A major assumption in many machine learning and data mining algorithms is that the training and future data must be in the same feature space and have the same distribution. However, in many real-world applications, this assumption may not hold. For example, we sometimes have a classification task in one domain of interest, but we only have sufficient training data in another domain of interest, where the latter data may be in a different feature space or follow a different data distribution. In such cases, knowledge transfer, if done successfully, would greatly improve the performance of learning by avoiding much expensive data-labeling efforts. In recent years, transfer learning has emerged as a new learning framework to address this problem. This survey focuses on categorizing and reviewing the current progress on transfer learning for classification, regression, and clustering problems. In this survey, we discuss the relationship between transfer learning and other related machine learning techniques such as domain adaptation, multitask learning and sample selection bias, as well as covariate shift. We also explore some potential future issues in transfer learning research.

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A Survey on Transfer Learning

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Scalable Molecular Dynamics with NAMD

In this article, we describe an automatic differentiation module of PyTorch — a library designed to enable rapid research on machine learning models. It builds upon a few projects, most notably Lua Torch, Chainer, and HIPS Autograd [4], and provides a high performance environment with easy access to automatic differentiation of models executed on different devices (CPU and GPU). To make prototyping easier, PyTorch does not follow the symbolic approach used in many other deep learning frameworks, but focuses on differentiation of purely imperative programs, with a focus on extensibility and low overhead. Note that this preprint is a draft of certain sections from an upcoming paper covering all PyTorch features.

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Automatic differentiation in PyTorch

Deep learning frameworks have often focused on either usability or speed, but not both. PyTorch is a machine learning library that shows that these two goals are in fact compatible: it provides an imperative and Pythonic programming style that supports code as a model, makes debugging easy and is consistent with other popular scientific computing libraries, while remaining efficient and supporting hardware accelerators such as GPUs. 
In this paper, we detail the principles that drove the implementation of PyTorch and how they are reflected in its architecture. We emphasize that every aspect of PyTorch is a regular Python program under the full control of its user. We also explain how the careful and pragmatic implementation of the key components of its runtime enables them to work together to achieve compelling performance. 
We demonstrate the efficiency of individual subsystems, as well as the overall speed of PyTorch on several common benchmarks.

PyTorch: An Imperative Style, High-Performance Deep Learning Library

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

We propose a simple approach to combining first-order logic and probabilistic graphical models in a single representation. A Markov logic network (MLN) is a first-order knowledge base with a weight attached to each formula (or clause). Together with a set of constants representing objects in the domain, it specifies a ground Markov network containing one feature for each possible grounding of a first-order formula in the KB, with the corresponding weight. Inference in MLNs is performed by MCMC over the minimal subset of the ground network required for answering the query. Weights are efficiently learned from relational databases by iteratively optimizing a pseudo-likelihood measure. Optionally, additional clauses are learned using inductive logic programming techniques. Experiments with a real-world database and knowledge base in a university domain illustrate the promise of this approach.

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Markov logic networks

One of the major applications of data mining is in helping companies determine which potential customers to market to. If the expected profit from a customer is greater than the cost of marketing to her, the marketing action for that customer is executed. So far, work in this area has considered only the intrinsic value of the customer (i.e, the expected profit from sales to her). We propose to model also the customer's network value: the expected profit from sales to other customers she may influence to buy, the customers those may influence, and so on recursively. Instead of viewing a market as a set of independent entities, we view it as a social network and model it as a Markov random field. We show the advantages of this approach using a social network mined from a collaborative filtering database. Marketing that exploits the network value of customers---also known as viral marketing---can be extremely effective, but is still a black art. Our work can be viewed as a step towards providing a more solid foundation for it, taking advantage of the availability of large relevant databases.

http://cs-people.bu.edu/evimaria/cs591/domingos01mining.pdf

Mining the network value of customers

Viral marketing takes advantage of networks of influence among customers to inexpensively achieve large changes in behavior. Our research seeks to put it on a firmer footing by mining these networks from data, building probabilistic models of them, and using these models to choose the best viral marketing plan. Knowledge-sharing sites, where customers review products and advise each other, are a fertile source for this type of data mining. In this paper we extend our previous techniques, achieving a large reduction in computational cost, and apply them to data from a knowledge-sharing site. We optimize the amount of marketing funds spent on each customer, rather than just making a binary decision on whether to market to him. We take into account the fact that knowledge of the network is partial, and that gathering that knowledge can itself have a cost. Our results show the robustness and utility of our approach.

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Mining knowledge-sharing sites for viral marketing

Search engine advertising has become a significant element of the Web browsing experience. Choosing the right ads for the query and the order in which they are displayed greatly affects the probability that a user will see and click on each ad. This ranking has a strong impact on the revenue the search engine receives from the ads. Further, showing the user an ad that they prefer to click on improves user satisfaction. For these reasons, it is important to be able to accurately estimate the click-through rate of ads in the system. For ads that have been displayed repeatedly, this is empirically measurable, but for new ads, other means must be used. We show that we can use features of ads, terms, and advertisers to learn a model that accurately predicts the click-though rate for new ads. We also show that using our model improves the convergence and performance of an advertising system. As a result, our model increases both revenue and user satisfaction.

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Predicting clicks: estimating the click-through rate for new ads

Though research on the Semantic Web has progressed at a steady pace, its promise has yet to be realized. One major difficulty is that, by its very nature, the Semantic Web is a large, uncensored system to which anyone may contribute. This raises the question of how much credence to give each source. We cannot expect each user to know the trustworthiness of each source, nor would we want to assign top-down or global credibility values due to the subjective nature of trust. We tackle this problem by employing a web of trust, in which each user maintains trusts in a small number of other users. We then compose these trusts into trust values for all other users. The result of our computation is not an agglomerate "trustworthiness" of each user. Instead, each user receives a personalized set of trusts, which may vary widely from person to person. We define properties for combination functions which merge such trusts, and define a class of functions for which merging may be done locally while maintaining these properties. We give examples of specific functions and apply them to data from Epinions and our BibServ bibliography server. Experiments confirm that the methods are robust to noise, and do not put unreasonable expectations on users. We hope that these methods will help move the Semantic Web closer to fulfilling its promise.

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Matthew Richardson

Papers

Markov logic networks

Mining the network value of customers

Mining knowledge-sharing sites for viral marketing

Predicting clicks: estimating the click-through rate for new ads

Trust management for the semantic web