2,641 research outputs found
Neural Networks for Complex Data
Artificial neural networks are simple and efficient machine learning tools.
Defined originally in the traditional setting of simple vector data, neural
network models have evolved to address more and more difficulties of complex
real world problems, ranging from time evolving data to sophisticated data
structures such as graphs and functions. This paper summarizes advances on
those themes from the last decade, with a focus on results obtained by members
of the SAMM team of Universit\'e Paris
Classifying sequences by the optimized dissimilarity space embedding approach: a case study on the solubility analysis of the E. coli proteome
We evaluate a version of the recently-proposed classification system named
Optimized Dissimilarity Space Embedding (ODSE) that operates in the input space
of sequences of generic objects. The ODSE system has been originally presented
as a classification system for patterns represented as labeled graphs. However,
since ODSE is founded on the dissimilarity space representation of the input
data, the classifier can be easily adapted to any input domain where it is
possible to define a meaningful dissimilarity measure. Here we demonstrate the
effectiveness of the ODSE classifier for sequences by considering an
application dealing with the recognition of the solubility degree of the
Escherichia coli proteome. Solubility, or analogously aggregation propensity,
is an important property of protein molecules, which is intimately related to
the mechanisms underlying the chemico-physical process of folding. Each protein
of our dataset is initially associated with a solubility degree and it is
represented as a sequence of symbols, denoting the 20 amino acid residues. The
herein obtained computational results, which we stress that have been achieved
with no context-dependent tuning of the ODSE system, confirm the validity and
generality of the ODSE-based approach for structured data classification.Comment: 10 pages, 49 reference
Developments in the theory of randomized shortest paths with a comparison of graph node distances
There have lately been several suggestions for parametrized distances on a
graph that generalize the shortest path distance and the commute time or
resistance distance. The need for developing such distances has risen from the
observation that the above-mentioned common distances in many situations fail
to take into account the global structure of the graph. In this article, we
develop the theory of one family of graph node distances, known as the
randomized shortest path dissimilarity, which has its foundation in statistical
physics. We show that the randomized shortest path dissimilarity can be easily
computed in closed form for all pairs of nodes of a graph. Moreover, we come up
with a new definition of a distance measure that we call the free energy
distance. The free energy distance can be seen as an upgrade of the randomized
shortest path dissimilarity as it defines a metric, in addition to which it
satisfies the graph-geodetic property. The derivation and computation of the
free energy distance are also straightforward. We then make a comparison
between a set of generalized distances that interpolate between the shortest
path distance and the commute time, or resistance distance. This comparison
focuses on the applicability of the distances in graph node clustering and
classification. The comparison, in general, shows that the parametrized
distances perform well in the tasks. In particular, we see that the results
obtained with the free energy distance are among the best in all the
experiments.Comment: 30 pages, 4 figures, 3 table
Similarities on Graphs: Kernels versus Proximity Measures
We analytically study proximity and distance properties of various kernels
and similarity measures on graphs. This helps to understand the mathematical
nature of such measures and can potentially be useful for recommending the
adoption of specific similarity measures in data analysis.Comment: 16 page
Analysis of a data matrix and a graph: Metagenomic data and the phylogenetic tree
In biological experiments researchers often have information in the form of a
graph that supplements observed numerical data. Incorporating the knowledge
contained in these graphs into an analysis of the numerical data is an
important and nontrivial task. We look at the example of metagenomic
data---data from a genomic survey of the abundance of different species of
bacteria in a sample. Here, the graph of interest is a phylogenetic tree
depicting the interspecies relationships among the bacteria species. We
illustrate that analysis of the data in a nonstandard inner-product space
effectively uses this additional graphical information and produces more
meaningful results.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS402 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
Modelling and recognition of protein contact networks by multiple kernel learning and dissimilarity representations
Multiple kernel learning is a paradigm which employs a properly constructed chain of kernel functions able to simultaneously analyse different data or different representations of the same data. In this paper, we propose an hybrid classification system based on a linear combination of multiple kernels defined over multiple dissimilarity spaces. The core of the training procedure is the joint optimisation of kernel weights and representatives selection in the dissimilarity spaces. This equips the system with a two-fold knowledge discovery phase: by analysing the weights, it is possible to check which representations are more suitable for solving the classification problem, whereas the pivotal patterns selected as representatives can give further insights on the modelled system, possibly with the help of field-experts. The proposed classification system is tested on real proteomic data in order to predict proteins' functional role starting from their folded structure: specifically, a set of eight representations are drawn from the graph-based protein folded description. The proposed multiple kernel-based system has also been benchmarked against a clustering-based classification system also able to exploit multiple dissimilarities simultaneously. Computational results show remarkable classification capabilities and the knowledge discovery analysis is in line with current biological knowledge, suggesting the reliability of the proposed system
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