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David M. McCandlish
David M. McCandlish
David M. McCandlish
@TheDMMcC

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David M. McCandlish

@TheDMMcC

Mathematical biologist, assistant professor Cold Spring Harbor Laboratory

Huntington, NY
cshl.edu/research/facul…
Vrijeme pridruživanja: prosinac 2016.

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    David M. McCandlish‏ @TheDMMcC 11. lip 2019.
    • Prijavi Tweet

    I feel like the preprint that @keitokiddo and I posted this past week is a substantial advance in our understanding of epistasis and so I'd like to say a few things about it that might be better on twitter than in print 1/nhttps://www.biorxiv.org/content/10.1101/657841v2 …

    10:15 - 11. lip 2019.
    • 67 proslijeđenih tweetova
    • 116 oznaka „sviđa mi se”
    • Jesse Weber Mao-Lun Weng Alvin X. Han Saloni 🏳️‍🌈 Jonathan Vo Bloom Lab David Danko Amit Sinha Ravi
    67 proslijeđenih tweetova 116 korisnika označava da im se sviđa
      1. Novi razgovor
      2. David M. McCandlish‏ @TheDMMcC 11. lip 2019.
        • Prijavi Tweet

        On a personal level, this is just more of my long-standing obsession with trying to make rigorous versions of Sewall Wright's fitness landscape cartoons 2/npic.twitter.com/IOzLS8n6La

        1 reply 3 proslijeđena tweeta 13 korisnika označava da im se sviđa
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      3. David M. McCandlish‏ @TheDMMcC 11. lip 2019.
        • Prijavi Tweet

        And as part of the paper we do that, revealing the simple qualitative structure underlying a 20^4=160,000 genotype fitness landscape using data from @wchnicholas 3/npic.twitter.com/tSvK1lkvIE

        1 reply 3 proslijeđena tweeta 14 korisnika označava da im se sviđa
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      4. David M. McCandlish‏ @TheDMMcC 11. lip 2019.
        • Prijavi Tweet

        But the specific problem that we're dealing with in this paper is how to extend fitness or phenotypic measurements for specific sequences to a model for all of sequence space without making assumptions about the precise form of the model (e.g.pair-wise, global epistasis, etc) 4/n

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      5. David M. McCandlish‏ @TheDMMcC 11. lip 2019.
        • Prijavi Tweet

        Put simply, our proposed solution is that given known fitnesses for some subset of genotypes, we assign fitnesses to all unobserved genotypes in a manner that minimizes that total amount of epistasis in the landscape as a whole. 5/n

        1 reply 0 proslijeđenih tweetova 7 korisnika označava da im se sviđa
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      6. David M. McCandlish‏ @TheDMMcC 11. lip 2019.
        • Prijavi Tweet

        More precisely, we minimize the mean squared epistatic coefficient between pairs of random mutations in random genetic backgrounds, so that mutational effects change as little as possible between adjacent backgrounds 6/npic.twitter.com/lxS4OmWAL3

        1 reply 1 proslijeđeni tweet 7 korisnika označava da im se sviđa
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      7. David M. McCandlish‏ @TheDMMcC 11. lip 2019.
        • Prijavi Tweet

        Why does this work? One way of thinking about this is to suppose that the fitness landscape really is some kind of 2D surface like in Wright's cartoons. 7/n

        1 reply 0 proslijeđenih tweetova 4 korisnika označavaju da im se sviđa
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      8. David M. McCandlish‏ @TheDMMcC 11. lip 2019.
        • Prijavi Tweet

        If we sample some genotypes and want to reconstruct the landscape, one standard way of doing this is using thin plate splines, which estimates the landscape with the least overall curvature compatible with our observations 8/npic.twitter.com/VItppMAs9X

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      9. David M. McCandlish‏ @TheDMMcC 11. lip 2019.
        • Prijavi Tweet

        In particular, it chooses the surface that goes through the sampled points (gray dots above) but otherwise minimizes the integral of the sum of the squared second-order partial derivatives 9/n

        1 reply 0 proslijeđenih tweetova 4 korisnika označavaju da im se sviđa
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      10. David M. McCandlish‏ @TheDMMcC 11. lip 2019.
        • Prijavi Tweet

        It turns out that our minimum epistasis interpolation method is precisely the thin plate spline solution, adapted to the discreteness of sequence space. 10/n

        1 proslijeđeni tweet 6 korisnika označava da im se sviđa
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      11. David M. McCandlish‏ @TheDMMcC 11. lip 2019.
        • Prijavi Tweet

        In particular, the epistatic coefficient measures how much one mutation influences the effect of another, so it's just the discrete analog of a mixed partial derivative. 11/npic.twitter.com/Irw8rqnUwP

        1 reply 1 proslijeđeni tweet 4 korisnika označavaju da im se sviđa
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      12. David M. McCandlish‏ @TheDMMcC 11. lip 2019.
        • Prijavi Tweet

        And so minimizing the average squared value of these epistatic coefficients essentially results in a discrete thin plate spline problem (i.e. a boundary value problem for a second-order Laplace operator, whose solution comes down to solving a single matrix equation). 12/n

        1 reply 1 proslijeđeni tweet 3 korisnika označavaju da im se sviđa
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      13. David M. McCandlish‏ @TheDMMcC 11. lip 2019.
        • Prijavi Tweet

        Moreover, just as a thin-plate spline can take a complicated shape close to the data but becomes less curved the farther you get from the data, our method can be highly epistatic near the data, but becomes nearly additive where data is sparse or absent. 13/n

        1 reply 0 proslijeđenih tweetova 2 korisnika označavaju da im se sviđa
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      14. David M. McCandlish‏ @TheDMMcC 11. lip 2019.
        • Prijavi Tweet

        So that's why it works. But what is the broader significance of this advance? 14/n

        1 reply 0 proslijeđenih tweetova 1 korisnik označava da mu se sviđa
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      15. David M. McCandlish‏ @TheDMMcC 11. lip 2019.
        • Prijavi Tweet

        The key insight provided by this method has to do with the possibilities that are opened up by incorporating higher-order epistasis, i.e. genetic interactions between 3 or more sites. 15/n

        1 reply 1 proslijeđeni tweet 5 korisnika označava da im se sviđa
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      16. David M. McCandlish‏ @TheDMMcC 11. lip 2019.
        • Prijavi Tweet

        Historically, higher-order epistasis has been viewed as something complicated, something to be worried about @DanWeinreich 16/n https://doi.org/10.1016/j.gde.2013.10.007 …

        1 reply 1 proslijeđeni tweet 4 korisnika označavaju da im se sviđa
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      17. David M. McCandlish‏ @TheDMMcC 11. lip 2019.
        • Prijavi Tweet

        But more recently we've seen that even "smooth" single-peaked fitness landscapes can harbor a substantial amount of higher-order epistasis due to global or non-specific epistasis 17/n

        1 reply 0 proslijeđenih tweetova 4 korisnika označavaju da im se sviđa
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      18. David M. McCandlish‏ @TheDMMcC 11. lip 2019.
        • Prijavi Tweet

        and so the presence of higher-order epistasis doesn't necessarily mean that the landscape is complicated as shown by e.g. @EvolBiochemist 18/nhttps://doi.org/10.1534/genetics.116.195214 …

        1 reply 0 proslijeđenih tweetova 8 korisnika označava da im se sviđa
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      19. David M. McCandlish‏ @TheDMMcC 11. lip 2019.
        • Prijavi Tweet

        Our method turns this around -- minimum epistasis interpolation is the smoothest possible solution compatible with the data and achieves this smoothness by allowing epistatic interactions of all orders. 19/n

        1 reply 0 proslijeđenih tweetova 5 korisnika označava da im se sviđa
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      20. David M. McCandlish‏ @TheDMMcC 11. lip 2019.
        • Prijavi Tweet

        The way to see this is by viewing higher-order interactions as pair-wise interactions whose strength can vary across sequence space 20/n

        1 reply 0 proslijeđenih tweetova 4 korisnika označavaju da im se sviđa
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      21. David M. McCandlish‏ @TheDMMcC 11. lip 2019.
        • Prijavi Tweet

        And one possibility this opens up is interactions whose strength decays as you get farther from the data 21/n

        1 reply 0 proslijeđenih tweetova 2 korisnika označavaju da im se sviđa
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      22. David M. McCandlish‏ @TheDMMcC 11. lip 2019.
        • Prijavi Tweet

        Which allows our method to accommodate strong pair-wise interactions where the data require it, but have these interactions decay away in regions of sequence space where the evidence does not support them. 22/n

        1 reply 1 proslijeđeni tweet 2 korisnika označavaju da im se sviđa
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      23. David M. McCandlish‏ @TheDMMcC 11. lip 2019.
        • Prijavi Tweet

        This more broadly raises the possibility that fitness landscapes may qualitatively be compatible with relatively simple geometric models that nonetheless contain epistasis of all orders. 23/n

        1 reply 0 proslijeđenih tweetova 2 korisnika označavaju da im se sviđa
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      24. David M. McCandlish‏ @TheDMMcC 11. lip 2019.
        • Prijavi Tweet

        For instance in the paper we show that the GB1 landscape has three different high fitness regions, where the fitness landscape is approximately additive within each region (see inset scatter plots). 24/npic.twitter.com/QEUDWf9aUo

        1 reply 2 proslijeđena tweeta 4 korisnika označavaju da im se sviđa
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      25. David M. McCandlish‏ @TheDMMcC 11. lip 2019.
        • Prijavi Tweet

        The method we describe also suggests a way forward in terms of dealing with how to make local models within the vastness of sequence space (tagging @granex who helped convince me that this is a key problem) 25/n

        1 reply 0 proslijeđenih tweetova 4 korisnika označavaju da im se sviđa
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      26. David M. McCandlish‏ @TheDMMcC 11. lip 2019.
        • Prijavi Tweet

        Standard regularized regression models with pair-wise interactions have the problem that they work well near the data but give unreasonable predictions far from it. 26/n

        1 reply 0 proslijeđenih tweetova 1 korisnik označava da mu se sviđa
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      27. David M. McCandlish‏ @TheDMMcC 11. lip 2019.
        • Prijavi Tweet

        Our work suggests that higher-order epistasis can be harnessed to solve this problem, by allowing predictions that behave in a complex way near the data but "fail elegantly" far from it. 27/n

        1 reply 0 proslijeđenih tweetova 3 korisnika označavaju da im se sviđa
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      28. David M. McCandlish‏ @TheDMMcC 11. lip 2019.
        • Prijavi Tweet

        So one of the big lessons for me in doing this work is that the presence of higher-order epistasis can actually make fitness landscapes less complicated, and that we can exploit this to make better models 28/n

        1 reply 2 proslijeđena tweeta 11 korisnika označava da im se sviđa
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      29. David M. McCandlish‏ @TheDMMcC 11. lip 2019.
        • Prijavi Tweet

        or, in other words, "How I learned to stop worrying and love higher-order epistasis" 29/29 FIN

        1 reply 2 proslijeđena tweeta 30 korisnika označava da im se sviđa
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