https://www.cs.rice.edu/~nakhleh/COMP571/Fall05/DatabaseSearch/blast.pdf

Basic Local Alignment Search Tool

The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSIBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.

/pdf/gapped-blast-and-psi-blast-a-new-generation-of-protein-2ybl67x5yx.pdf

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

This tutorial provides an overview of the basic theory of hidden Markov models (HMMs) as originated by L.E. Baum and T. Petrie (1966) and gives practical details on methods of implementation of the theory along with a description of selected applications of the theory to distinct problems in speech recognition. Results from a number of original sources are combined to provide a single source of acquiring the background required to pursue further this area of research. The author first reviews the theory of discrete Markov chains and shows how the concept of hidden states, where the observation is a probabilistic function of the state, can be used effectively. The theory is illustrated with two simple examples, namely coin-tossing, and the classic balls-in-urns system. Three fundamental problems of HMMs are noted and several practical techniques for solving these problems are given. The various types of HMMs that have been studied, including ergodic as well as left-right models, are described. >

/pdf/a-tutorial-on-hidden-markov-models-and-selected-applications-1vlzbxbk68.pdf

A tutorial on hidden Markov models and selected applications in speech recognition

We will review some of the major results in random graphs and some of the more challenging open problems. We will cover algorithmic and structural questions. We will touch on newer models, including those related to the WWW.

Random graphs

Consider the upper tail probability that the homomorphism count of a fixed graph $H$ within a large sparse random graph $G_n$ exceeds its expected value by a fixed factor $1+\delta$. Going beyond the Erdős-Renyi model, we establish here explicit, sharp upper tail decay rates for sparse random $d_n$-regular graphs (provided $H$ has a regular $2$-core), and for sparse uniform random graphs. We further deal with joint upper tail probabilities for homomorphism counts of multiple graphs $H_1,\ldots, H_k$ (extending the known results for $k=1$), and for inhomogeneous graph ensembles (such as the stochastic block model), we bound the upper tail probability by a variational problem analogous to the one that determines its decay rate in the case of sparse Erdős-Renyi graphs.

Upper Tail For Homomorphism Counts In Constrained Sparse Random Graphs

We consider recurrence versus transience for models of random walks on domains of $\mathbb{Z}^d$, in which monotone interaction enforces domain growth as a result of visits by the walk (or probes it sent), to the neighborhood of domain boundary.

Monotone interaction of walk and graph: recurrence versus transience

We consider the ferromagnetic Ising model on a sequence of graphs $G_n$ converging locally weakly to a rooted random tree. Generalizing [Montanari, Mossel, Sly '11], under an appropriate "continuity" property, we show that the Ising measures on these graphs converge locally weakly to a measure, which is obtained by first picking a random tree, and then the symmetric mixture of Ising measures with $+$ and $-$ boundary conditions on that tree. Under the extra assumptions that $G_n$ are edge-expanders, we show that the local weak limit of the Ising measures conditioned on positive magnetization, is the Ising measure with $+$ boundary condition on the limiting tree. The "continuity" property holds except possibly for countably many choices of $\beta$, which for limiting trees of minimum degree at least three, are all within certain explicitly specified compact interval. We further show the edge-expander property for (most of) the configuration model graphs corresponding to limiting (multi-type) Galton Watson trees.

Ferromagnetic Ising Measures on Large Locally Tree-Like Graphs

Given a set of input-output training samples, we describe a procedure for determining the time sequence of weights for a dynamic neural network to model an arbitrary input-output process. We formulate the input-output mapping problem as an optimal control problem, defining a performance index to be minimized as a function of time-varying weights. We solve the resulting nonlinear two-point-boundary-value problem, and this yields the training rule. For the performance index chosen, this rule turns out to be a continuous time generalization of the outer product rule earlier suggested heuristically by Hopfield for designing associative memories. Learning curves for the new technique are presented.

/pdf/neural-network-weight-matrix-synthesis-using-optimal-control-1p9ms2hwos.pdf

Neural Network Weight Matrix Synthesis Using Optimal Control Techniques

The $N$ vertices of a quantum random graph are each a circle independently punctured at Poisson points of arrivals, with parallel connections derived through for each pair of these punctured circles by yet another independent Poisson process. Considering these graphs at their critical parameters, we show that the joint law of the re-scaled by $N^{2/3}$ and ordered sizes of their connected components, converges to that of the ordered lengths of excursions above zero for a reflected Brownian motion with drift. Thereby, this work forms the first example of an inhomogeneous random graph, beyond the case of effectively rank-1 models, which is rigorously shown to be in the Erd\H{o}s-R\'{e}nyi graphs universality class in terms of Aldous's results.

Amir Dembo

Papers

Upper Tail For Homomorphism Counts In Constrained Sparse Random Graphs

Monotone interaction of walk and graph: recurrence versus transience

Ferromagnetic Ising Measures on Large Locally Tree-Like Graphs

Neural Network Weight Matrix Synthesis Using Optimal Control Techniques

Component sizes for large quantum erdos renyi graph near criticality