Strong compound-risk factors: Efficient discovery through emerging patterns and contrast sets

Odds ratio (OR), relative risk (RR) (risk ratio), and absolute risk reduction (ARR) (risk difference) are biostatistics measurements that are widely used for identifying significant risk factors in dichotomous groups of subjects. In the past, they have often been used to assess simple risk factors. In this paper, we introduce the concept of compound-risk factors to broaden the applicability of these statistical tests for assessing factor interplays. We observe that compound-risk factors with a high risk ratio or a big risk difference have an one-to-one correspondence to strong emerging patterns or strong contrast sets-two types of patterns that have been extensively studied in the data mining field. Such a relationship has been unknown to researchers in the past, and efficient algorithms for discovering strong compound-risk factors have been lacking. In this paper, we propose a theoretical framework and a new algorithm that unify the discovery of compound-risk factors that have a strong OR, risk ratio, or a risk difference. Our method guarantees that all patterns meeting a certain test threshold can be efficiently discovered. Our contribution thus represents the first of its kind in linking the risk ratios and ORs to pattern mining algorithms, making it possible to find compound-risk factors in large-scale data sets. In addition, we show that using compound-risk factors can improve classification accuracy in probabilistic learning algorithms on several disease data sets, because these compound-risk factors capture the interdependency between important data attributes. © 2007 IEEE

Ассоциативная классификация: аналитический обзор. Часть 1

The paper topic is associative classification intended for processing of big data. It formulates corresponding problem statement and introduces basic concepts and formal notation used in associative classification. An extended overview and comparative analysis of the early approaches, models and algorithms for associative classification form the main paper contents. The paper assesses the contribution of the first papers devoted to associative classification to the development of this area and formulates goals of the further research.В работе описаны основные результаты, модели и методы, разработанные в области ассоциативной классификации, ориентированные на обработку данных большого объема. В работе дается постановка задачи ассоциативной классификации, вводится необходимая терминология и формальные обозначения, используемые в ассоциативной классификации. Приводится описание и сравнительный анализ ранних подходов, методов и конкретных алгоритмов ассоциативной классификации. Дается оценка вклада первых работ, посвящённых ассоциативной классификации, в развитие этого направления

Emerging Chemical Patterns for Virtual Screening and Knowledge Discovery

The adaptation and evaluation of contemporary data mining methods to chemical and biological problems is one of major areas of research in chemoinformatics. Currently, large databases containing millions of small organic compounds are publicly available, and the need for advanced methods to analyze these data increases. Most methods used in chemoinformatics, e.g. quantitative structure activity relationship (QSAR) modeling, decision trees and similarity searching, depend on the availability of large high-quality training data sets. However, in biological settings, the availability of these training sets is rather limited. This is especially true for early stages of drug discovery projects where typically only few active molecules are available. The ability of chemoinformatic methods to generalize from small training sets and accurately predict compound properties such as activity, ADME or toxicity is thus crucially important. Additionally, biological data such as results from high-throughput screening (HTS) campaigns is heavily biased towards inactive compounds. This bias presents an additional challenge for the adaptation of data mining methods and distinguishes chemoinformatics data from the standard benchmark scenarios in the data mining community. Even if a highly accurate classifier would be available, it is still necessary to evaluate the predictions experimentally. These experiments are both costly and time-consuming and the need to optimize resources has driven the development of integrated screening protocols which try to minimize experimental efforts but still reaching high hit rates of active compounds. This integration, termed “sequential screening” benefits from the complementary nature of experimental HTS and computational virtual screening (VS) methods. In this thesis, a current data mining framework based on class-specific nominal combinations of attributes (emerging patterns) is adapted to chemoinformatic problems and thoroughly evaluated. Combining emerging pattern methodology and the well-known notion of chemical descriptors, emerging chemical patterns (ECP) are defined as class- specific descriptor value range combinations. Each pattern can be thought of as a region in chemical space which is dominated by compounds from one class only. Based on chemical patterns, several experiments are presented which evaluate the performance of pattern-based knowledge mining, property prediction, compound ranking and sequential screening. ECP-based classification is implemented and evaluated on four activity classes for the prediction of compound potency levels. Compared to decision trees and a Bayesian binary QSAR method, ECP-based classification produces high accuracy in positive and negative classes even on the basis of very small training set, a result especially valuable to chemoinformatic problems. The simple nature of ECPs as class-specific descriptor value range combinations makes them easily interpretable. This is used to related ECPs to changes in the interaction network of protein-ligand complexes when the binding conformation is replaced by a computer-modeled conformation in a knowledge mining experiment. ECPs capture well-known energetic differences between binding and energy-minimized conformations and additionally present new insight into these differences on a class level analysis. Finally, the integration of ECPs and HTS is evaluated in simulated lead-optimization and sequential screening experiments. The high accuracy on very small training sets is exploited to design an iterative simulated lead optimization experiment based on experimental evaluation of randomly selected small training sets. In each iteration, all compounds predicted to be weakly active are removed and the remaining compound set is enriched with highly potent compounds. On this basis, a simulated sequential screening experiment shows that ECP-based ranking recovers 19% of available compounds while reducing the “experimental” effort to 0.2%. These findings illustrate the potential of sequential screening protocols and hopefully increase the popularity of this relatively new methodology

Ассоциативная классификация: аналитический обзор. Часть 2

The paper continues the survey of associative classification in context of big data processing. An extended overview and comparative analysis of the modern approaches, models and algorithms developed for associative classification form the main paper contents. In conclusion, the paper outlines the main advantages and drawbacks of associative classification, as well as evaluates its capabilities from big data processing perspective.В работе продолжается рассмотрение основных результатов, моделей и методов, разработанных в области ассоциативной классификации, ориентированных на обработку данных большого объема. Дается анализ подходов, методов и алгоритмов, разработанных в области ассоциативной классификации к настоящему времени. В заключении формулируются достоинства и недостатки ассоциативной классификации как модели машинного обучения, а также дается оценка перспектив ее использования в интеллектуальном анализе больших данных

LODE: A distance-based classifier built on ensembles of positive and negative observations

International audienceCurrent work on assembling a set of local patterns such as rules and class association rules into a global model for the prediction of a target usually focuses on the identification of the minimal set of patterns that cover the training data. In this paper we present a different point of view: the model of a class has been built with the purpose to emphasise the typical features of the examples of the class. Typical features are modelled by frequent itemsets extracted from the examples and constitute a new representation space of the examples of the class. Prediction of the target class of test examples occurs by computation of the distance between the vector representing the example in the space of the itemsets of each class and the vectors representing the classes. It is interesting to observe that in the distance computation the critical contribution to the discrimination between classes is given not only by the itemsets of the class model that match the example but also by itemsets that do not match the example. These absent features constitute some pieces of information on the examples that can be considered for the prediction and should not be disregarded. Second, absent features are more abundant in the wrong classes than in the correct ones and their number increases the distance between the example vector and the negative class vectors. Furthermore, since absent features are frequent features in their respective classes, they make the prediction more robust against over-fitting and noise. The usage of features absent in the test example is a novel issue in classification: existing learners usually tend to select the best local pattern that matches the example - and do not consider the abundance of other patterns that do not match it. We demonstrate the validity of our observations and the effectiveness of LODE, our learner, by means of extensive empirical experiments in which we compare the prediction accuracy ofLODE with a consistent set of classifiers of the state of the art. In this paper we also report the methodology that we adopted in order to determine automatically the setting of the learner and of its parameters

Attribute Oriented Induction High Level Emerging Pattern (AOI-HEP)

Attribute-Oriented Induction of High-level Emerging Pattern(AOI-HEP) is a combination of Attribute Oriented Induction (AOI) and Emerging Patterns (EP). AOI is a summarisation algorithm that compact a given dataset into small conceptual descriptions, where each attribute has a defined concept hierarchy. This presents patterns are easily readable and understandable.Emerging patterns are patterns discovered between two datasets and between two time periods such that patterns found in the first dataset have either grown (or reduced) in size, totally disappeared or new ones have emerged. AOI-HEP is not influenced by border-based algorithm like in EP mining algorithms. It is desirable therefore that we obtain summarised emerging patterns between two datasets. We propose High-level Emerging Pattern (HEP) algorithm. The main purpose of combining AOI and EP is to use the typical strength of AOI and EP to extract important high-level emerging patterns from data. The AOI characteristic rule algorithm was run twice with two input datasets,to create two rulesets which are then processed with the HEP algorithm. Firstly, the HEP algorithm starts with cartesian product between two rulesets which eliminates rules in rulesets by computing similarity metric (a categorization of attribute comparisons). Secondly, the output rules between two rulesets from the metric similarity are discriminated by computing a growth rate value to find ratio of supports between rules from two rulesets. The categorization of attribute comparisons is based on similarity hierarchy level. The categorisation of attributes was found to be with three options in how they subsume each other. These were Total Subsumption HEP (TSHEP), Subsumption Overlapping HEP (SOHEP) and Total Overlapping HEP (TOHEP) patterns. Meanwhile, from certain similarity hierarchy level and values, we can mine frequent and similar patterns that create discriminant rules. We used four large real datasets from UCI machine learning repository and discovered valuable HEP patterns including strong discriminant rules, frequent and similar patterns. Moreover, the experiments showed that most datasets have SOHEP but not TSHEP and TOHEP and the most rarely found were TOHEP. Since AOI- iii HEP can strongly discriminate high-level data, assuredly AOI-HEP can be implemented to discriminate datasets such as finding bad and good customers for banking loan systems or credit card applicants etc. Moreover, AOI-HEP can be implemented to mine similar patterns, for instance, mining similar customer loan patterns etc

Unmasking Clever Hans Predictors and Assessing What Machines Really Learn

Current learning machines have successfully solved hard application problems, reaching high accuracy and displaying seemingly "intelligent" behavior. Here we apply recent techniques for explaining decisions of state-of-the-art learning machines and analyze various tasks from computer vision and arcade games. This showcases a spectrum of problem-solving behaviors ranging from naive and short-sighted, to well-informed and strategic. We observe that standard performance evaluation metrics can be oblivious to distinguishing these diverse problem solving behaviors. Furthermore, we propose our semi-automated Spectral Relevance Analysis that provides a practically effective way of characterizing and validating the behavior of nonlinear learning machines. This helps to assess whether a learned model indeed delivers reliably for the problem that it was conceived for. Furthermore, our work intends to add a voice of caution to the ongoing excitement about machine intelligence and pledges to evaluate and judge some of these recent successes in a more nuanced manner.Comment: Accepted for publication in Nature Communication