Finding Mutations in DNA and Proteins (Bioinformatics VI) Coursera


About this course: In previous courses in the Specialization, we have discussed how to sequence and compare genomes. This course will cover advanced topics in finding mutations lurking within DNA and proteins. In the first half of the course, we would like to ask how an individual's genome differs from the "reference genome" of the species. Our goal is to take small fragments of DNA from the individual and "map" them to the reference genome. We will see that the combinatorial pattern matching algorithms solving this problem are elegant and extremely efficient, requiring a surprisingly small amount of runtime and memory.

Online learning in episodic Markovian decision processes by relative entropy policy search

Neural Information Processing Systems

We study the problem of online learning in finite episodic Markov decision processes (MDPs)where the loss function is allowed to change between episodes. The natural performance measure in this learning problem is the regret defined as the difference between the total loss of the best stationary policy and the total loss suffered by the learner. We assume that the learner is given access to a finite action space A and the state space X has a layered structure with L layers, so that state transitions are only possible between consecutive layers. We describe a variant of the recently proposed Relative Entropy Policy Search algorithm and show that its regret after T episodes is 2 L X A T log( X A /L) in the bandit setting and 2L T log( X A /L) in the full information setting, given that the learner has perfect knowledge of the transition probabilities of the underlying MDP. These guarantees largely improve previously known results under much milder assumptions andcannot be significantly improved under general assumptions.

Online Learning in Kernelized Markov Decision Processes Machine Learning

We consider online learning for minimizing regret in unknown, episodic Markov decision processes (MDPs) with continuous states and actions. We develop variants of the UCRL and posterior sampling algorithms that employ nonparametric Gaussian process priors to generalize across the state and action spaces. When the transition and reward functions of the true MDP are either sampled from Gaussian process priors (fully Bayesian setting) or are members of the associated Reproducing Kernel Hilbert Spaces of functions induced by symmetric psd kernels (frequentist setting), we show that the algorithms enjoy sublinear regret bounds. The bounds are in terms of explicit structural parameters of the kernels, namely a novel generalization of the information gain metric from kernelized bandit, and highlight the influence of transition and reward function structure on the learning performance. Our results are applicable to multi-dimensional state and action spaces with composite kernel structures, and generalize results from the literature on kernelized bandits, and the adaptive control of parametric linear dynamical systems with quadratic costs.

Online Learning in Markov Decision Processes with Adversarially Chosen Transition Probability Distributions Machine Learning

We study the problem of learning Markov decision processes with finite state and action spaces when the transition probability distributions and loss functions are chosen adversarially and are allowed to change with time. We introduce an algorithm whose regret with respect to any policy in a comparison class grows as the square root of the number of rounds of the game, provided the transition probabilities satisfy a uniform mixing condition. Our approach is efficient as long as the comparison class is polynomial and we can compute expectations over sample paths for each policy. Designing an efficient algorithm with small regret for the general case remains an open problem.