13,159 research outputs found
Training Support Vector Machines Using Frank-Wolfe Optimization Methods
Training a Support Vector Machine (SVM) requires the solution of a quadratic
programming problem (QP) whose computational complexity becomes prohibitively
expensive for large scale datasets. Traditional optimization methods cannot be
directly applied in these cases, mainly due to memory restrictions.
By adopting a slightly different objective function and under mild conditions
on the kernel used within the model, efficient algorithms to train SVMs have
been devised under the name of Core Vector Machines (CVMs). This framework
exploits the equivalence of the resulting learning problem with the task of
building a Minimal Enclosing Ball (MEB) problem in a feature space, where data
is implicitly embedded by a kernel function.
In this paper, we improve on the CVM approach by proposing two novel methods
to build SVMs based on the Frank-Wolfe algorithm, recently revisited as a fast
method to approximate the solution of a MEB problem. In contrast to CVMs, our
algorithms do not require to compute the solutions of a sequence of
increasingly complex QPs and are defined by using only analytic optimization
steps. Experiments on a large collection of datasets show that our methods
scale better than CVMs in most cases, sometimes at the price of a slightly
lower accuracy. As CVMs, the proposed methods can be easily extended to machine
learning problems other than binary classification. However, effective
classifiers are also obtained using kernels which do not satisfy the condition
required by CVMs and can thus be used for a wider set of problems
Bioinformatics tools in predictive ecology: Applications to fisheries
This article is made available throught the Brunel Open Access Publishing Fund - Copygith @ 2012 Tucker et al.There has been a huge effort in the advancement of analytical techniques for molecular biological data over the past decade. This has led to many novel algorithms that are specialized to deal with data associated with biological phenomena, such as gene expression and protein interactions. In contrast, ecological data analysis has remained focused to some degree on off-the-shelf statistical techniques though this is starting to change with the adoption of state-of-the-art methods, where few assumptions can be made about the data and a more explorative approach is required, for example, through the use of Bayesian networks. In this paper, some novel bioinformatics tools for microarray data are discussed along with their ‘crossover potential’ with an application to fisheries data. In particular, a focus is made on the development of models that identify functionally equivalent species in different fish communities with the aim of predicting functional collapse
Hierarchical Losses and New Resources for Fine-grained Entity Typing and Linking
Extraction from raw text to a knowledge base of entities and fine-grained
types is often cast as prediction into a flat set of entity and type labels,
neglecting the rich hierarchies over types and entities contained in curated
ontologies. Previous attempts to incorporate hierarchical structure have
yielded little benefit and are restricted to shallow ontologies. This paper
presents new methods using real and complex bilinear mappings for integrating
hierarchical information, yielding substantial improvement over flat
predictions in entity linking and fine-grained entity typing, and achieving new
state-of-the-art results for end-to-end models on the benchmark FIGER dataset.
We also present two new human-annotated datasets containing wide and deep
hierarchies which we will release to the community to encourage further
research in this direction: MedMentions, a collection of PubMed abstracts in
which 246k mentions have been mapped to the massive UMLS ontology; and TypeNet,
which aligns Freebase types with the WordNet hierarchy to obtain nearly 2k
entity types. In experiments on all three datasets we show substantial gains
from hierarchy-aware training.Comment: ACL 201
Active Sampling of Pairs and Points for Large-scale Linear Bipartite Ranking
Bipartite ranking is a fundamental ranking problem that learns to order
relevant instances ahead of irrelevant ones. The pair-wise approach for
bi-partite ranking construct a quadratic number of pairs to solve the problem,
which is infeasible for large-scale data sets. The point-wise approach, albeit
more efficient, often results in inferior performance. That is, it is difficult
to conduct bipartite ranking accurately and efficiently at the same time. In
this paper, we develop a novel active sampling scheme within the pair-wise
approach to conduct bipartite ranking efficiently. The scheme is inspired from
active learning and can reach a competitive ranking performance while focusing
only on a small subset of the many pairs during training. Moreover, we propose
a general Combined Ranking and Classification (CRC) framework to accurately
conduct bipartite ranking. The framework unifies point-wise and pair-wise
approaches and is simply based on the idea of treating each instance point as a
pseudo-pair. Experiments on 14 real-word large-scale data sets demonstrate that
the proposed algorithm of Active Sampling within CRC, when coupled with a
linear Support Vector Machine, usually outperforms state-of-the-art point-wise
and pair-wise ranking approaches in terms of both accuracy and efficiency.Comment: a shorter version was presented in ACML 201
Decoding Sequence Classification Models for Acquiring New Biological Insights
Classifying biological sequences is one of the most important tasks in computational biology. In the last decade, support vector machines (SVMs) in combination with sequence kernels have emerged as a de-facto standard. These methods are theoretically well-founded, reliable, and provide high-accuracy solutions at low computational cost. However, obtaining a highly accurate classifier is rarely the end of the story in many practical situations. Instead, one often aims to acquire biological knowledge about the principles underlying a given classification task. SVMs with traditional sequence kernels do not offer a straightforward way of accessing this knowledge.

In this contribution, we propose a new approach to analyzing biological sequences on the basis of support vector machines with sequence kernels. We first extract explicit pattern weights from a given SVM. When classifying a sequence, we then compute a prediction profile by distributing the weight of each pattern to the sequence positions that match the pattern. The final profile not only allows assessing the importance of a position, but also determining for which class it is indicative. Since it is unfeasible to analyze profiles of all sequences in a given data set, we advocate using affinity propagation (AP) clustering to narrow down the analysis to a small set of typical sequences.

The proposed approach is applicable to a wide range of biological sequences and a wide selection of sequence kernels. To illustrate our framework, we present the prediction of oligomerization tendencies of coiled coil proteins as a case study.

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