50,494 research outputs found
Methods for protein complex prediction and their contributions towards understanding the organization, function and dynamics of complexes
Complexes of physically interacting proteins constitute fundamental
functional units responsible for driving biological processes within cells. A
faithful reconstruction of the entire set of complexes is therefore essential
to understand the functional organization of cells. In this review, we discuss
the key contributions of computational methods developed till date
(approximately between 2003 and 2015) for identifying complexes from the
network of interacting proteins (PPI network). We evaluate in depth the
performance of these methods on PPI datasets from yeast, and highlight
challenges faced by these methods, in particular detection of sparse and small
or sub- complexes and discerning of overlapping complexes. We describe methods
for integrating diverse information including expression profiles and 3D
structures of proteins with PPI networks to understand the dynamics of complex
formation, for instance, of time-based assembly of complex subunits and
formation of fuzzy complexes from intrinsically disordered proteins. Finally,
we discuss methods for identifying dysfunctional complexes in human diseases,
an application that is proving invaluable to understand disease mechanisms and
to discover novel therapeutic targets. We hope this review aptly commemorates a
decade of research on computational prediction of complexes and constitutes a
valuable reference for further advancements in this exciting area.Comment: 1 Tabl
VoG: Summarizing and Understanding Large Graphs
How can we succinctly describe a million-node graph with a few simple
sentences? How can we measure the "importance" of a set of discovered subgraphs
in a large graph? These are exactly the problems we focus on. Our main ideas
are to construct a "vocabulary" of subgraph-types that often occur in real
graphs (e.g., stars, cliques, chains), and from a set of subgraphs, find the
most succinct description of a graph in terms of this vocabulary. We measure
success in a well-founded way by means of the Minimum Description Length (MDL)
principle: a subgraph is included in the summary if it decreases the total
description length of the graph.
Our contributions are three-fold: (a) formulation: we provide a principled
encoding scheme to choose vocabulary subgraphs; (b) algorithm: we develop
\method, an efficient method to minimize the description cost, and (c)
applicability: we report experimental results on multi-million-edge real
graphs, including Flickr and the Notre Dame web graph.Comment: SIAM International Conference on Data Mining (SDM) 201
Efficiently Clustering Very Large Attributed Graphs
Attributed graphs model real networks by enriching their nodes with
attributes accounting for properties. Several techniques have been proposed for
partitioning these graphs into clusters that are homogeneous with respect to
both semantic attributes and to the structure of the graph. However, time and
space complexities of state of the art algorithms limit their scalability to
medium-sized graphs. We propose SToC (for Semantic-Topological Clustering), a
fast and scalable algorithm for partitioning large attributed graphs. The
approach is robust, being compatible both with categorical and with
quantitative attributes, and it is tailorable, allowing the user to weight the
semantic and topological components. Further, the approach does not require the
user to guess in advance the number of clusters. SToC relies on well known
approximation techniques such as bottom-k sketches, traditional graph-theoretic
concepts, and a new perspective on the composition of heterogeneous distance
measures. Experimental results demonstrate its ability to efficiently compute
high-quality partitions of large scale attributed graphs.Comment: This work has been published in ASONAM 2017. This version includes an
appendix with validation of our attribute model and distance function,
omitted in the converence version for lack of space. Please refer to the
published versio
{VoG}: {Summarizing} and Understanding Large Graphs
How can we succinctly describe a million-node graph with a few simple sentences? How can we measure the "importance" of a set of discovered subgraphs in a large graph? These are exactly the problems we focus on. Our main ideas are to construct a "vocabulary" of subgraph-types that often occur in real graphs (e.g., stars, cliques, chains), and from a set of subgraphs, find the most succinct description of a graph in terms of this vocabulary. We measure success in a well-founded way by means of the Minimum Description Length (MDL) principle: a subgraph is included in the summary if it decreases the total description length of the graph. Our contributions are three-fold: (a) formulation: we provide a principled encoding scheme to choose vocabulary subgraphs; (b) algorithm: we develop \method, an efficient method to minimize the description cost, and (c) applicability: we report experimental results on multi-million-edge real graphs, including Flickr and the Notre Dame web graph
Techniques for clustering gene expression data
Many clustering techniques have been proposed for the analysis of gene expression data obtained from microarray experiments. However, choice of suitable method(s) for a given experimental dataset is not straightforward. Common approaches do not translate well and fail to take account of the data profile. This review paper surveys state of the art applications which recognises these limitations and implements procedures to overcome them. It provides a framework for the evaluation of clustering in gene expression analyses. The nature of microarray data is discussed briefly. Selected examples are presented for the clustering methods considered
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