Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These methods are starting to become a bottleneck in some analysis pipelines when faced with data sets of the size of many thousands of sequences. Some methods allow computation of larger data sets while sacrificing quality, and others produce high-quality alignments, but scale badly with the number of sequences. In this paper, we describe a new program called Clustal Omega, which can align virtually any number of protein sequences quickly and that delivers accurate alignments. The accuracy of the package on smaller test cases is similar to that of the high-quality aligners. On larger data sets, Clustal Omega outperforms other packages in terms of execution time and quality. Clustal Omega also has powerful features for adding sequences to and exploiting information in existing alignments, making use of the vast amount of precomputed information in public databases like Pfam.

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Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega

Today's Web-enabled deluge of electronic data calls for automated methods of data analysis. Machine learning provides these, developing methods that can automatically detect patterns in data and then use the uncovered patterns to predict future data. This textbook offers a comprehensive and self-contained introduction to the field of machine learning, based on a unified, probabilistic approach. The coverage combines breadth and depth, offering necessary background material on such topics as probability, optimization, and linear algebra as well as discussion of recent developments in the field, including conditional random fields, L1 regularization, and deep learning. The book is written in an informal, accessible style, complete with pseudo-code for the most important algorithms. All topics are copiously illustrated with color images and worked examples drawn from such application domains as biology, text processing, computer vision, and robotics. Rather than providing a cookbook of different heuristic methods, the book stresses a principled model-based approach, often using the language of graphical models to specify models in a concise and intuitive way. Almost all the models described have been implemented in a MATLAB software package--PMTK (probabilistic modeling toolkit)--that is freely available online. The book is suitable for upper-level undergraduates with an introductory-level college math background and beginning graduate students.

Machine Learning : A Probabilistic Perspective

The k-means method is a widely used clustering technique that seeks to minimize the average squared distance between points in the same cluster. Although it offers no accuracy guarantees, its simplicity and speed are very appealing in practice. By augmenting k-means with a very simple, randomized seeding technique, we obtain an algorithm that is Θ(logk)-competitive with the optimal clustering. Preliminary experiments show that our augmentation improves both the speed and the accuracy of k-means, often quite dramatically.

/pdf/k-means-the-advantages-of-careful-seeding-4p8vluc5ni.pdf

k-means++: the advantages of careful seeding

Models for the processes by which ideas and influence propagate through a social network have been studied in a number of domains, including the diffusion of medical and technological innovations, the sudden and widespread adoption of various strategies in game-theoretic settings, and the effects of "word of mouth" in the promotion of new products. Recently, motivated by the design of viral marketing strategies, Domingos and Richardson posed a fundamental algorithmic problem for such social network processes: if we can try to convince a subset of individuals to adopt a new product or innovation, and the goal is to trigger a large cascade of further adoptions, which set of individuals should we target?We consider this problem in several of the most widely studied models in social network analysis. The optimization problem of selecting the most influential nodes is NP-hard here, and we provide the first provable approximation guarantees for efficient algorithms. Using an analysis framework based on submodular functions, we show that a natural greedy strategy obtains a solution that is provably within 63% of optimal for several classes of models; our framework suggests a general approach for reasoning about the performance guarantees of algorithms for these types of influence problems in social networks.We also provide computational experiments on large collaboration networks, showing that in addition to their provable guarantees, our approximation algorithms significantly out-perform node-selection heuristics based on the well-studied notions of degree centrality and distance centrality from the field of social networks.

/pdf/maximizing-the-spread-of-influence-through-a-social-network-47y1ehuvwi.pdf

Maximizing the Spread of Influence through a Social Network

In this paper, we present {GraRep}, a novel model for learning vertex representations of weighted graphs. This model learns low dimensional vectors to represent vertices appearing in a graph and, unlike existing work, integrates global structural information of the graph into the learning process. We also formally analyze the connections between our work and several previous research efforts, including the DeepWalk model of Perozzi et al. as well as the skip-gram model with negative sampling of Mikolov et al. We conduct experiments on a language network, a social network as well as a citation network and show that our learned global representations can be effectively used as features in tasks such as clustering, classification and visualization. Empirical results demonstrate that our representation significantly outperforms other state-of-the-art methods in such tasks.

GraRep: Learning Graph Representations with Global Structural Information

The k-means method is an old but popular clustering algorithm known for its observed speed and its simplicity. Until recently, however, no meaningful theoretical bounds were known on its running time. In this paper, we demonstrate that the worst-case running time of k-means is superpolynomial by improving the best known lower bound from Ω(n) iterations to 2Ω(√n).

/pdf/how-slow-is-the-k-means-method-43b07v1yln.pdf

How slow is the k-means method?

The k-means method is one of the most widely used clustering algorithms, drawing its popularity from its speed in practice. Recently, however, it was shown to have exponential worst-case running time. In order to close the gap between practical performance and theoretical analysis, the k-means method has been studied in the model of smoothed analysis. But even the smoothed analyses so far are unsatisfactory as the bounds are still super-polynomial in the number n of data points. In this paper, we settle the smoothed running time of the k-means method. We show that the smoothed number of iterations is bounded by a polynomial in n and 1/sigma, where sigma is the standard deviation of the Gaussian perturbations. This means that if an arbitrary input data set is randomly perturbed, then the k-means method will run in expected polynomial time on that input set.

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k-Means Has Polynomial Smoothed Complexity

We study the use of viral marketing strategies on social networks that seek to maximize revenue from the sale of a single product. We propose a model in which the decision of a buyer to buy the product is influenced by friends that own the product and the price at which the product is offered. The influence model we analyze is quite general, naturally extending both the Linear Threshold model and the Independent Cascade model, while also incorporating price information. We consider sales proceeding in a cascading manner through the network, i.e. a buyer is offered the product via recommendations from its neighbors who own the product. In this setting, the seller influences events by offering a cashback to recommenders and by setting prices (via coupons or discounts) for each buyer in the social network. This choice of prices for the buyers is termed as the seller's strategy.

Finding a seller strategy which maximizes the expected revenue in this setting turns out to be NP-hard. However, we propose a seller strategy that generates revenue guaranteed to be within a constant factor of the optimal strategy in a wide variety of models. The strategy is based on an influence-and-exploit idea, and it consists of finding the right trade-off at each time step between: generating revenue from the current user versus offering the product for free and using the influence generated from this sale later in the process.

/pdf/pricing-strategies-for-viral-marketing-on-social-networks-vwac12rqv5.pdf

Pricing Strategies for Viral Marketing on Social Networks

We study the use of viral marketing strategies on social networks to maximize revenue from the sale of a single product. We propose a model in which the decision of a buyer to buy the product is influenced by friends that own the product and the price at which the product is offered. The influence model we analyze is quite general, naturally extending both the Linear Threshold model and the Independent Cascade model, while also incorporating price information. We consider sales proceeding in a cascading manner through the network, i.e. a buyer is offered the product via recommendations from its neighbors who own the product. In this setting, the seller influences events by offering a cashback to recommenders and by setting prices (via coupons or discounts) for each buyer in the social network. 
Finding a seller strategy which maximizes the expected revenue in this setting turns out to be NP-hard. However, we propose a seller strategy that generates revenue guaranteed to be within a constant factor of the optimal strategy in a wide variety of models. The strategy is based on an influence-and-exploit idea, and it consists of finding the right trade-off at each time step between: generating revenue from the current user versus offering the product for free and using the influence generated from this sale later in the process. We also show how local search can be used to improve the performance of this technique in practice.

David Arthur

Papers

k-means++: the advantages of careful seeding

How slow is the k-means method?

k-Means Has Polynomial Smoothed Complexity

Pricing Strategies for Viral Marketing on Social Networks

Pricing strategies for viral marketing on Social Networks