9,745 research outputs found
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
Identification of functionally related enzymes by learning-to-rank methods
Enzyme sequences and structures are routinely used in the biological sciences
as queries to search for functionally related enzymes in online databases. To
this end, one usually departs from some notion of similarity, comparing two
enzymes by looking for correspondences in their sequences, structures or
surfaces. For a given query, the search operation results in a ranking of the
enzymes in the database, from very similar to dissimilar enzymes, while
information about the biological function of annotated database enzymes is
ignored.
In this work we show that rankings of that kind can be substantially improved
by applying kernel-based learning algorithms. This approach enables the
detection of statistical dependencies between similarities of the active cleft
and the biological function of annotated enzymes. This is in contrast to
search-based approaches, which do not take annotated training data into
account. Similarity measures based on the active cleft are known to outperform
sequence-based or structure-based measures under certain conditions. We
consider the Enzyme Commission (EC) classification hierarchy for obtaining
annotated enzymes during the training phase. The results of a set of sizeable
experiments indicate a consistent and significant improvement for a set of
similarity measures that exploit information about small cavities in the
surface of enzymes
Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction.
BackgroundOne of the most powerful methods for the prediction of protein structure from sequence information alone is the iterative construction of profile-type models. Because profiles are built from sequence alignments, the sequences included in the alignment and the method used to align them will be important to the sensitivity of the resulting profile. The inclusion of highly diverse sequences will presumably produce a more powerful profile, but distantly related sequences can be difficult to align accurately using only sequence information. Therefore, it would be expected that the use of protein structure alignments to improve the selection and alignment of diverse sequence homologs might yield improved profiles. However, the actual utility of such an approach has remained unclear.ResultsWe explored several iterative protocols for the generation of profile hidden Markov models. These protocols were tailored to allow the inclusion of protein structure alignments in the process, and were used for large-scale creation and benchmarking of structure alignment-enhanced models. We found that models using structure alignments did not provide an overall improvement over sequence-only models for superfamily-level structure predictions. However, the results also revealed that the structure alignment-enhanced models were complimentary to the sequence-only models, particularly at the edge of the "twilight zone". When the two sets of models were combined, they provided improved results over sequence-only models alone. In addition, we found that the beneficial effects of the structure alignment-enhanced models could not be realized if the structure-based alignments were replaced with sequence-based alignments. Our experiments with different iterative protocols for sequence-only models also suggested that simple protocol modifications were unable to yield equivalent improvements to those provided by the structure alignment-enhanced models. Finally, we found that models using structure alignments provided fold-level structure assignments that were superior to those produced by sequence-only models.ConclusionWhen attempting to predict the structure of remote homologs, we advocate a combined approach in which both traditional models and models incorporating structure alignments are used
Fine-grained Search Space Classification for Hard Enumeration Variants of Subset Problems
We propose a simple, powerful, and flexible machine learning framework for
(i) reducing the search space of computationally difficult enumeration variants
of subset problems and (ii) augmenting existing state-of-the-art solvers with
informative cues arising from the input distribution. We instantiate our
framework for the problem of listing all maximum cliques in a graph, a central
problem in network analysis, data mining, and computational biology. We
demonstrate the practicality of our approach on real-world networks with
millions of vertices and edges by not only retaining all optimal solutions, but
also aggressively pruning the input instance size resulting in several fold
speedups of state-of-the-art algorithms. Finally, we explore the limits of
scalability and robustness of our proposed framework, suggesting that
supervised learning is viable for tackling NP-hard problems in practice.Comment: AAAI 201
- …