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Here we collect our writing on various topics from our day-to-day work and our reading clubs.

Today: OMICS and Deep Learning

we had 3 papers to read for today, but only discussed one “Predicting the effects of non-coding variants..” (2015) Zhou and Troyanskaya. It had impressive results but was frustrating to read since details of both data and model were not described.

Wednesday 9AM we will discuss “END-TO-END DIFFERENTIABLE LEARNING OF PROTEIN STRUCTURE” (2018) by Mohammed AlQuraishi who has solved the protein folding problem. And “Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model” (2017)

Deep Learning Study Group

Since early May we have met Monday Wednesday and Friday 9AM reading books and papers relevant to DL. We started with reading/discussing 700 pages in Goodfellow (2016) et al : Deep Learning and Giron (2017) Hands-On using TensorFlow. after that we switch to papers from different application areas and have taken papers on Games (GO, Backgammon, Atari), Biosciences (Baldi, 2018) and are now in the middle of Genotype–>Phenotype mapping. We have 4 weeks to go and hope to cover protein structure, chemoinformatics, finance and a few deeper methodological papers from people in the Department. Any can join and come with suggestions about what to read.


I hope I am wrong – I worked hard for this not to be the case, but maybe not hard enough. I am giving a graduate lecture – 4th in 18 months on “Algorithms, Combinatorics in ChemoInformatics”.

Title: Combinatorics and Algorithms in ChemoInformatics Venue: May 17th 3.30 PM Department of Statistics, LG.04

Summary: Chemoinformatics is central to Drug Development and Design. In this lecture, we will go through key algorithms and combinatorics related to Chemoinformatics. Such algorithms are graph isomorphism, subgraph isomorphism, maximal common subgraphs and double pushout graph grammars. Combinatorics include generating functions for counting/enumerating special classes of molecules starting with alkanes, Polya-counting/enumerating molecules with symmetries, recursive enumeration of molecular graphs. We will also mention calculation of synthetic pathways, prediction of reactions and catalysis, exploration of chemical space and the potential for the use of Deep Learning. The talk attempts to survey these techniques in a way that should be useful for users that normally don’t venture into these techniques but maybe use chemoinformatics tools. 90 minutes – 30 slides:



We are done with Roemer (1996): “Theories of Distributive Justice”.  It was hard to digest to say the least and we might still have a wrap-up dinner at University College, if I find an expert who are willing to discuss with the 4 readers.

We are real happy to move on and somehow we found the above topic appealing.  I have avoided reading on this as I feel the Brain extremely complex, textbooks on Neuroscience are often huge, I am sceptical about the contribution about philosophy to the kind of knowledge I strive for.  I personally feel absolutely fine with a life without consciousness and have repeatedly recommended it to others.

But it is one of the BIG QUESTIONS and the ability to simulate the brain grows, so it would be real exciting to scratch the surface of this topic.   I have also included 4 lectures in my course Topics in Computational Biology in 2019, so I better get started reading the background literature and for once this fits right in.

I emailed 5 Professors of Neuroscience I knew, for recommendations and so far this book got unambigous praise, but I hope for a bit more feedback and advice on supplementary readings.  We are real careful with the books we read and it is not easy to get through the needle’s eye.  It has to be hard to read so it needs thorough discussion for each chapter.  In Roemer we at times used 30 minutes per page…..

But if I don’t find a better book by Monday morning, we will start Friday May 4th 6.30AM UK time per skype to discuss Stan Dehaene (2014): “Consciousness and the Brain: Deciphering How the Brain Codes Our Thoughts”.  We might supplement this with technical literature if need be.


He will talk on an correlation model for RNA evolution 3.30PM in the lower floor of Department of Statistics. The slides can be seen here: https://goo.gl/e6r4gx I spoke a week ago on the work I did in Israel: https://tinyurl.com/longisrael

Four Topics in Computational Biology

I will be giving a course with these lecture in TH18 at a advanced undergraduate course at the Department of Statistics

1 Enumeration in Phylogenetics
2. Tree Generating Processes
3. Compatibility
4. Statistical Alignment

5 Physics of Molecules: QM and MM
6 Integrators and Approximations
7 Applications I: Reactions
8 Applications II: Protein Folding

9 Small Molecules
10 Polya Enumeration
11 Graph Grammars and Reaction Prediction
12 3D Prediction from Graphs

13 Modeling the Evolution of Complex Objects: Languages, Patterns, Movements
14 The Comparative Method
15 Example I: Proteins
16 Example II: Networks

They will appear on this page as I finish them:


Skype Book Discussion Group in “Computational Complexity of Sampling”

The present version can be found here:


The author – Istvan Miklos – believes he will always be ahead of the readers in writing. We would then write a review that would be published about the same time as the book was published and we put an extended report on this page:


We also give a summarizing lecture when we have finished the book. Earlier when we did this, we met every 2nd day doing about 20 pages each time, but it can depend on the individual book. We did a similar thing to Mike Steels 2016-book, which I believe was beneficial to both authors and readers.

The ideal number of participants in such a group is 3-5. It would have to be online since I will be Israel. I like to choose a time that is either starting or ending of working day so it interpheres minimally with work. If you know somebody interested in participating in this, please tell me. If it proves a crappy book, we will stop reading, but that is not what I expect.