Chloé-Agathe Azencott

Researcher at the Centre for Computational Biology (CBIO) of Mines ParisTech, Institut Curie and INSERM.


Installing PyGTK on Mac OS X 10.7

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This is how I installed PyGTK on my office machine, a Mac with OS X 10.7.5 (aka Lion) on which I've never managed to properly use fink or macports and gave up trying to install homebrew. In other words, without a package manager. Look, mommy, no hands!

I'm putting those notes here in case it might help someone struggling with similar problems. Please try using a package manager first, and save yourself some headache.

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Spring Travels

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I will be away from Tübingen in the next three weeks, attending SMILE in Paris on Monday, March 18th, as well as the Workshop in Computation, Inference and Optimization at IHÉS on Wednesday, March 20th in Bures-sur-Yvette (France).

I'm also looking very much forward to visiting EBI Cambridge at the end of the month. I will be giving a talk on network-guided multi-locus genome-wide mapping on Tuesday, March 27th at 11am.


Data Mining in Bioinformatics Course

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I will be teaching a few of the lectures in the course "Data Mining in der Bioinformatik" from February 18 to March 1st.

Lecture slides:


NIPS 2012

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I'll be attending NIPS next week, and am very much looking forward to what promises to be a great scientific week.

I will also be presenting a poster on my first results in graph-based feature selection[1] at the Machine Learning in Computational Biology workshop on December 7. I've been working with Dominik Grimm, Yoshinobu Kawahara and Karsten Borgwardt on the problem of finding single-point mutations that are maximally, jointly associated with an observed trait, while being connected in an underlying (predefined) biological network. We've been rather successful at dealing with the large (10^5 to 10^7) number of features involved, as in our experiments the method turns out to be fast, robust, and generally lead to better recall than our state-of-the-art comparison partner, the overlapping group lasso, for very similar precisions.

The method is currently called SOS for Subnetworks of Optimal SNPs, but I'm not very happy with the name and I'm considering renaming it SConES (Selection of Connected Explanatory SNPs).


[1] Although I have a lot of experience treating problems in which the objects themselves are represented by graphs (and the way they are connected is very much object dependent), I had never studied a setting in which the objects are not graph-like, but there is an underlying network that connecte their features (completely independently of the objects).


Lindau Nobel Laureates Meeting 2012

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I was last week one of the lucky ("has qualified in a global competition among young scientists worldwide to participate", my certificate of attendance says emphatically and somewhat repetitively) six hundred or so young researchers participating in the Nobel laureates meeting in Lindau. Twenty-seven laureates were attending this sixty-second edition focused on physics. Physics, as you may know, is something I've stopped studying as soon as I was allowed to, and quite frankly I was a bit afraid that I wouldn't understand anything. Thankfully, most of the conversations remained pretty high-level and I was able to follow quite more than I was expecting.

What a week! It was an exciting place to be, especially the week when the CERN (the idea of which apparently arose at a similar meeting in Lindau) announced having found a (possibly Higgs) boson (you can watch the reactions of a few of the laureates here). It was an inspiring meeting, what with the great conversation with a bunch of damn smart people (and I don't only mean the laureates), memorable talks, and an impressive amount of social occasions... I've never been (and will probably never again be) so well treated at a conference. There were, of course, quite a good amount of welcome addresses and other inaugural talks, and a few uncomfortable moments — such as the induction of the new members to the honorary senate of the foundation organizing the meetings: the President of Singapore, a country that might be doing cool science but which democracy remains questionable at best, and the CEO of Volkswagen, introduced by a video that was to my eyes nothing but a commercial for his company.

Lindau Hafen

Lindau harbor

Great memories

I came back with many great memories... where to begin? Explaining support vector machines to Brian Schmidt (2011 Physics Nobel laureate, for the discovery that the universe's rate of expansion is accelerating) is certainly one of my favorites. Another one, far from scientific concerns, would be the few words I exchanged with Hans-Peter Ochsenhofer, violist of the Vienna Philharmonic, and member of the ensemble that played a Haydn string quartet and a Mozart clarinet quintet at the concert following the opening ceremony. Countess Bettina, daughter of Count Lennart who initiated those meetings and President of the Council for the Lindau Nobel Laureate Meetings, did after all insist in her welcome address on the similarities between art and science, which both open minds, breech frontiers, and involve creativity.

Just before the Nobel laureate meeting started, the research ministers of the G8+5 countries were meeting in Constance to discuss international research policy; a few of them took part in a boat tour on the lake to which a few dozens of us young researchers were invited as well, together of course with the laureates who had already arrived. I talked with Geneviève Fioraso (the French Minister of Research and Education), mostly about the lack of consideration for PhD holders in France, as well as with John Holdren (chief scientific advisor to President Obama), who had very interesting things to say about deciding of a science budget and trying to convince politicians that scientists must take risks (and fail often) for real advances to be made.

I also attended a dinner hosted by the Max Planck Society (my academic sponsor), at which I sat close to Theodor Hänsch (Physics Nobel laureate 2005, for the development of laser-based precision spectroscopy), and I have fond memories of the conversations, from his eagerness to discuss science to his memories of California. Sadly, Hänsch did confirm what I'm hearing way too often these days: that your postdoc is the best time of your career...

Conversations highlights

The usual themes (science, academia vs. industry, balancing science and the rest of one's life, women in STEM, teaching, publish or perish, the two-body problem, navigating different cultures, and pretty much anything else under the sun, including, of course, soccer) were very present in the conversations among young researchers (so it turns out that computer scientists aren't that different from physicists after all).

Atomkraft protest

A protest against nuclear energy in Lindau — a great kick off to a week filled with many discussios on energy!

In what follows I'll try to briefly summarize my favorite talks and discussions. The talks should be available in the Mediatheque (which, unfortunately, requires Silverlight to run, and doesn't seem to work with Moonlight on my Ubuntu laptop — yes, I have complained about it already. At least it works on my Mac.).

Monday Science Breakfast: On the Brink of an Era of Quantum Technologies With Colin Teo (PhD Student at NUS), Artur Ekert (Director of the Centre for Quantum Technologies at NUS), and Bill Phillips (1997 Physics Nobel Laureate for his work on cooling and trapping atoms with lasers, and NIST/JQI fellow). A discussion on quantum cryptography and the necessity to close the loopholes (detection, locality, and free will) in Bell tests experiments. As much as I love the free will loophole (is there an entity able to fool us into believing that we observe a violation of Bells inequalities?), someone (Phillips, maybe?) made an excellent point by asking which of human factors or quantum mechanics loopholes is more likely to compromise quantum cryptography. Eckert admitted that the idea that a property truly does not exist until measured is confusing as hell. I don't know whether I should find this comforting or not, but I'm glad it's not just laypeople like me who have a hard time wrapping their mind around this concept. (Same goes for the temperature of a single atom, which even as someone used to manipulating probability distributions I find disturbing.) This was followed by a conversation on Qubits. Phillips stated that in his opinion there's a 50-50 chance we'll have a quantum computer able to factorize numbers in polynomial time 50 years from now. He suspects the Qubit will be a combination of quantum objects.

Monday morning, Part I: Cosmology Three plenary lectures by Brian Schimdt, John Mather and George Smoot (both 2006 Physics Nobel laureates for the discovery of the anisotropy of the cosmic microwave background, consistent with the Big Bang model).

Schmidt condensed an entire series of lecture in 30 minutes about the standard model; Mather gave us a long list of the telescopes that allow us to see farther and farther; and Smoot discussed the mapping of the Universe in both time and space. To be honest I mostly remember the very pretty pictures and the excerpt from Contact that Smoot showed. Well, taking pretty pictures of our universe is a large part of what cosmologists do, right?

Monday morning, Part II: Climate Change, Global Warming, and Energy Four plenary lectures by Paul Crutzen, Mario Molina (both 1995 Chemistry Nobel laureate for the discovery of the role of nitrogen oxide in the ozone hole), Ivar Giaever (1973 Physics Nobel laureate for his work tunneling in supraconductors) and Hartmut Michel (1988 Chemistry Nobel laureate for his work on membrane proteins involved on photosynthesis).

While Crutzen gave a very sobering picture of the Anthropocene, this geological age we have entered that is influenced by mankind, and concluded that "a daunting task lies ahead for scientists and engineers", Giaever defended the exact opposite view, took offense at the American Physics Society's statement that evidence for global warming is incontrovertible ("unlike," he added, "the mass of the proton"), and delivered a provocative lecture about the alarmist fallacies of global warming. Unfortunately, this address was, as far as I could tell, peppered with inaccuracies and gross generalizations; self-admittedly, it stems from a few hours spent on Google rather than a careful review of the literature. Here's a pretty good deconstruction.

Molina, who preemptively dismissed the position defended by Giaever in a famous Wall Street Journal editorial, presented some scientific evidence of climate change (in particular of the increasing incidence of extreme climatic events), discussed possible strategies to reduce the emission of CO2 (including a new generation of more secure nuclear power plants with better waste management), and addressed some political issues, with an emphasis on the regrettable position of U.S. Republicans.

Eventually, Michel closed the morning session with a lecture on photosynthesis, biomass and biofuels, essentially demonstrating how inefficient they are (natural photosynthesis, which we are far from being able to approximate, included). He also spent some time addressing the production of palm oil biofuels, which he deemed to be "one of the most stupid things" (for it destroys the rain forest and actually leads to the emission of more CO2). His vision for the future includes genetic engineering of plants to improve their CO2 fixation and light absorption capabilities, the improved transport of solar energy produced in deserts (using superconducting cables), and the development of better batteries to improve electricity storage.

Monday afternoon discussion with Mario Molina Lots and lots of ideas in that conversation! Here are a few of the topics we touched: climate change as a symbol of government intervention for the Tea Party, the distrust of scientists (Molina pointed out that people also distrust Al Gore because he's not a scientist), developing countries (good solutions can accelerate development rather than slow it down), geo-engineering (there's nothing wrong with having a plan B but the community should be very, very cautious), nuclear waste (which biggest problem is known as "NIMB", or Not In My Backyard). Molina talked a lot about rephrasing the problem to overcome political barriers: working with the media (which is what so-called interest groups are doing), mentioning air quality improvement, and presenting optimistic solutions. For instance, in response to the ever increasing human population, he prefers addressing the improvement of the standard of living and women empowerment rather than advocating (as does Giaever) a one children per family policy.

When asked how to form one's own opinion in scientific controversies, Molina gave us two choices: either dwell in the literature yourself, or trust the way the peer-reviewed scientific community works... later on, he reminded us that there have been much more controversial scientific theories than climate change (Boltzmann in the early 20th century was fighting groups of scientists who did not believe that molecules exist).

Lindau Hafen

Lindau harbor

Tuesday morning session: Quantum Mechanics Six plenary lectures (and a coffee break) with Martinus Veltman (1999 Physics Nobel laureate for the elucidation of electroweak interactions), Carlo Rubbia (1984 Physics Nobel laureate for the discovery of W and Z particles), David Gross (2004 Physics Nobel laureate for the discovery of asymptotic freedom), Albert Fert (2007 Physics Nobel laureate for the discovery of giant magnetoresistance), Bill Phillips and Brian Josephson (1973 Physics Nobel laureate for the discovery of, well, the Josephson effect of a supercurrent through a tunnel barrier).

The topic could not have been more aptly chosen; while the breakfast room at my hotel was already bustling with the news of the incoming CERN conference, Veltman brandished a copy of a local paper, telling us that this was now where one could read the latest scientific news. "This week might later be known as Higgs week", he added, before starting his lecture which, being titled The LHC at CERN and the Higgs, was a pretty good introduction to the unfolding events. He concluded with a few words of the implications of a Higgs field on cosmology; either the universe started out curved the other way around and was "flattened out" when the Higgs field came, or there is no such thing as a Higgs field, or our understanding of gravity is wrong, he explained.

Rubbia followed with a lecture on neutrinos which he thinks must fill many of the gaps of our understanding of the standard model. His talk focused on the LSND anomaly and electron neutrino disappearance in Gallium experiments, and the work to explore them at Fermilab (ICARUS), CEA (Lucifer reactor), and Daya Bay.

Gross then presented a history of quantum mechanics, which he assesses to be 100 years old in average (as their starting point can be either chosen as 1900, Planck, or 1925, Heisenberg), and many pictures of the Solvay Conference. He contrasted the anguish of the early 20th century at the idea of the failure of classical physics (illustrated by this sentence by Lorentz: "The old theories have been showed to be powerless to pierce the darkness that surrounds us on all sides") and the current enthusiastic agreement that QM works, makes sense, and resists (for now) attempts to break it. He pointed out, however, that we still lack a unified theory of physics that encompasses string theory, QM, and spacetime, which makes it exciting times for young physicists, with still so many amazing questions to answer.

In a more practically-oriented lecture, Fert followed with a presentation of spintronics in modern ICT, focused mostly on STT-RAM, spin-transfer oscillators, spintronics on graphene and carbon nanotubes, and memristors for neuromorphic computing.

Eventually, Phillips delivered a rather neat lecture on artificial magnetic fields. Unfortunately my notes are pretty obscure at that point, so I won't say more than recommend you watch it if you're interested.

Whether or not Josephson's lecture fits under the "quantum mechanics" label I could not say; his talk about a unifying theory of physics and spirituality, based on the idea of a disconnect between mathematics and reality, featuring expressions such as "subtle biosphere", and partly relying on a dancing metaphor of what seemed to me very much like self-organizing multi-agent systems minus the maths, left me (and all I discussed it with) rather confused.

Tuesday afternoon discussion with Albert Fert Mostly, a conversation about the future of CMOS: memristors, spintronics on graphene for displays, spintronics on diamond for quantum computing, oxides (such as LSMO) for spintronics, spin-LEDs, ferroelectric tunnel junction, and STT-RAM vs. PC-RAM for non-volatile memory (apparently Samsung stopped their research on phase-change and is putting all their effort on STT-RAM).

Lindau from the lake

Lindau — lakeview

Wednesday morning session: Spectroscopy Six plenary lectures, by Kurt Wüthrich (2002 Physics Nobel laureate for the development of NMR spectroscopy), John Hall, Theodor Hänsch (both 2005 Physics Nobel laureates for their work on laser spectroscopy and the frequency comb), Douglas Osheroff (1996 Physics Nobel laureate for the discovery of the superfluidity of Helium 3), Roy Glauber (2005 Physics Nobel laureate for his work on the quantum theory of optical coherence) and James Cronin (1980 Physics Nobel laureate for the discovery of CP violations).

Wüthrich started with a rather energetic lecture on structural genomics — surprising the audience by taking his belt off to illustrate protein folding, a trick I might want to remember in the future. He emphasized the size of the gap between the large number of known protein sequences (14 million) and the much smaller number of known protein structures (75,000), not forgetting the abysmally smaller number of known protein functions. He made the case for the development of NMR and multi-dimensional NMR (ie. NMR repeated at incremental time points), which work on protein solutions, as a great alternative to X-ray crystallography (and anybody who has ever tried to make a protein crystallize can see why). Eventually he introduced TROSY, which doesn't have the traditional NMR drawbacks with respect to size and makes it possible to analyze large protein complexes, by these words: "We always talk about the relativity but Einstein also did important work," meaning the Stokes-Einstein equation on Brownian motion.

Hall then celebrated fifty years of laser, and marveled at the still growing excitement in the field. And yes, his slides, like those of Bill Phillips, were in Comic Sans.

He was followed by Hänsch and his lecture on laser spectroscopy. I strongly recommend you watch his amazing animation explaining frequency combs with a series of pendulums (which you can see starting at the 5th minute of this Youtube video if Silverlight is giving you trouble), which led the audience to applaud for the first time in the middle of a lecture. "How do you find something new?" Hänsch asked, and gave a fairly simple answer to that: either you look where no one has looked before, or you make more precise measurements — whenever you measure something to more decimal places than anybody before you, chances are you'll find something there.

The first half of the morning session was closed by Osheroff and his lecture on how science discoveries are made. Using examples from supraconductivity to cosmic microwave background radiation and, of course, the superfluidity of Helium 3, he gave the following advice: use the best instrumentation; don't reinvent the wheel; look into unexplored regions; failures are a hint to try something new; don't dismiss subtle unexplained behaviors; understand what it is that you are measuring; and rely on the scientific community. Piece o' pie! Osheroff also told us of running in the building at 2am after discovering BCS transition in liquid 3He, not finding anybody to share his results with, and calling his supervisor around 2:30am — about the same time he received a call from Stockholm 25 years later—, complete with a copy of his lab notebook from back then.

The coffee break followed, taken over by the live stream of the CERN press conference that was screened in the lecture hall. I think most of us would have preferred watching the scientific talk that was given before, but it was still a rather exciting moment! (By the way, the Higgs field as a crowd of journalist analogy comes from David Miller.)

Back to lectures, Glauber — "I'm well aware that this is not show business. But let me say this is certainly a hard act to follow." — gave a pretty interesting history of quantum mechanics through a list of apparent paradoxes of optics. Unfortunately he ran out of time and I was never able to figure out what the ghosts in his title (The Quantum Mechanics of Light: Interference, Entanglement — and Ghosts) were.

Cronin closed that intense morning session with a history of our understanding of cosmic rays, showing us how scientific theories evolve as we gather knowledge and experiments — "when you do physics for 50 years of your life, you realize it's not so easy to do".

Wednesday afternoon discussion with Kurt Wüthrich Well, we did talk a lot about NMR, X-ray crystallography, TROSY, and electron microscopy. A few bits of advice for physicists interested in biology: learn how to communicate with biologists; learn what the important problems are; your role is to develop techniques and tools — you need to figure out by yourself what for. Another piece of advice: studying publications for errors will give you some insights as to what to do next. Wüthrich is a big fan of regularly changing fields in your training (and I can't say I disagree with him on that point... we clearly have different views on open source software).

Lindauer Löwe

The Lion of Lindau

Thursday morning session Six plenary lectures by Dan Schechtman (2011 Chemistry Nobel laureate for his discovery of quasi-crystals), Dudley Hershbach (1986 Chemistry Nobel laureate, for the development of molecular beams to analyze the kinetics of chemical reactions), Erwin Neher (1991 Physiology/Medicine Nobel laureate for explaining the role of ion channels in cells), Robert Laughlin (1998 Physics Nobel laureate for the explanation of fractional quantum Hall effect), Walter Kohn (1998 Chemistry Nobel laureate for the development of density functional theory) and Sir Harold Kroto (1996 Chemistry Nobel laureate for the discovery of fullerenes, a.k.a. "the buckyball guy" in some circles).

I think my favorite of all the lectures was Schechtman's talk on his discovery of quasi-periodicity. Stunning science, complete with beautiful diffraction patterns and Fibonacci rabbits ("The greatest mathematician of all times, but Italians called him 'Blockhead'"), and the history that led from the initial disbelief of the community ("There are no quasi-crystals, but only quasi-scientists," said Linus Pauling) to his Nobel, both wrapped in Schechtman's talents as an orator, made for a wonderful lecture in my opinion. "A good scientist is a humble scientist," he said, addressing the redefinition of crystals by the International Union of Crystallography from "a regular repeating array of atoms" to "any solid having an essentially discrete diffraction pattern" (notice the vagueness of this "essentially"). "Choose something you like, become an expert at it, and you will have a wonderful career," Schechtman told us young researchers. I'll have this talk in mind next time I review a paper that presents itself as "paradigm shifting"!

The most acclaimed bit of advice to young researcher was however, without a doubt, Herschbach's closing advice of "Experiment!", very nicely illustrated by the eponymous Cole Porter song and dedicated to Schechtman. I do wonder however how many people in the audience realized at the time the song is from Nymph Errant and about a woman being advised to experiment with men... One sure thing: I've been humming "Experiment, make it your motto day and night, experiment, and it will take you to the light" to myself ever since. Herschbach started his lecture on ''Chemical Wizardry'' (an appealing title for this chemoinformatician) with a jab at MIT, for their logo with mens and manus looking away from each other instead of working together, then told us of three "molecular parables": the synthesis of palytoxin, the single biologically active form of a compound that has 5.10^21 isomers, akin to '"Beethoven writing a symphony"; how the lack of a single methyl group on a particular amino acid on the Y chromosome of a human fœtus results in an infertile female rather than a male, and how little estrogen and testosterone differ; and the synthesis of indigo, back in 1853, when chemists didn't know anything about atomic structure.

Neher followed with a lecture on the biophysics of neurotransmitter release (which I haven't found in the Mediatheque), preceded to match the spirit of previous lecturers by a history of neurotransmitter science from Galvani's experiments on frogs (which, to me, brought back long-forgotten memories of high school biology) to his discovery of sodium ion channel currents. He told us how ion channels opening and closing is linked to the perception of hot and cold (including heat detection in vampire bats) but also substances such as menthol or capsaicine (found in chili peppers), before moving on to his current research on synaptic plasticity.

After a very much needed coffee break (you know how you just end up getting less and less sleep at those events in spite of all your good intentions), Laughlin gave an energetic lecture on "powering the future" (not so incidentally the title of his book — "I have many hobbies, one of them writing books," he explained, before adding that writing books, with proper references of course, is often the best way to understand a topic). He insisted on the difference between "saving the Earth" and the issue of energy (which is all but a brief geological instant) and took us through a "science-fiction experiment" of imagining year 2200. Would people still drive cars, fly in airplanes and have light come up when pressing a switch? Most of the audience answered positively to these questions, without any regard for how this would be made possible. That the main reason for this answer boils down to "because we want to" demonstrates how political and economic the question is. "What happens if the lights go off?" he asked next, answering with the impeachment of Davis and the election of Schwarzenegger in California. Laughlin also made the case that ordinary fuels are physically optimal, comparing them to fat as a compact, efficient energy source, and pointed out that synthetic fuels are in his opinion the only way to keep airplanes flying.

Kohn then gave a never before seen lecture (also not in the Mediatheque at the time of this writing) on developing devices to compensate macular degeneration, a topic he has been working on for the past seven years, driven by his wife's affection by the illness. He described a software tool which presents the patient with a straight grid, which she will distort with the mouse until she sees it straight. The transformation can then be automatically applied to any image in a hand-held device akin to a magnifying glass.

Eventually Kroto gave the last lecture of the week ("three talks packed in one!"), about science education and the scientific method. He quoted Feynman, insisted on the importance of making use of our freedom to doubt, and to ask ourselves what we accept without evidence. From chilling pictures of the Creationism museum to one liners too numerous to list ("We introduced a new concept of TV debates: that participants should actually know something about the topic."), he kept his audience attention tight. His final advice to researchers? "Satisfy yourself, not your boss, and you'll do good." This was a great, enthusiastic talk, which I recommend even to not-scientists. Oh, and have a look at and GEOSET.

Thursday afternoon discussion with Erwin Neher We touched to a variety of topics, from vesicle recycling to man machine interfaces, the connectome, the universality of Ca++ as a messenger, patch clamps, free will, and neuromorphic chips. My favorite part was probably the conversation( initiated during this discussion and followed afterwards in the streets of Lindau) about simulating biologically realistic neural systems vs. developing artificial neural networks for optimal approximation of function.

Mainau Schmetterling

Butterfly on Mainau

Friday panel discussion: The Future of Energy Supply and Storage For the last scientific event of the meeting, we were all put on a huge boat to head to the island of Mainau where a panel discussion on the the future of energy supply and storage, moderated by Geoffrey Carr ( Science Editor at The Economist), and featuring Martin Keilhacker (German Physics Society), Carlo Rubbia, Georg Schütte (State Secretary of the German Ministry of Eduction and Research) and Robert Laughlin, was held. Taking in questions from the young researchers, they discussed the reality of phasing out nuclear energy in Germany, the role to be played by developing and third-world countries, safer nuclear energy, the difficulty of estimating the costs of various energy sources, and improving the yield of photovoltaic cells. Rubbia and Laughlin strongly disagreed on the future of superconductivity as a way to transport energy (Laughlin even qualifying the idea of stupid).


Bye-bye Mainau — The boat back to Lindau

Head to Flickr for more pictures of Lindau and Mainau (I only had my compact, so do not expect anything too impressive — of course there's always the #lnlm12 hashtag there as well).

Disclaimer — All view expressed my own (unless otherwise stated) and inaccuracies my sole responsibility.

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