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Buckminster Fuller: there is no such thing as artificial sweetener
“All the chemist can do is to find out what Nature permits, and any substances that are thus developed or discovered are inherently natural. It is very important to remember that.”
— Buckminster Fuller (1963, p. 76)
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Andrews on the irrelevancy of numbers in mathematics
“To the unsophisticated observer of mathematics, it may appear that the use of numbers is the critical characteristic of disciplines which use mathematics, and that one can thus make a discipline more scientific by involving numbers in it more deeply. However, the really fundamental feature of mathematics is not numbers but logical rigor. While arguments involving numbers are often rigorous, it will be seen that a standard of rigor can be defined and maintained whether numbers are involved or not.”
— Andrews (2002, p. 3)
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Martin-Löf says mathematics is informal
“Our main aim is to build up a system of formal rules representing in the best possible way informal (mathematical) reasoning.”
— Martin-Löf (1984, p. 4)
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Toward Interactive Statistical Modeling
Abstract
When solving machine learning problems, there is currently little automated support for easily experimenting with alternative statistical models or solution strategies. This is because this activity often requires expertise from several different ï¬elds (e.g., statistics, optimization, linear algebra), and the level of formalism required for automation is much higher than for a human solving problems on paper. We present a system toward addressing these issues, which we achieve by (1) formalizing a type theory for probability and optimization, and (2) providing an interactive rewrite system for applying problem reformulation theorems. Automating solution strategies this way enables not only manual experimentation but also higher-level, automated activities, such as autotuning.
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Sooraj Bhat, Ashish Agarwal, Alexander Gray, Richard Vuduc (2010). Toward Interactive Statistical Modeling, In Procedia Computer Science, International Conference on Computational Science ICCS 2010, 1(1): 1892-1838.
My new website
My new WordPress powered website is up! There’s now a chance it will be updated more than once every 3 years.
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Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response
Abstract
Transcription factors are key components of regulatory networks that control development, as well as the response to environmental stimuli. We have established an experimental pipeline in Caenorhabditis elegans that permits global identification of the binding sites for transcription factors using chromatin immunoprecipitation and deep sequencing. We describe and validate this strategy, and apply it to the transcription factor PHA-4, which plays critical roles in organ development and other cellular processes. We identified thousands of binding sites for PHA-4 during formation of the embryonic pharynx, and also found a role for this factor during the starvation response. Many binding sites were found to shift dramatically between embryos and starved larvae, from developmentally regulated genes to genes involved in metabolism. These results indicate distinct roles for this regulator in two different biological processes and demonstrate the versatility of transcription factors in mediating diverse biological roles.
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Mei Zhong, Wei Niu, Zhi John Lu, Mihail Sarov, John I. Murray, Judith Janette, Debasish Raha, Karyn L. Sheaffer, Hugo Y. K. Lam, Elicia Preston, Cindie Slightham, LaDeana W. Hillier, Trisha Brock, Ashish Agarwal, Raymond Auerbach, Anthony A. Hyman, Mark Gerstein, Susan E. Mango, Stuart K. Kim, Robert H. Waterston, Valerie Reinke, Michael Snyder (2010). Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response, PLoS Genetics, 6(2): 1-13.
Automating Mathematical Program Transformations
Abstract
Mathematical programs (MPs) are a class of constrained optimization problems that include linear, mixed-integer, and disjunctive programs. Strategies for solving MPs rely heavily on various transformations between these subclasses, but most are not automated because MP theory does not presently treat programs as syntactic objects. In this work, we present the ï¬rst syntactic deï¬nition of MP and of some widely used MP transformations, most notably the big-M and convex hull methods for converting disjunctive constraints. We use an embedded OCaml DSL on problems from chemical process engineering and operations research to compare our automated transformations to existing technology—ï¬nding that no one technique is always best—and also to manual reformulations—ï¬nding that our mechanizations are comparable to human experts. This work enables higher-level solution strategies that can use these transformations as subroutines.
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Ashish Agarwal, Sooraj Bhat, Alexander Gray, Ignacio E. Grossmann (2010). Automating Mathematical Program Transformations, in Proceedings of the 12th International Symposium on Practical Aspects of Declarative Languages, PADL 2010, Vol 5937 of Lecture Notes in Computer Science, pp. 134-148.
Machiavelli: we always think it was better before
“It is the common practice of Mankind, to commend the ancient, and condemn the present …”
— Machiavelli (~1513, preface of Discourses on Livy II)
I find this especially amusing because it was stated in the 1500’s.
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Our PADL paper was accepted.
See you in Madrid! Paper details are here.
