openboundlabs.com

Michael Paul Stewart Brown

Research Interests:
- Bioinformatics. Application of probabilistic and machine learning techniques to new bioinformatics problems with large amounts of data. - Probabilistic models. Hidden Markov models, stochastic context-free grammars, graphical models, Fisher features. - Classifiers, Machine Learning. Support vector machines, Guassian processes, information geometries, boosting. - Unsupervised learning of concepts. Mixture and product models, simulated annealing, Expectation Maximization. - Characterization of information flow and mechanisms of living things. Genomic organization, pathway inference, RNA structure, transcription, translation, regulation, RNAi, cross species analysis. - Information retrieval and modeling. Vector space models, large vocabulary modeling, efficient search, link structure analysis.
Publications:
Papers: Hidden Markov Models, stochastic context-free grammars, Dirichlet mixtures, support vector machines, RNA modeling including ribosomal RNA, RNA pseudoknot modeling, and DNA microarray data analysis....
Me:
- http://www.openboundlabs.com/mpsbHomepage/ - Email: michaelbrownid "at" gmail.com - CV: cv.pdf -
Site Map:
Just wait until I start using this site for real... :-)
- http://www.openboundlabs.com/surf/ Collect together some data to check the surf!
- http://www.openboundlabs.com/simplest-embedding/ Use neural network embedding techniques in tensorflow to show you can learn linear orderings. Animations and Math included! - http://www.openboundlabs.com/deepdream-flowers/ Apply tensorflow deepdream to some images for a flower effect.
- http://www.openboundlabs.com/rare-variant-power/ Calculate how confident you are of biological truth when you want to detect the presence of a minor variant but there is sequencing noise. Is it real or noise? - http://www.openboundlabs.com/buckets/ A python solution to a simple combinatorial math problem. - http://www.openboundlabs.com/box2d-js/ Simple physics simulation using box2d in javascript. - http://www.openboundlabs.com/image_batch/ A short summary of how to use imagemagick to do image manipulations. - http://www.openboundlabs.com/README_kez_computer.html General computer buying guide - http://www.openboundlabs.com/linksFeb2017.html Some random links on Irreproducible Research, physics and machine learning, discrete math, Tensegrity.
- http://www.openboundlabs.com/bcr-abl-paperfigs/ Results on examining minor variants in the kinase domain of the BCR-ABL fusion from leukemia (a drug target), time series and clustering plots. - http://www.openboundlabs.com/bcrAblBarcodesFull/ Results on examining minor variants in the kinase domain of the BCR-ABL fusion from leukemia (a drug target). - http://www.openboundlabs.com/bcrabl-datatable-results/ Results on examining minor variants in the kinase domain of the BCR-ABL fusion from leukemia (a drug target). - http://www.openboundlabs.com/washubcrabl/ Results on looking at BCR-ABL kinase domain sequencing from leukemia samples.
- http://www.openboundlabs.com/hivMI/ Compute mutual information for all pairs of bases in HIV genome. Plot everything and move around it like Google maps. - http://www.openboundlabs.com/NIAID-closehivAnalysis Results on resolving mixtures of full length HIV genomes (9kb) that differ only by a base or two - http://www.openboundlabs.com/emory2012Feb/ Results on examining HIV sequencing data: full HIV genome 9kb and GAG regions. - http://www.openboundlabs.com/niaid/ Results on deconvoluting mixture of 20 full HIV genomes. - http://www.openboundlabs.com/niaid-lids/ Results on HIV genomes in patients have Large Internal Deletions! - http://www.openboundlabs.com/niaid-lids-validation/ Results on HIV genomes in patients have Large Internal Deletions! - http://www.openboundlabs.com/partner/ Results on HIV sequences that shows 300 base deletions in ENV. - http://www.openboundlabs.com/ucsd/ Results on looking at HIV ENV sequencing.