A Regularized Method for Selecting Nested Groups of Relevant Genes from Microarray Data

Gene expression analysis aims at identifying the genes able to accurately predict biological parameters like, for example, disease subtyping or progression. While accurate prediction can be achieved by means of many different techniques, gene identification, due to gene correlation and the limited number of available samples, is a much more elusive problem. Small changes in the expression values often produce different gene lists, and solutions which are both sparse and stable are difficult to obtain. We propose a two-stage regularization method able to learn linear models characterized by a high prediction performance. By varying a suitable parameter these linear models allow to trade sparsity for the inclusion of correlated genes and to produce gene lists which are almost perfectly nested. Experimental results on synthetic and microarray data confirm the interesting properties of the proposed method and its potential as a starting point for further biological investigationsComment: 17 pages, 8 Post-script figure

A general guide to applying machine learning to computer architecture

The resurgence of machine learning since the late 1990s has been enabled by significant advances in computing performance and the growth of big data. The ability of these algorithms to detect complex patterns in data which are extremely difficult to achieve manually, helps to produce effective predictive models. Whilst computer architects have been accelerating the performance of machine learning algorithms with GPUs and custom hardware, there have been few implementations leveraging these algorithms to improve the computer system performance. The work that has been conducted, however, has produced considerably promising results. The purpose of this paper is to serve as a foundational base and guide to future computer architecture research seeking to make use of machine learning models for improving system efficiency. We describe a method that highlights when, why, and how to utilize machine learning models for improving system performance and provide a relevant example showcasing the effectiveness of applying machine learning in computer architecture. We describe a process of data generation every execution quantum and parameter engineering. This is followed by a survey of a set of popular machine learning models. We discuss their strengths and weaknesses and provide an evaluation of implementations for the purpose of creating a workload performance predictor for different core types in an x86 processor. The predictions can then be exploited by a scheduler for heterogeneous processors to improve the system throughput. The algorithms of focus are stochastic gradient descent based linear regression, decision trees, random forests, artificial neural networks, and k-nearest neighbors.This work has been supported by the European Research Council (ERC) Advanced Grant RoMoL (Grant Agreemnt 321253) and by the Spanish Ministry of Science and Innovation (contract TIN 2015-65316P).Peer ReviewedPostprint (published version

Identifying Real Estate Opportunities using Machine Learning

The real estate market is exposed to many fluctuations in prices because of existing correlations with many variables, some of which cannot be controlled or might even be unknown. Housing prices can increase rapidly (or in some cases, also drop very fast), yet the numerous listings available online where houses are sold or rented are not likely to be updated that often. In some cases, individuals interested in selling a house (or apartment) might include it in some online listing, and forget about updating the price. In other cases, some individuals might be interested in deliberately setting a price below the market price in order to sell the home faster, for various reasons. In this paper, we aim at developing a machine learning application that identifies opportunities in the real estate market in real time, i.e., houses that are listed with a price substantially below the market price. This program can be useful for investors interested in the housing market. We have focused in a use case considering real estate assets located in the Salamanca district in Madrid (Spain) and listed in the most relevant Spanish online site for home sales and rentals. The application is formally implemented as a regression problem that tries to estimate the market price of a house given features retrieved from public online listings. For building this application, we have performed a feature engineering stage in order to discover relevant features that allows for attaining a high predictive performance. Several machine learning algorithms have been tested, including regression trees, k-nearest neighbors, support vector machines and neural networks, identifying advantages and handicaps of each of them.Comment: 24 pages, 13 figures, 5 table

Machine Learning Classification of SDSS Transient Survey Images

We show that multiple machine learning algorithms can match human performance in classifying transient imaging data from the Sloan Digital Sky Survey (SDSS) supernova survey into real objects and artefacts. This is a first step in any transient science pipeline and is currently still done by humans, but future surveys such as the Large Synoptic Survey Telescope (LSST) will necessitate fully machine-enabled solutions. Using features trained from eigenimage analysis (principal component analysis, PCA) of single-epoch g, r and i-difference images, we can reach a completeness (recall) of 96 per cent, while only incorrectly classifying at most 18 per cent of artefacts as real objects, corresponding to a precision (purity) of 84 per cent. In general, random forests performed best, followed by the k-nearest neighbour and the SkyNet artificial neural net algorithms, compared to other methods such as na\"ive Bayes and kernel support vector machine. Our results show that PCA-based machine learning can match human success levels and can naturally be extended by including multiple epochs of data, transient colours and host galaxy information which should allow for significant further improvements, especially at low signal-to-noise.Comment: 14 pages, 8 figures. In this version extremely minor adjustments to the paper were made - e.g. Figure 5 is now easier to view in greyscal

k-Nearest Neighbour Classifiers: 2nd Edition (with Python examples)

Perhaps the most straightforward classifier in the arsenal or machine learning techniques is the Nearest Neighbour Classifier -- classification is achieved by identifying the nearest neighbours to a query example and using those neighbours to determine the class of the query. This approach to classification is of particular importance because issues of poor run-time performance is not such a problem these days with the computational power that is available. This paper presents an overview of techniques for Nearest Neighbour classification focusing on; mechanisms for assessing similarity (distance), computational issues in identifying nearest neighbours and mechanisms for reducing the dimension of the data. This paper is the second edition of a paper previously published as a technical report. Sections on similarity measures for time-series, retrieval speed-up and intrinsic dimensionality have been added. An Appendix is included providing access to Python code for the key methods.Comment: 22 pages, 15 figures: An updated edition of an older tutorial on kN