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Motivation: Cancer is not a single disease and involves different subtypes characterized by different sets of molecules. Patients with different subtypes of cancer often react heterogeneously towards the same treatment. Currently, clinical diagnoses rather than molecular profiles are used to determine the most suitable treatment. A molecular level approach will allow a more precise and informed way for making treatment decisions, leading to a better survival chance and less suffering of patients. Although many computational methods have been proposed to identify cancer subtypes at molecular level, to the best of our knowledge none of them are designed to discover subtypes with heterogeneous treatment responses., Results: In this article we propose the Survival Causal Tree (SCT) method. SCT is designed to discover patient subgroups with heterogeneous treatment effects from censored observational data. Results on TCGA breast invasive carcinoma and glioma datasets have shown that for each subtype identified by SCT, the patients treated with radiotherapy exhibit significantly different relapse free survival pattern when compared to patients without the treatment. With the capability to identify cancer subtypes with heterogeneous treatment responses, SCT is useful in helping to choose the most suitable treatment for individual patients., Availability and Implementation: Data and code are available at https://github.com/WeijiaZhang24/SurvivalCausalTree ., Contact: weijia.zhang@mymail.uinsa.edu.au., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com)

The use of distance metrics such as the Euclidean or Manhattan distance for nearest neighbour algorithms allows for interpretation as a geometric model, and it has been widely assumed that the metric axioms are a necessary condition for many data mining tasks. We show that this assumption can in fact be an impediment to producing effective models. We propose to use mass-based dissimilarity, which employs estimates of the probability mass to measure dissimilarity, to replace the distance metric. This substitution effectively converts nearest neighbour (NN) algorithms into lowest probability mass neighbour (LMN) algorithms. Both types of algorithms employ exactly the same algorithmic procedures, except for the substitution of the dissimilarity measure. We show that LMN algorithms overcome key shortcomings of NN algorithms in classification and clustering tasks. Unlike existing generalised data independent metrics (e.g., quasi-metric, meta-metric, semi-metric, peri-metric) and data dependent metrics, the proposed mass-based dissimilarity is unique because its self-dissimilarity is data dependent and non-constant. [ABSTRACT FROM AUTHOR]

In a multi-label learning task, an object possesses multiple concepts where each concept is represented by a class label. Previous studies on multi-label learning have focused on a fixed set of class labels, i.e., the class label set of test data is the same as that in the training set. In many applications, however, the environment is dynamic and new concepts may emerge in a data stream. In order to maintain a good predictive performance in this environment, a multi-label learning method must have the ability to detect and classify instances with emerging new labels. To this end, we propose a new approach called Multi-label learning with Emerging New Labels (MuENL). It has three functions: classify instances on currently known labels, detect the emergence of a new label, and construct a new classifier for each new label that works collaboratively with the classifier for known labels. In addition, we show that MuENL can be easily extended to handle sparse high dimensional data streams by simply reducing the original dimensionality, and then applying MuENL on the reduced dimensional space. Our empirical evaluation shows the effectiveness of MuENL on several benchmark datasets and MuENLHD on the sparse high dimensional Weibo dataset. [ABSTRACT FROM AUTHOR]

It is well-known that exploiting label correlations is important to multi-label learning. Existing approaches either assume that the label correlations are global and shared by all instances; or that the label correlations are local and shared only by a data subset. In fact, in the real-world applications, both cases may occur that some label correlations are globally applicable and some are shared only in a local group of instances. Moreover, it is also a usual case that only partial labels are observed, which makes the exploitation of the label correlations much more difficult. That is, it is hard to estimate the label correlations when many labels are absent. In this paper, we propose a new multi-label approach GLOCAL dealing with both the full-label and the missing-label cases, exploiting global and local label correlations simultaneously, through learning a latent label representation and optimizing label manifolds. The extensive experimental studies validate the effectiveness of our approach on both full-label and missing-label data. [ABSTRACT FROM PUBLISHER]

One of the fundamental issues in crowdsourcing is the trade-off between the number of workers needed for high-accuracy aggregation and the budget to pay. To save cost, it is important to ensure high quality of the crowd-sourced labels, hence the total cost on label collection will be reduced. Since the confidence of the workers often has a close relationship with their abilities, a possible way for quality control is to request the workers to return the labels only when they feel confident, by means of providing them with an ‘unsure’ option. On the other hand, allowing workers to choose the unsure option can potentially waste part of the budget. In this work, we conduct an analysis towards understanding when providing the unsure option indeed leads to significant cost reduction, as well as how the confidence threshold might be set. We also propose an online mechanism, which is an alternative for threshold selection when the estimation of the crowd ability distribution is difficult. [ABSTRACT FROM AUTHOR]

Multi-label learning studies the problem where each example is represented by a single instance while associated with a set of labels simultaneously. During the past decade, significant amount of progresses have been made toward this emerging machine learning paradigm. This paper aims to provide a timely review on this area with emphasis on state-of-the-art multi-label learning algorithms. Firstly, fundamentals on multi-label learning including formal definition and evaluation metrics are given. Secondly and primarily, eight representative multi-label learning algorithms are scrutinized under common notations with relevant analyses and discussions. Thirdly, several related learning settings are briefly summarized. As a conclusion, online resources and open research problems on multi-label learning are outlined for reference purposes. [ABSTRACT FROM PUBLISHER]

The problem of multilabel classification has attracted great interest in the last decade, where each instance can be assigned with a set of multiple class labels simultaneously. It has a wide variety of real-world applications, e.g., automatic image annotations and gene function analysis. Current research on multilabel classification focuses on supervised settings which assume existence of large amounts of labeled training data. However, in many applications, the labeling of multilabeled data is extremely expensive and time consuming, while there are often abundant unlabeled data available. In this paper, we study the problem of transductive multilabel learning and propose a novel solution, called Trasductive Multilabel Classification (TraM), to effectively assign a set of multiple labels to each instance. Different from supervised multilabel learning methods, we estimate the label sets of the unlabeled instances effectively by utilizing the information from both labeled and unlabeled data. We first formulate the transductive multilabel learning as an optimization problem of estimating label concept compositions. Then, we derive a closed-form solution to this optimization problem and propose an effective algorithm to assign label sets to the unlabeled instances. Empirical studies on several real-world multilabel learning tasks demonstrate that our TraM method can effectively boost the performance of multilabel classification by using both labeled and unlabeled data. [ABSTRACT FROM AUTHOR]

Abstract-Undersampling is a popular method in dealing with class-imbalance problems, which uses only a subset of the majority class and thus is very efficient. The main deficiency is that many majority class examples are ignored. We propose two algorithms to overcome this deficiency. EasyEnsemble samples several subsets from the majority class, trains a learner using each of them, and combines the outputs of those learners. BalanceCascade trains the learners sequentially, where in each step, the majority class examples that are correctly classified by the current trained learners are removed from further consideration. Experimental results show that both methods have higher Area Under the ROC Curve, F-measure, and G-mean values than many existing classimbalance learning methods. Moreover, they have approximately the same training time as that of undersampling when the same number of weak classifiers is used, which is significantly faster than other methods. [ABSTRACT FROM AUTHOR]

This paper reviews three recent books on data mining written from three different perspectives, i.e., databases, machine learning, and statistics. Although the exploration in this paper is suggestive instead of conclusive, it reveals that besides some common properties, different perspectives lay strong emphases on different aspects of data mining. The emphasis of the database perspective is on efficiency because this perspective strongly concerns the whole discovery process and huge data volume. The emphasis of the machine learning perspective is on effectiveness because this perspective is heavily attracted by substantive heuristics working well in data analysis although they may not always be useful. As for the statistics perspective, its emphasis is on validity because this perspective cares much for mathematical soundness behind mining methods. [Copyright &y& Elsevier]

Cotraining, a paradigm of semisupervised learning, is promised to alleviate effectively the shortage of labeled examples in supervised learning. The standard two-view cotraining requires the data set to be described by two views of features, and previous studies have shown that cotraining works well if the two views satisfy the sufficiency and independence assumptions. In practice, however, these two assumptions are often not known or ensured (even when the two views are given). More commonly, most supervised data sets are described by one set of attributes (one view). Thus, they need be split into two views in order to apply the standard two-view cotraining. In this paper, we first propose a novel approach to empirically verify the two assumptions of cotraining given two views. Then, we design several methods to split single view data sets into two views, in order to make cotraining work reliably well. Our empirical results show that, given a whole or a large labeled training set, our view verification and splitting methods are quite effective. Unfortunately, cotraining is called for precisely when the labeled training set is small. However, given small labeled training sets, we show that the two cotraining assumptions are difficult to verify, and view splitting is unreliable. Our conclusions for cotraining's effectiveness are mixed. If two views are given, and known to satisfy the two assumptions, cotraining works well. Otherwise, based on small labeled training sets, verifying the assumptions or splitting single view into two views are unreliable; thus, it is uncertain whether the standard cotraining would work or not. [ABSTRACT FROM AUTHOR]