • biology, biotechnology, bioinformatics: transcription factors (TFs) as regulators and non-transcription factors (TFs) as targets, modular networks, biological priors, in-silico data, second generation bio-fuel production, DREAM4 challenge, DREAM5 challenge
  • use to biofuels and green chemistry production (with fungus Trichoderma reesei)
Supervising team:
PhD Thesis reporters

PhD Thesis Examiners
More links:

September 9, 2018

Kultur Pop 44 : Brain et évolution

[Mise à jour, 29/09/2018, pour Pascale Casanova] Elle anima les mardis littéraires, les jeudis littéraires, l'atelier littéraire. Une vie n'est pas coutume, Kultur Pop ajoute un neuvième morceau, leur générique, à Kultur Pop 44, Brain. Qui était déjà dans Kultur Pop 01, il y a 11 ans déjà, en 2007. Car 3^2-2^3 = 1 est une égalité rare.
"We are using your brain's electrical system as a receiver,We are unable to transmit to your conscious neural interference"
Tandis :
le 44e volume, Brain, des génériques Kultur Pop (France Culture/France Inter, et parfois des intruses), vient (enfin) de paraître,



Au programme : Kultur Pop 2018.44 : Brain
  • France Culture, Interlude nuits : Alain Romans, Quel Temps Fait-il a Paris? (Les vacances de monsieur Hulot)
  • France Culture, Culture protestante : Ensemble Lucidarium, O prebstres, prebstres
  • France Culture,  Science publique : Brian Eno & David Byrne, The Jezebel Spirit
  • France Culture, Condordance des temps : Louis Sclavis Sextet, Charmes
  • France Culture, Interlude nuits : Alexandre Desplat, Camera Obscura (Girl With A Pearl Earring)
  • France Culture, Agora : L'Orchestre de Contrebasses, Sablier
  • France Culture, Grands reportages : Bonobo, Kerala
  • France Culture,  Culture de soi, cultures des autres : Music Ensemble of Benares, Kathak Nritya, part 1 & 2
  • Ghost track. France Culture,  Atelier littéraire, mardis littéraires, jeudis littéraires (Pascale Casanova, 29 septembre 2018) : DJ Shadow, Stem long stem

There is no hope, there's only chaos and evolution (Evereve, Fade to grey, Visage cover)


Et en même temps (c'est la mode), nous célébrons the BRANE Power, et l'évolution : Gene network inference with graph optimization

July 29, 2018

Multiscale representation of hexahedral meshes & compression

Companion pages:
A full-scale geological grid (or 3D Hexahedral mesh in Corner-Point grid) structure is decomposed onto embedded wavelet-like scales while preserving discontinuities, here geological faults (red), using a morphological 2D wavelet:
Geological grid structures and discontinuities preservation (red painted faults)
Categorical properties like rock types (sandstone, limestone, shale)  can be upscaled according to a dedicated non-linear decomposition called modelet (patent #20170344676: Method of exploitation of hydrocarbons of an underground formation by means of optimized scaling):


Hexahedral mesh categorical property: rock type

Continuous properties (saturation, porosity, permeability, temperature) can be homogenized with a 3D Haar wavelet:

Hexahedral mesh continuous property: porosity

The HexaShrink methodology described above is detailed in the recently published paper: 
With huge data acquisition progresses realized in the past decades and acquisition systems now able to produce high resolution point clouds, the digitization of physical terrains becomes increasingly more precise. Such extreme quantities of generated and modeled data greatly impact computational performances on many levels: storage media, memory requirements, transfer capability, and finally simulation interactivity, necessary to exploit this instance of big data. Efficient representations and storage are thus becoming "enabling technologies" in simulation science. We propose HexaShrink, an original decomposition scheme for structured hexahedral volume meshes. The latter are used for instance in biomedical engineering, materials science, or geosciences. HexaShrink provides a comprehensive framework allowing efficient mesh visualization and storage. Its exactly reversible multiresolution decomposition yields a hierarchy of meshes of increasing levels of details, in terms of either geometry, continuous or categorical properties of cells. Starting with an overview of volume meshes compression techniques, our contribution blends coherently different multiresolution wavelet schemes. It results in a global framework preserving discontinuities (faults) across scales, implemented as a fully reversible upscaling. Experimental results are provided on meshes of varying complexity. They emphasize the consistency of the proposed representation, in terms of visualization, attribute downsampling and distribution at different resolutions. Finally, HexaShrink yields gains in storage space when combined to lossless compression techniques.
And there is a patent associated to HexaShrink, Method of exploitation of hydrocarbons of an underground formation by means of optimized scaling:

Method of exploitation of hydrocarbons of an underground formation by means of optimized scaling


July 10, 2018

Bioinformatics & datascience: Internship & PhD on multi-omics data

An PhD position is still available on Graph-based learning from integrated multi-omics and multi-species data (genomic, transcriptomic, epigenetic) between IFP Energies nouvelles and CentraleSupélec/INRIA Saclay. All the information is gathered at this address.

Some information is duplicated below:
Micro-organisms are studied here for their application to bio-based chemistry from renewable sources. Such organisms are driven by their genome expression, with very diverse mechanisms acting at various biological scales, sensitive to external conditions (nutrients, environment). The irruption of novel high-throughput experimental technologies provides complementary omics data and, therefore, a better capability for understanding for the studied biological systems. Innovative analysis methods are required for such highly integrated data. Their handling increasingly require advanced bioinformatics, data science and optimization tools to provide insights into the multi-level regulation mechanisms (Editorial: Multi-omic data integration). The main objective of this subject is to offer an improved understanding of the different regulation levels in the cell (from model organisms to Trichoderma reesei strains). The underlying prediction task requires the normalization and the integration of heterogeneous biological data (genomic, transcriptomic and epigenetic) from different microorganisms. The path chosen is that of graph modelling and network optimization techniques, allowing the combination of different natures of data, with the incorporation of biological a priori (in the line of BRANE Cut and BRANE Clust algorithms). Learning models relating genomic and transcriptomic data to epigenomic traits could be associated to network inference, source separation and clustering techniques to achieve this aim. The methodology would inherit from a wealth of techniques developed over graphs for scattered data, social networks. Attention will also be paid to novel evaluation metrics, as their standardization remains a crucial stake in bioinformatics. A preliminary internship position (summer/fall 2018) is suggested before engaging the PhD program. Information at: http://www.laurent-duval.eu/lcd-2018-intern-phd-epigenetics-omics-graph-processing.html

SPOQ: norm ratio sparsity restoration

So SPOQ means, in Swedish, "Svenskt Pediatriskt Ortopediskt Qvalitetsregister "  (Swedish Pediatric  Orthopaedic  Quality regist...