Włodzisław Duch

A shared task involving multi-label classification of clinical free text

This paper reports on a shared task involving the assignment of ICD-9-CM codes to radiology reports. Two features distinguished this task from previous shared tasks in the biomedical domain. One is that it resulted in the first freely distributable corpus of fully anonymized clinical text. This resource is permanently available and will (we hope) facilitate future research. The other key feature of the task is that it required categorization with respect to a large and commercially significant set of labels. The number of participants was larger than in any previous biomedical challenge task. We describe the data production process and the evaluation measures, and give a preliminary analysis of the results. Many systems performed at levels approaching the inter-coder agreement, suggesting that human-like performance on this task is within the reach of currently available technologies.

Computational Intelligence Methods For Rule-Based Data Understanding

In many applications, black-box prediction is not satisfactory, and understanding the data is of critical importance. Typically, approaches useful for understanding of data involve logical rules, evaluate similarity to prototypes, or are based on visualization or graphical methods. This paper is focused on the extraction and use of logical rules for data understanding. All aspects of rule generation, optimization, and application are described, including the problem of finding good symbolic descriptors for continuous data, tradeoffs between accuracy and simplicity at the rule-extraction stage, and tradeoffs between rejection and error level at the rule optimization stage. Stability of rule-based description, calculation of probabilities from rules, and other related issues are also discussed. Major approaches to extraction of logical rules based on neural networks, decision trees, machine learning, and statistical methods are introduced. Optimization and application issues for sets of logical rules are described. Applications of such methods to benchmark and real-life problems are reported and illustrated with simple logical rules for many datasets. Challenges and new directions for research are outlined.

Feature space mapping as a universal adaptive system

Abstract The most popular realizations of adaptive systems are based on the neural network type of algorithms, in particular feedforward multilayered perceptrons trained by backpropagation of error procedures. In this paper an alternative approach based on multidimensional separable localized functions centered at the data clusters is proposed. In comparison with the neural networks that use delocalized transfer functions this approach allows for full control of the basins of attractors of all stationary points. Slow learning procedures are replaced by the explicit construction of the landscape function followed by the optimization of adjustable parameters using gradient techniques or genetic algorithms. Retrieving information does not require searches in multidimensional subspaces but it is factorized into a series of one-dimensional searches. Feature Space Mapping is applicable to learning not only from facts but also from general laws and may be treated as a fuzzy expert system (neurofuzzy system). The number of nodes (fuzzy rules) is growing as the network creates new nodes for novel data but the search time is sublinear in the number of rules or data clusters stored. Such a system may work as a universal classificator, approximator and reasoning system. Examples of applications for the identification of spectra (classification), intelligent databases (association) and for the analysis of simple electrical circuits (expert system type) are given.

Artificial Neural Networks and Machine Learning – ICANN 2012

A complex-valued multilayer perceptron (MLP) can approximate a periodic or unbounded function, which cannot be easily realized by a real-valued MLP. Its search space is full of crevasse-like forms having huge condition numbers; thus, it is very hard for existing methods to perform efficient search in such a space. The space also includes the structure of reducibility mapping. The paper proposes a new search method for a complex-valued MLP, which employs both eigen vector descent and reducibility mapping, aiming to stably find excellent solutions in such a space. Our experiments showed the proposed method worked well.

Feature Selection for High-Dimensional Data — A Pearson Redundancy Based Filter

An algorithm for filtering information based on the Pearson χ2 test approach has been implemented and tested on feature selection. This test is frequently used in biomedical data analysis and should be used only for nominal (discretized) features. This algorithm has only one parameter, statistical confidence level that two distributions are identical. Empirical comparisons with four other state-of-the-art features selection algorithms (FCBF, CorrSF, ReliefF and ConnSF) are very encouraging.

Comparison of Shannon, Renyi and Tsallis Entropy Used in Decision Trees

Shannon entropy used in standard top-down decision trees does not guarantee the best generalization. Split criteria based on generalized entropies offer different compromise between purity of nodes and overall information gain. Modified C4.5 decision trees based on Tsallis and Renyi entropies have been tested on several high-dimensional microarray datasets with interesting results. This approach may be used in any decision tree and information selection algorithm.

Machine learning competition in immunology – Prediction of HLA class I binding peptides

Experimental studies of immune system and related applications such as characterization of immune responses against pathogens, vaccine design, or optimization of therapies are combinatorially complex, time-consuming and expensive. The main methods for large-scale identification of T-cell epitopes from pathogens or cancer proteomes involve either reverse immunology or high-throughput mass spectrometry (HTMS). Reverse immunology approaches involve pre-screening of proteomes by computational algorithms, followed by experimental validation of selected targets (Mora et al., 2006; De Groot et al., 2008; Larsen et al., 2010). HTMS involves HLA typing, immunoaffinity chromatography of HLA molecules, HLA extraction, and chromatography combined with tandem mass spectrometry, followed by the application of computational algorithms for peptide characterization (Bassani-Sternberg et al., 2010). Hundreds of naturally processed HLA class I associated peptides have been identified in individual studies using HTMS in normal (Escobar et al., 2008), cancer (Antwi et al., 2009; Bassani-Sternberg et al., 2010), autoimmunity-related (Ben Dror et al., 2010), and infected samples (Wahl et al, 2010). Computational algorithms are essential steps in highthroughput identification of T-cell epitope candidates using both reverse immunology and HTMS approaches. Peptide binding to MHC molecules is the single most selective step in defining T cell epitope and the accuracy of computational algorithms for prediction of peptide binding, therefore, determines the accuracy of the overall method. Computational predictions of peptide binding to HLA, both class I and class II, use a variety of algorithms ranging from binding motifs to advanced machine learning techniques (Brusic et al., 2004; Lafuente and Reche, 2009) and standards for their

Comparison of feature ranking methods based on information entropy

A comparison between five feature ranking methods based on entropy is presented on artificial and real datasets. Feature ranking method using /spl chi//sup 2/ statistics gives results that are very similar to the entropy-based methods. The quality of feature rankings obtained by these methods is evaluated using the decision tree and the nearest neighbor classifier with growing number of most important features. Significant differences are found in some cases, but there is no single best index that works best for all data and all classifiers. Therefore to be sure that a subset of features giving highest accuracy has been selected requires the use of many different indices.

GRMS or Graphical Representation of Model Spaces

1. Preface.- 2. Introduction.- I: Architecture of Model Spaces.- 1.1 Introducing graphical representation.- 1.2 Labeling and ordering the paths.- 1.3 ? z-adapted graphs in different forms.- 1.4