Machine Learning is the study of methods for programming computers to learn. Computers are applied to a wide range of tasks, and for most of these it is relatively easy for programmers to design and implement the necessary software. However, there are many tasks for which this is difficult or impossible. These can be divided into four general categories. First, there are problems for which there exist no human experts. For example, in modern automated manufacturing facilities, there is a need to predict machine failures before they occur by analyzing sensor readings. Because the machines are new, there are no human experts who can be interviewed by a programmer to provide the knowledge necessary to build a computer system. A machine learning system can study recorded data and subsequent machine failures and learn prediction rules. Second, there are problems where human experts exist, but where they are unable to explain their expertise. This is the case in many perceptual tasks, such as speech recognition, hand-writing recognition, and natural language understanding. Virtually all humans exhibit expert-level abilities on these tasks, but none of them can describe the detailed steps that they follow as they perform them. Fortunately, humans can provide machines with examples of the inputs and correct outputs for these tasks, so machine learning algorithms can learn to map the inputs to the outputs. Third, there are problems where phenomena are changing rapidly. In finance, for example, people would like to predict the future behavior of the stock market, of consumer purchases, or of exchange rates. These behaviors change frequently, so that even if a programmer could construct a good predictive computer program, it would need to be rewritten frequently. A learning program can relieve the programmer of this burden by constantly modifying and tuning a set of learned prediction rules. Fourth, there are applications that need to be customized for each computer user separately. Consider, for example, a program to filter unwanted electronic mail messages. Different users will need different filters. It is unreasonable to expect each user to program his or her own rules, and it is infeasible to provide every user with a software engineer to keep the rules up-to-date. A machine learning system can learn which mail messages the user rejects and maintain the filtering rules automatically. Machine learning addresses many of the same research questions as the fields of statistics, data mining, and psychology, but with differences of emphasis. Statistics focuses on understanding the phenomena that have generated the data, often with the goal of testing different hypotheses about those phenomena. Data mining seeks to find patterns in the data that are understandable by people. Psychological studies of human learning aspire to understand the mechanisms underlying the various learning behaviors exhibited by people (concept learning, skill acquisition, strategy change, etc.).

Machine learning

Probability Distributions.- Linear Models for Regression.- Linear Models for Classification.- Neural Networks.- Kernel Methods.- Sparse Kernel Machines.- Graphical Models.- Mixture Models and EM.- Approximate Inference.- Sampling Methods.- Continuous Latent Variables.- Sequential Data.- Combining Models.

Pattern Recognition and Machine Learning

So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

Human biochemical genetics

In the past decade, extracellular vesicles (EVs) have been recognized as potent vehicles of intercellular communication, both in prokaryotes and eukaryotes. This is due to their capacity to transfer proteins, lipids and nucleic acids, thereby influencing various physiological and pathological functions of both recipient and parent cells. While intensive investigation has targeted the role of EVs in different pathological processes, for example, in cancer and autoimmune diseases, the EV-mediated maintenance of homeostasis and the regulation of physiological functions have remained less explored. Here, we provide a comprehensive overview of the current understanding of the physiological roles of EVs, which has been written by crowd-sourcing, drawing on the unique EV expertise of academia-based scientists, clinicians and industry based in 27 European countries, the United States and Australia. This review is intended to be of relevance to both researchers already working on EV biology and to newcomers who will encounter this universal cell biological system. Therefore, here we address the molecular contents and functions of EVs in various tissues and body fluids from cell systems to organs. We also review the physiological mechanisms of EVs in bacteria, lower eukaryotes and plants to highlight the functional uniformity of this emerging communication system.

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Biological properties of extracellular vesicles and their physiological functions

This paper addresses the problem of the classification of hyperspectral remote sensing images by support vector machines (SVMs) First, we propose a theoretical discussion and experimental analysis aimed at understanding and assessing the potentialities of SVM classifiers in hyperdimensional feature spaces Then, we assess the effectiveness of SVMs with respect to conventional feature-reduction-based approaches and their performances in hypersubspaces of various dimensionalities To sustain such an analysis, the performances of SVMs are compared with those of two other nonparametric classifiers (ie, radial basis function neural networks and the K-nearest neighbor classifier) Finally, we study the potentially critical issue of applying binary SVMs to multiclass problems in hyperspectral data In particular, four different multiclass strategies are analyzed and compared: the one-against-all, the one-against-one, and two hierarchical tree-based strategies Different performance indicators have been used to support our experimental studies in a detailed and accurate way, ie, the classification accuracy, the computational time, the stability to parameter setting, and the complexity of the multiclass architecture The results obtained on a real Airborne Visible/Infrared Imaging Spectroradiometer hyperspectral dataset allow to conclude that, whatever the multiclass strategy adopted, SVMs are a valid and effective alternative to conventional pattern recognition approaches (feature-reduction procedures combined with a classification method) for the classification of hyperspectral remote sensing data

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Classification of hyperspectral remote sensing images with support vector machines

Due to advances in sensor technology, it is now possible to acquire hyperspectral data simultaneously in hundreds of bands. Algorithms that both reduce the dimensionality of the data sets and handle highly correlated bands are required to exploit the information in these data sets effectively. the authors propose a set of best-bases feature extraction algorithms that are simple, fast, and highly effective for classification of hyperspectral data. These techniques intelligently combine subsets of adjacent bands into a smaller number of features. Both top-down and bottom-up algorithms are proposed. The top-down algorithm recursively partitions the bands into two (not necessarily equal) sets of bands and then replaces each final set of bands by its mean value. The bottom-up algorithm builds an agglomerative tree by merging highly correlated adjacent bands and projecting them onto their Fisher direction, yielding high discrimination among classes. Both these algorithms are used in a pairwise classifier framework where the original C-class problem is divided into a set of (/sub 2//sup C/) two-class problems. The new algorithms (1) find variable length bases localized in wavelength, (2) favor grouping highly correlated adjacent bands that, when merged either by taking their mean or Fisher linear projection, yield maximum discrimination, and (3) seek orthogonal bases for each of the (/sub 2//sup C/) two-class problems into which a C-class problem can be decomposed. Experiments on an AVIRIS data set for a 12-class problem show significant improvements in classification accuracies while using a much smaller number of features.

Best-bases feature extraction algorithms for classification of hyperspectral data

The invention, referred to herein as PeaCoCk, uses a unique blend of technologies from statistics, information theory, and graph theory to quantify and discover patterns in relationships between entities, such as products and customers, as evidenced by purchase behavior. In contrast to traditional purchase-frequency based market basket analysis techniques, such as association rules which mostly generate obvious and spurious associations, PeaCoCk employs information-theoretic notions of consistency and similarity, which allows robust statistical analysis of the true, statistically significant, and logical associations between products. Therefore, PeaCoCk lends itself to reliable, robust predictive analytics based on purchase-behavior.

Method and apparatus for recommendation engine using pair-wise co-occurrence consistency

Many classification problems involve high dimensional inputs and a large number of classes. Multiclassifier fusion approaches to such difficult problems typically centre around smart feature extraction, input resampling methods, or input space partitioning to exploit modular learning. In this paper, we investigate how partitioning of the output space (i.e. the set of class labels) can be exploited in a multiclassifier fusion framework to simplify such problems and to yield better solutions. Specifically, we introduce a hierarchical technique to recursively decompose a C-class problem into C_1 two-(meta) class problems. A generalised modular learning framework is used to partition a set of classes into two disjoint groups called meta-classes. The coupled problems of finding a good partition and of searching for a linear feature extractor that best discriminates the resulting two meta-classes are solved simultaneously at each stage of the recursive algorithm. This results in a binary tree whose leaf nodes represent the original C classes. The proposed hierarchical multiclassifier framework is particularly effective for difficult classification problems involving a moderately large number of classes. The proposed method is illustrated on a problem related to classification of landcover using hyperspectral data: a 12-class AVIRIS subset with 180 bands. For this problem, the classification accuracies obtained were superior to most other techniques developed for hyperspectral classification. Moreover, the class hierarchies that were automatically discovered conformed very well with human domain experts’ opinions, which demonstrates the potential of using such a modular learning approach for discovering domain knowledge automatically from data.

Hierarchical Fusion of Multiple Classifiers for Hyperspectral Data Analysis

Method and apparatus for retail data mining using pair-wise co-occurrence consistency

Previous studies have established that the vasopres- sin-regulated water channel of the collecting duct, aquaporin-2, is excreted in the urine, providing a means for assessment of regulation and dysregulation of aquaporin-2 in humans. This article addresses the hypothesis that membrane transporters from upstream nephron segments are normally detectable in urine. The experiments employed rabbit polyclonal antibodies against the major Na transporters of the proximal tubule (the type 3 Na-H exchanger (NHE3)), the thick ascending limb of Henle's loop (the bumetanide-sensitive Na-K-2Cl cotrans- porter (NKCC2)), and the distal convoluted tubule (the thia- zide-sensitive Na-Cl cotransporter (NCC)) in immunoblotting experiments. All three of these transporters were readily de- tectable as high molecular weight complexes present in low- density membrane fractions from urine of normal rats. Cross linking studies of NHE3, NKCC2, and NCC revealed that high molecular weight complexes are normally present in renal tissue. The molecular weights of the complexes in urine matched those of the cross-linked complexes in native kidney tissue. The presence in urine of integral membrane proteins representative of each nephron segment raises the possibility that limited or comprehensive proteomic analysis of urine samples may be useful in clinical settings.

Shailesh Kumar

Papers

Best-bases feature extraction algorithms for classification of hyperspectral data

Method and apparatus for recommendation engine using pair-wise co-occurrence consistency

Hierarchical Fusion of Multiple Classifiers for Hyperspectral Data Analysis

Method and apparatus for retail data mining using pair-wise co-occurrence consistency

Detection of Na+ Transporter Proteins in Urine