drinking the koolaid
A little over one year ago, Frey and Dueck published a paper in Science where they describe an algorithm called affinity propagation which clusters data points via passing messages between the points. In their paper they first describe the algorithm and then apply it to a few different examples of clustering problems from diverse fields. Read the rest of this entry »
Segal et. al. recently published a paper in Nature describing a computational framework that models transcriptional regulation in an attempt to predict expression. They apply their framework to the well characterized problem of segmentation of a Drosophila embryo. Read the rest of this entry »
I recently read “The Treeterbi and Parallel Treeterbi algorithms: efficient, optimal decoding for ordinary, generalized, and pair HMMs” by Keibler, Arumugam and Brent which was published in Bioinformatics 23(5):545-554 (2007). This paper outlines an algorithm for optimal decoding of HMMs which reduces memory requirements compared to the more standard Viterbi decoding. Furthermore, unlike the Hirschberg algorithm (aka Myers-Miller) it does not result in a significant increase in runtime.
Yeang and Haussler have developed an interesting model of coevolution … the selective constraints on components of a molecular apparatus which require coordinated changes of its components. The best studied of these being the compensatory mutations required in RNA secondary structure. Yeang uses a general continuous-time Markov process to model substitution at two sites. The null hypothesis being that the sites evolve neutrally. The alternative model is one where the changes observed between the two sites are co-occuring … favoring double changes over singles. The resulting probabilistic graphical model is relatively general, as demonstrated by their two recent publications.
