26,413 research outputs found
Mining data quality rules based on T-dependence
Since their introduction in 1976, edit rules have been a standard tool in statistical analysis. Basically, edit rules are a compact representation of non-permitted combinations of values in a dataset. In this paper, we propose a technique to automatically find edit rules by use of the concept of T-dependence. We first generalize the traditional notion of lift, to that of T-lift, where stochastic independence is generalized to T-dependence. A combination of values is declared as an edit rule under a t-norm T if there is a strong negative correlation under T-dependence. We show several interesting properties of this approach. In particular, we show that under the minimum t-norm, edit rules can be computed efficiently by use of frequent pattern trees. Experimental results show that there is a weak to medium correlation in the rank order of edit rules obtained under T_M and T_P, indicating that the semantics of these kinds of dependencies are different
Overview of Random Forest Methodology and Practical Guidance with Emphasis on Computational Biology and Bioinformatics
The Random Forest (RF) algorithm by Leo Breiman has become a
standard data analysis tool in bioinformatics. It has shown excellent performance in settings where the number of variables is much larger than the number of observations, can cope with complex interaction structures as well as highly correlated variables and returns measures of variable importance. This paper synthesizes ten years of RF development with emphasis on applications to bioinformatics and computational biology. Special attention is given to practical aspects such as the selection of parameters, available RF implementations, and important pitfalls and biases of RF and its variable importance measures (VIMs). The paper surveys recent developments of the methodology relevant to bioinformatics as well as some representative examples of RF applications in this context and possible directions for future research
Learning Interpretable Rules for Multi-label Classification
Multi-label classification (MLC) is a supervised learning problem in which,
contrary to standard multiclass classification, an instance can be associated
with several class labels simultaneously. In this chapter, we advocate a
rule-based approach to multi-label classification. Rule learning algorithms are
often employed when one is not only interested in accurate predictions, but
also requires an interpretable theory that can be understood, analyzed, and
qualitatively evaluated by domain experts. Ideally, by revealing patterns and
regularities contained in the data, a rule-based theory yields new insights in
the application domain. Recently, several authors have started to investigate
how rule-based models can be used for modeling multi-label data. Discussing
this task in detail, we highlight some of the problems that make rule learning
considerably more challenging for MLC than for conventional classification.
While mainly focusing on our own previous work, we also provide a short
overview of related work in this area.Comment: Preprint version. To appear in: Explainable and Interpretable Models
in Computer Vision and Machine Learning. The Springer Series on Challenges in
Machine Learning. Springer (2018). See
http://www.ke.tu-darmstadt.de/bibtex/publications/show/3077 for further
informatio
Mining Fix Patterns for FindBugs Violations
In this paper, we first collect and track a large number of fixed and unfixed
violations across revisions of software.
The empirical analyses reveal that there are discrepancies in the
distributions of violations that are detected and those that are fixed, in
terms of occurrences, spread and categories, which can provide insights into
prioritizing violations.
To automatically identify patterns in violations and their fixes, we propose
an approach that utilizes convolutional neural networks to learn features and
clustering to regroup similar instances. We then evaluate the usefulness of the
identified fix patterns by applying them to unfixed violations.
The results show that developers will accept and merge a majority (69/116) of
fixes generated from the inferred fix patterns. It is also noteworthy that the
yielded patterns are applicable to four real bugs in the Defects4J major
benchmark for software testing and automated repair.Comment: Accepted for IEEE Transactions on Software Engineerin
FixMiner: Mining Relevant Fix Patterns for Automated Program Repair
Patching is a common activity in software development. It is generally
performed on a source code base to address bugs or add new functionalities. In
this context, given the recurrence of bugs across projects, the associated
similar patches can be leveraged to extract generic fix actions. While the
literature includes various approaches leveraging similarity among patches to
guide program repair, these approaches often do not yield fix patterns that are
tractable and reusable as actionable input to APR systems. In this paper, we
propose a systematic and automated approach to mining relevant and actionable
fix patterns based on an iterative clustering strategy applied to atomic
changes within patches. The goal of FixMiner is thus to infer separate and
reusable fix patterns that can be leveraged in other patch generation systems.
Our technique, FixMiner, leverages Rich Edit Script which is a specialized tree
structure of the edit scripts that captures the AST-level context of the code
changes. FixMiner uses different tree representations of Rich Edit Scripts for
each round of clustering to identify similar changes. These are abstract syntax
trees, edit actions trees, and code context trees. We have evaluated FixMiner
on thousands of software patches collected from open source projects.
Preliminary results show that we are able to mine accurate patterns,
efficiently exploiting change information in Rich Edit Scripts. We further
integrated the mined patterns to an automated program repair prototype,
PARFixMiner, with which we are able to correctly fix 26 bugs of the Defects4J
benchmark. Beyond this quantitative performance, we show that the mined fix
patterns are sufficiently relevant to produce patches with a high probability
of correctness: 81% of PARFixMiner's generated plausible patches are correct.Comment: 31 pages, 11 figure
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