Gene expression-based prediction of malignancies

Molecular classification of malignancies can potentially stratify patients into distinct subclasses not detectable using traditional classification of tumors, opening new perspectives on the diagnosis and personalized therapy of polygenic diseases. In this paper we present a brief overview of our work on gene expression based prediction of malignancies, starting from the dichotomic classification problem of normal versus tumoural tissues, to multiclasss cancer diagnosis and to functional class discovery and gene selection problems. The last part of this work present preliminary results about the applicatin of ensembles of SVMs based on bias-variance decomposition of the error to the analysis of gene expression data of malignant tissues

Multi-class Heterogeneous Domain Adaptation

© 2019 Joey Tianyi Zhou, Ivor W. Tsang, Sinno Jialin Pan, Mingkui Tan. A crucial issue in heterogeneous domain adaptation (HDA) is the ability to learn a feature mapping between different types of features across domains. Inspired by language translation, a word translated from one language corresponds to only a few words in another language, we present an efficient method named Sparse Heterogeneous Feature Representation (SHFR) in this paper for multi-class HDA to learn a sparse feature transformation between domains with multiple classes. Specifically, we formulate the problem of learning the feature transformation as a compressed sensing problem by building multiple binary classifiers in the target domain as various measurement sensors, which are decomposed from the target multi-class classification problem. We show that the estimation error of the learned transformation decreases with the increasing number of binary classifiers. In other words, for adaptation across heterogeneous domains to be successful, it is necessary to construct a sufficient number of incoherent binary classifiers from the original multi-class classification problem. To achieve this, we propose to apply the error correcting output correcting (ECOC) scheme to generate incoherent classifiers. To speed up the learning of the feature transformation across domains, we apply an efficient batch-mode algorithm to solve the resultant nonnegative sparse recovery problem. Theoretically, we present a generalization error bound of our proposed HDA method under a multi-class setting. Lastly, we conduct extensive experiments on both synthetic and real-world datasets to demonstrate the superiority of our proposed method over existing state-of-the-art HDA methods in terms of prediction accuracy and training efficiency

Learning error-correcting representations for multi-class problems

[eng] Real life is full of multi-class decision tasks. In the Pattern Recognition field, several method- ologies have been proposed to deal with binary problems obtaining satisfying results in terms of performance. However, the extension of very powerful binary classifiers to the multi-class case is a complex task. The Error-Correcting Output Codes framework has demonstrated to be a very powerful tool to combine binary classifiers to tackle multi-class problems. However, most of the combinations of binary classifiers in the ECOC framework overlook the underlay- ing structure of the multi-class problem. In addition, is still unclear how the Error-Correction of an ECOC design is distributed among the different classes. In this dissertation, we are interested in tackling critic problems of the ECOC framework, such as the definition of the number of classifiers to tackle a multi-class problem, how to adapt the ECOC coding to multi-class data and how to distribute error-correction among different pairs of categories. In order to deal with this issues, this dissertation describes several proposals. 1) We define a new representation for ECOC coding matrices that expresses the pair-wise codeword separability and allows for a deeper understanding of how error-correction is distributed among classes. 2) We study the effect of using a logarithmic number of binary classifiers to treat the multi-class problem in order to obtain very efficient models. 3) In order to search for very compact ECOC coding matrices that take into account the distribution of multi-class data we use Genetic Algorithms that take into account the constraints of the ECOC framework. 4) We propose a discrete factorization algorithm that finds an ECOC configuration that allocates the error-correcting capabilities to those classes that are more prone to errors. The proposed methodologies are evaluated on different real and synthetic data sets: UCI Machine Learning Repository, handwriting symbols, traffic signs from a Mobile Mapping System, and Human Pose Recovery. The results of this thesis show that significant perfor- mance improvements are obtained on traditional coding ECOC designs when the proposed ECOC coding designs are taken into account. [[spa] En la vida cotidiana las tareas de decisión multi-clase surgen constantemente. En el campo de Reconocimiento de Patrones muchos métodos de clasificación binaria han sido propuestos obteniendo resultados altamente satisfactorios en términos de rendimiento. Sin embargo, la extensión de estos sofisticados clasificadores binarios al contexto multi-clase es una tarea compleja. En este ámbito, las estrategias de Códigos Correctores de Errores (CCEs) han demostrado ser una herramienta muy potente para tratar la combinación de clasificadores binarios. No obstante, la mayoría de arquitecturas de combinación de clasificadores binarios negligen la estructura del problema multi-clase. Sin embargo, el análisis de la distribución de corrección de errores entre clases es aún un problema abierto. En esta tesis doctoral, nos centramos en tratar problemas críticos de los códigos correctores de errores; la definición del número de clasificadores necesarios para tratar un problema multi-clase arbitrario; la adaptación de los problemas binarios al problema multi-clase y cómo distribuir la corrección de errores entre clases. Para dar respuesta a estas cuestiones, en esta tesis doctoral describimos varias propuestas. 1) Definimos una nueva representación para CCEs que expresa la separabilidad entre pares de códigos y nos permite una mejor comprensión de cómo se distribuye la corrección de errores entre distintas clases. 2) Estudiamos el efecto de usar un número logarítmico de clasificadores binarios para tratar el problema multi-clase con el objetivo de obtener modelos muy eficientes. 3) Con el objetivo de encontrar modelos muy eficientes que tienen en cuenta la estructura del problema multi-clase utilizamos algoritmos genéticos que tienen en cuenta las restricciones de los ECCs. 4) Pro- ponemos un algoritmo de factorización de matrices discreta que encuentra ECCs con una configuración que distribuye corrección de error a aquellas categorías que son más propensas a tener errores. Las metodologías propuestas son evaluadas en distintos problemas reales y sintéticos como por ejemplo: Repositorio UCI de Aprendizaje Automático, reconocimiento de símbolos escritos, clasificación de señales de tráfico y reconocimiento de la pose humana. Los resultados obtenidos en esta tesis muestran mejoras significativas en rendimiento comparados con los diseños tradiciones de ECCs cuando las distintas propuestas se tienen en cuenta

Error-correcting codes and applications to large scale classification systems

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2009.Includes bibliographical references (p. 37-39).In this thesis, we study the performance of distributed output coding (DOC) and error-Correcting output coding (ECOC) as potential methods for expanding the class of tractable machine-learning problems. Using distributed output coding, we were able to scale a neural-network-based algorithm to handle nearly 10,000 output classes. In particular, we built a prototype OCR engine for Devanagari and Korean texts based upon distributed output coding. We found that the resulting classifiers performed better than existing algorithms, while maintaining small size. Error-correction, however, was found to be ineffective at increasing the accuracy of the ensemble. For each language, we also tested the feasibility of automatically finding a good codebook. Unfortunately, the results in this direction were primarily negative.by Jeremy Scott Hurwitz.M.Eng

ROC curves for regression

“NOTICE: this is the author’s version of a work that was accepted for publication in Pattern Recognition. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Pattern Recognition Volume 46, Issue 12, December 2013, Pages 3395–3411 DOI: 10.1016/j.patcog.2013.06.014Receiver Operating Characteristic (ROC) analysis is one of the most popular tools for the visual assessment and understanding of classifier performance. In this paper we present a new representation of regression models in the so-called regression ROC (RROC) space. The basic idea is to represent over-estimation against under-estimation. The curves are just drawn by adjusting a shift, a constant that is added (or subtracted) to the predictions, and plays a similar role as a threshold in classification. From here, we develop the notions of optimal operating condition, convexity, dominance, and explore several evaluation metrics that can be shown graphically, such as the area over the RROC curve (AOC). In particular, we show a novel and significant result: the AOC is equivalent to the error variance. We illustrate the application of RROC curves to resource estimation, namely the estimation of software project effort.I would like to thank Peter Flach and Nicolas Lachiche for some very useful comments and corrections on earlier versions of this paper, especially the suggestion of drawing normalised curves (dividing x-axis and y-axis by n). This work was supported by the MEC/MINECO projects CONSOLIDER-INGENIO CSD2007-00022 and TIN 2010-21062-C02-02, GVA project Prometeo/2008/051, the COST - European Cooperation in the field of Scientific and Technical Research IC0801 AT, and the REFRAME project granted by the European Coordinated Research on Long-term Challenges in Information and Communication Sciences & Technologies ERA-Net (CHIST-ERA), and funded by the respective national research councils and ministries.Hernández-Orallo, J. (2013). ROC curves for regression. Pattern Recognition. 46(12):3395-3411. https://doi.org/10.1016/j.patcog.2013.06.014S33953411461

Multi-feature approach for writer-independent offline signature verification

Some of the fundamental problems facing handwritten signature verification are the large number of users, the large number of features, the limited number of reference signatures for training, the high intra-personal variability of the signatures and the unavailability of forgeries as counterexamples. This research first presents a survey of offline signature verification techniques, focusing on the feature extraction and verification strategies. The goal is to present the most important advances, as well as the current challenges in this field. Of particular interest are the techniques that allow for designing a signature verification system based on a limited amount of data. Next is presented a novel offline signature verification system based on multiple feature extraction techniques, dichotomy transformation and boosting feature selection. Using multiple feature extraction techniques increases the diversity of information extracted from the signature, thereby producing features that mitigate intra-personal variability, while dichotomy transformation ensures writer-independent classification, thus relieving the verification system from the burden of a large number of users. Finally, using boosting feature selection allows for a low cost writer-independent verification system that selects features while learning. As such, the proposed system provides a practical framework to explore and learn from problems with numerous potential features. Comparison of simulation results from systems found in literature confirms the viability of the proposed system, even when only a single reference signature is available. The proposed system provides an efficient solution to a wide range problems (eg. biometric authentication) with limited training samples, new training samples emerging during operations, numerous classes, and few or no counterexamples