Blood type classification using computer vision and machine learning

In emergency situations, where time for blood transfusion is reduced, the O negative blood type (the universal donor) is administrated. However, sometimes even the universal donor can cause transfusion reactions that can be fatal to the patient. As commercial systems do not allow fast results and are not suitable for emergency situations, this paper presents the steps considered for the development and validation of a prototype, able to determine blood type compatibilities, even in emergency situations. Thus it is possible, using the developed system, to administer a compatible blood type, since the first blood unit transfused. In order to increase the system’s reliability, this prototype uses different approaches to classify blood types, the first of which is based on Decision Trees and the second one based on support vector machines. The features used to evaluate these classifiers are the standard deviation values, histogram, Histogram of Oriented Gradients and fast Fourier transform, computed on different regions of interest. The main characteristics of the presented prototype are small size, lightweight, easy transportation, ease of use, fast results, high reliability and low cost. These features are perfectly suited for emergency scenarios, where the prototype is expected to be used.

Rough set-based reasoning and pattern mining for information filtering

An information filtering (IF) system monitors an incoming document stream to find the documents that match the information needs specified by the user profiles. To learn to use the user profiles effectively is one of the most challenging tasks when developing an IF system. With the document selection criteria better defined based on the users’ needs, filtering large streams of information can be more efficient and effective. To learn the user profiles, term-based approaches have been widely used in the IF community because of their simplicity and directness. Term-based approaches are relatively well established. However, these approaches have problems when dealing with polysemy and synonymy, which often lead to an information overload problem. Recently, pattern-based approaches (or Pattern Taxonomy Models (PTM) [160]) have been proposed for IF by the data mining community. These approaches are better at capturing sematic information and have shown encouraging results for improving the effectiveness of the IF system. On the other hand, pattern discovery from large data streams is not computationally efficient. Also, these approaches had to deal with low frequency pattern issues. The measures used by the data mining technique (for example, “support” and “confidences”) to learn the profile have turned out to be not suitable for filtering. They can lead to a mismatch problem. This thesis uses the rough set-based reasoning (term-based) and pattern mining approach as a unified framework for information filtering to overcome the aforementioned problems. This system consists of two stages - topic filtering and pattern mining stages. The topic filtering stage is intended to minimize information overloading by filtering out the most likely irrelevant information based on the user profiles. A novel user-profiles learning method and a theoretical model of the threshold setting have been developed by using rough set decision theory. The second stage (pattern mining) aims at solving the problem of the information mismatch. This stage is precision-oriented. A new document-ranking function has been derived by exploiting the patterns in the pattern taxonomy. The most likely relevant documents were assigned higher scores by the ranking function. Because there is a relatively small amount of documents left after the first stage, the computational cost is markedly reduced; at the same time, pattern discoveries yield more accurate results. The overall performance of the system was improved significantly. The new two-stage information filtering model has been evaluated by extensive experiments. Tests were based on the well-known IR bench-marking processes, using the latest version of the Reuters dataset, namely, the Reuters Corpus Volume 1 (RCV1). The performance of the new two-stage model was compared with both the term-based and data mining-based IF models. The results demonstrate that the proposed information filtering system outperforms significantly the other IF systems, such as the traditional Rocchio IF model, the state-of-the-art term-based models, including the BM25, Support Vector Machines (SVM), and Pattern Taxonomy Model (PTM).

Learning the kernel matrix with semidefinite programming

Kernel-based learning algorithms work by embedding the data into a Euclidean space, and then searching for linear relations among the embedded data points. The embedding is performed implicitly, by specifying the inner products between each pair of points in the embedding space. This information is contained in the so-called kernel matrix, a symmetric and positive semidefinite matrix that encodes the relative positions of all points. Specifying this matrix amounts to specifying the geometry of the embedding space and inducing a notion of similarity in the input space - classical model selection problems in machine learning. In this paper we show how the kernel matrix can be learned from data via semidefinite programming (SDP) techniques. When applied to a kernel matrix associated with both training and test data this gives a powerful transductive algorithm -using the labeled part of the data one can learn an embedding also for the unlabeled part. The similarity between test points is inferred from training points and their labels. Importantly, these learning problems are convex, so we obtain a method for learning both the model class and the function without local minima. Furthermore, this approach leads directly to a convex method for learning the 2-norm soft margin parameter in support vector machines, solving an important open problem.

Rademacher and Gaussian complexities: Risk bounds and structural results

We investigate the use of certain data-dependent estimates of the complexity of a function class, called Rademacher and Gaussian complexities. In a decision theoretic setting, we prove general risk bounds in terms of these complexities. We consider function classes that can be expressed as combinations of functions from basis classes and show how the Rademacher and Gaussian complexities of such a function class can be bounded in terms of the complexity of the basis classes. We give examples of the application of these techniques in finding data-dependent risk bounds for decision trees, neural networks and support vector machines.

Classification with a reject option using a hinge loss

We consider the problem of binary classification where the classifier can, for a particular cost, choose not to classify an observation. Just as in the conventional classification problem, minimization of the sample average of the cost is a difficult optimization problem. As an alternative, we propose the optimization of a certain convex loss function φ, analogous to the hinge loss used in support vector machines (SVMs). Its convexity ensures that the sample average of this surrogate loss can be efficiently minimized. We study its statistical properties. We show that minimizing the expected surrogate loss—the φ-risk—also minimizes the risk. We also study the rate at which the φ-risk approaches its minimum value. We show that fast rates are possible when the conditional probability P(Y=1|X) is unlikely to be close to certain critical values.

Sparseness vs estimating conditional probabilities : some asymptotic results

One of the nice properties of kernel classifiers such as SVMs is that they often produce sparse solutions. However, the decision functions of these classifiers cannot always be used to estimate the conditional probability of the class label. We investigate the relationship between these two properties and show that these are intimately related: sparseness does not occur when the conditional probabilities can be unambiguously estimated. We consider a family of convex loss functions and derive sharp asymptotic results for the fraction of data that becomes support vectors. This enables us to characterize the exact trade-off between sparseness and the ability to estimate conditional probabilities for these loss functions.

Learning the Kernel Matrix with Semi-Definite Programming

Kernel-based learning algorithms work by embedding the data into a Euclidean space, and then searching for linear relations among the embedded data points. The embedding is performed implicitly, by specifying the inner products between each pair of points in the embedding space. This information is contained in the so-called kernel matrix, a symmetric and positive definite matrix that encodes the relative positions of all points. Specifying this matrix amounts to specifying the geometry of the embedding space and inducing a notion of similarity in the input space -- classical model selection problems in machine learning. In this paper we show how the kernel matrix can be learned from data via semi-definite programming (SDP) techniques. When applied to a kernel matrix associated with both training and test data this gives a powerful transductive algorithm -- using the labelled part of the data one can learn an embedding also for the unlabelled part. The similarity between test points is inferred from training points and their labels. Importantly, these learning problems are convex, so we obtain a method for learning both the model class and the function without local minima. Furthermore, this approach leads directly to a convex method to learn the 2-norm soft margin parameter in support vector machines, solving another important open problem. Finally, the novel approach presented in the paper is supported by positive empirical results.

Microarray expression profiling in melanoma reveals a BRAF mutation signature

We have used microarray gene expression profiling and machine learning to predict the presence of BRAF mutations in a panel of 61 melanoma cell lines. The BRAF gene was found to be mutated in 42 samples (69%) and intragenic mutations of the NRAS gene were detected in seven samples (11%). No cell line carried mutations of both genes. Using support vector machines, we have built a classifier that differentiates between melanoma cell lines based on BRAF mutation status. As few as 83 genes are able to discriminate between BRAF mutant and BRAF wild-type samples with clear separation observed using hierarchical clustering. Multidimensional scaling was used to visualize the relationship between a BRAF mutation signature and that of a generalized mitogen-activated protein kinase (MAPK) activation (either BRAF or NRAS mutation) in the context of the discriminating gene list. We observed that samples carrying NRAS mutations lie somewhere between those with or without BRAF mutations. These observations suggest that there are gene-specific mutation signals in addition to a common MAPK activation that result from the pleiotropic effects of either BRAF or NRAS on other signaling pathways, leading to measurably different transcriptional changes.

Supplementary Information : Hogan, Holland, Holloway, Petit and Read : Read Classification for Next Generation Sequencing, ESANN 2013, April 2013

This item provides supplementary materials for the paper mentioned in the title, specifically a range of organisms used in the study. The full abstract for the main paper is as follows: Next Generation Sequencing (NGS) technologies have revolutionised molecular biology, allowing clinical sequencing to become a matter of routine. NGS data sets consist of short sequence reads obtained from the machine, given context and meaning through downstream assembly and annotation. For these techniques to operate successfully, the collected reads must be consistent with the assumed species or species group, and not corrupted in some way. The common bacterium Staphylococcus aureus may cause severe and life-threatening infections in humans,with some strains exhibiting antibiotic resistance. In this paper, we apply an SVM classifier to the important problem of distinguishing S. aureus sequencing projects from alternative pathogens, including closely related Staphylococci. Using a sequence k-mer representation, we achieve precision and recall above 95%, implicating features with important functional associations.

A fast dual algorithm for kernel logistic regression

This paper gives a new iterative algorithm for kernel logistic regression. It is based on the solution of a dual problem using ideas similar to those of the Sequential Minimal Optimization algorithm for Support Vector Machines. Asymptotic convergence of the algorithm is proved. Computational experiments show that the algorithm is robust and fast. The algorithmic ideas can also be used to give a fast dual algorithm for solving the optimization problem arising in the inner loop of Gaussian Process classifiers.

Reducing the babel in plant volatile communication: using the forest to see the trees

While plants of a single species emit a diversity of volatile organic compounds (VOCs) to attract or repel interacting organisms, these specific messages may be lost in the midst of the hundreds of VOCs produced by sympatric plants of different species, many of which may have no signal content. Receivers must be able to reduce the babel or noise in these VOCs in order to correctly identify the message. For chemical ecologists faced with vast amounts of data on volatile signatures of plants in different ecological contexts, it is imperative to employ accurate methods of classifying messages, so that suitable bioassays may then be designed to understand message content. We demonstrate the utility of `Random Forests' (RF), a machine-learning algorithm, for the task of classifying volatile signatures and choosing the minimum set of volatiles for accurate discrimination, using datam from sympatric Ficus species as a case study. We demonstrate the advantages of RF over conventional classification methods such as principal component analysis (PCA), as well as data-mining algorithms such as support vector machines (SVM), diagonal linear discriminant analysis (DLDA) and k-nearest neighbour (KNN) analysis. We show why a tree-building method such as RF, which is increasingly being used by the bioinformatics, food technology and medical community, is particularly advantageous for the study of plant communication using volatiles, dealing, as it must, with abundant noise.

Rough Core Vector Clustering

Support Vector Clustering has gained reasonable attention from the researchers in exploratory data analysis due to firm theoretical foundation in statistical learning theory. Hard Partitioning of the data set achieved by support vector clustering may not be acceptable in real world scenarios. Rough Support Vector Clustering is an extension of Support Vector Clustering to attain a soft partitioning of the data set. But the Quadratic Programming Problem involved in Rough Support Vector Clustering makes it computationally expensive to handle large datasets. In this paper, we propose Rough Core Vector Clustering algorithm which is a computationally efficient realization of Rough Support Vector Clustering. Here Rough Support Vector Clustering problem is formulated using an approximate Minimum Enclosing Ball problem and is solved using an approximate Minimum Enclosing Ball finding algorithm. Experiments done with several Large Multi class datasets such as Forest cover type, and other Multi class datasets taken from LIBSVM page shows that the proposed strategy is efficient, finds meaningful soft cluster abstractions which provide a superior generalization performance than the SVM classifier.

Efficient Algorithms for Linear Summed Error Structural SVMs

Structural Support Vector Machines (SSVMs) have become a popular tool in machine learning for predicting structured objects like parse trees, Part-of-Speech (POS) label sequences and image segments. Various efficient algorithmic techniques have been proposed for training SSVMs for large datasets. The typical SSVM formulation contains a regularizer term and a composite loss term. The loss term is usually composed of the Linear Maximum Error (LME) associated with the training examples. Other alternatives for the loss term are yet to be explored for SSVMs. We formulate a new SSVM with Linear Summed Error (LSE) loss term and propose efficient algorithms to train the new SSVM formulation using primal cutting-plane method and sequential dual coordinate descent method. Numerical experiments on benchmark datasets demonstrate that the sequential dual coordinate descent method is faster than the cutting-plane method and reaches the steady-state generalization performance faster. It is thus a useful alternative for training SSVMs when linear summed error is used.

Hybrid Working Set Algorithm for SVM Learning With a Kernel Coprocessor on FPGA

Support vector machines (SVM) are a popular class of supervised models in machine learning. The associated compute intensive learning algorithm limits their use in real-time applications. This paper presents a fully scalable architecture of a coprocessor, which can compute multiple rows of the kernel matrix in parallel. Further, we propose an extended variant of the popular decomposition technique, sequential minimal optimization, which we call hybrid working set (HWS) algorithm, to effectively utilize the benefits of cached kernel columns and the parallel computational power of the coprocessor. The coprocessor is implemented on Xilinx Virtex 7 field-programmable gate array-based VC707 board and achieves a speedup of upto 25x for kernel computation over single threaded computation on Intel Core i5. An application speedup of upto 15x over software implementation of LIBSVM and speedup of upto 23x over SVMLight is achieved using the HWS algorithm in unison with the coprocessor. The reduction in the number of iterations and sensitivity of the optimization time to variation in cache size using the HWS algorithm are also shown.

Síntese de árvores de padrões Fuzzy através de Programação Genética Cartesiana.

Esta dissertação apresenta um sistema de indução de classificadores fuzzy. Ao invés de utilizar a abordagem tradicional de sistemas fuzzy baseados em regras, foi utilizado o modelo de Árvore de Padrões Fuzzy(APF), que é um modelo hierárquico, com uma estrutura baseada em árvores que possuem como nós internos operadores lógicos fuzzy e as folhas são compostas pela associação de termos fuzzy com os atributos de entrada. O classificador foi obtido sintetizando uma árvore para cada classe, esta árvore será uma descrição lógica da classe o que permite analisar e interpretar como é feita a classificação. O método de aprendizado originalmente concebido para a APF foi substituído pela Programação Genética Cartesiana com o intuito de explorar melhor o espaço de busca. O classificador APF foi comparado com as Máquinas de Vetores de Suporte, K-Vizinhos mais próximos, florestas aleatórias e outros métodos Fuzzy-Genéticos em diversas bases de dados do UCI Machine Learning Repository e observou-se que o classificador APF apresenta resultados competitivos. Ele também foi comparado com o método de aprendizado original e obteve resultados comparáveis com árvores mais compactas e com um menor número de avaliações.