31 research outputs found
Enhancing the functional content of protein interaction networks
Protein interaction networks are a promising type of data for studying
complex biological systems. However, despite the rich information embedded in
these networks, they face important data quality challenges of noise and
incompleteness that adversely affect the results obtained from their analysis.
Here, we explore the use of the concept of common neighborhood similarity
(CNS), which is a form of local structure in networks, to address these issues.
Although several CNS measures have been proposed in the literature, an
understanding of their relative efficacies for the analysis of interaction
networks has been lacking. We follow the framework of graph transformation to
convert the given interaction network into a transformed network corresponding
to a variety of CNS measures evaluated. The effectiveness of each measure is
then estimated by comparing the quality of protein function predictions
obtained from its corresponding transformed network with those from the
original network. Using a large set of S. cerevisiae interactions, and a set of
136 GO terms, we find that several of the transformed networks produce more
accurate predictions than those obtained from the original network. In
particular, the measure proposed here performs particularly well for
this task. Further investigation reveals that the two major factors
contributing to this improvement are the abilities of CNS measures, especially
, to prune out noisy edges and introduce new links between
functionally related proteins
Association Analysis Techniques for Discovering Functional Modules from Microarray Data
An application of great interest in microarray data analysis is the identification of a group of genes that show very similar patterns of expression in a data set, and are expected to represent groups of genes that perform common/similar functions, also known as functional modules. Although clustering offers a natural solution to this problem, it suffers from the limitation that it uses all the conditions to compare two genes, whereas only a subset of them may be relevant. Association analysis offers an alternative route for finding such groups of genes that may be co-expressed only over a subset of the experimental conditions used to prepare the data set. The techniques in this field attempt to find groups of data objects that contain coherent values across a set of attributes, in an exhaustive and efficient manner. In this paper, we illustrate how a generalization of the techniques in association analysis for real-valued data can be utilized to extract coherent functional modules from large microarray data sets
SLIM : Scalable Linkage of Mobility Data
We present a scalable solution to link entities across mobility datasets using their spatio-temporal information. This is a fundamental problem in many applications such as linking user identities for security, understanding privacy limitations of location based services, or producing a unified dataset from multiple sources for urban planning. Such integrated datasets are also essential for service providers to optimise their services and improve business intelligence. In this paper, we first propose a mobility based representation and similarity computation for entities. An efficient matching process is then developed to identify the final linked pairs, with an automated mechanism to decide when to stop the linkage. We scale the process with a locality-sensitive hashing (LSH) based approach that significantly reduces candidate pairs for matching. To realize the effectiveness and efficiency of our techniques in practice, we introduce an algorithm called SLIM. In the experimental evaluation, SLIM outperforms the two existing state-of-the-art approaches in terms of precision and recall. Moreover, the LSH-based approach brings two to four orders of magnitude speedup
Mining Novel Multivariate Relationships in Time Series Data Using Correlation Networks
In many domains, there is significant interest in capturing novel
relationships between time series that represent activities recorded at
different nodes of a highly complex system. In this paper, we introduce
multipoles, a novel class of linear relationships between more than two time
series. A multipole is a set of time series that have strong linear dependence
among themselves, with the requirement that each time series makes a
significant contribution to the linear dependence. We demonstrate that most
interesting multipoles can be identified as cliques of negative correlations in
a correlation network. Such cliques are typically rare in a real-world
correlation network, which allows us to find almost all multipoles efficiently
using a clique-enumeration approach. Using our proposed framework, we
demonstrate the utility of multipoles in discovering new physical phenomena in
two scientific domains: climate science and neuroscience. In particular, we
discovered several multipole relationships that are reproducible in multiple
other independent datasets and lead to novel domain insights.Comment: This is the accepted version of article submitted to IEEE
Transactions on Knowledge and Data Engineering 201
Progress in developing a hybrid deep learning algorithm for identifying and locating primary vertices
The locations of proton-proton collision points in LHC experiments are called
primary vertices (PVs). Preliminary results of a hybrid deep learning algorithm
for identifying and locating these, targeting the Run 3 incarnation of LHCb,
have been described at conferences in 2019 and 2020. In the past year we have
made significant progress in a variety of related areas. Using two newer Kernel
Density Estimators (KDEs) as input feature sets improves the fidelity of the
models, as does using full LHCb simulation rather than the "toy Monte Carlo"
originally (and still) used to develop models. We have also built a deep
learning model to calculate the KDEs from track information. Connecting a
tracks-to-KDE model to a KDE-to-hists model used to find PVs provides a
proof-of-concept that a single deep learning model can use track information to
find PVs with high efficiency and high fidelity. We have studied a variety of
models systematically to understand how variations in their architectures
affect performance. While the studies reported here are specific to the LHCb
geometry and operating conditions, the results suggest that the same approach
could be used by the ATLAS and CMS experiments
Complex biomarker discovery in neuroimaging data: Finding a needle in a haystack
AbstractNeuropsychiatric disorders such as schizophrenia, bipolar disorder and Alzheimer's disease are major public health problems. However, despite decades of research, we currently have no validated prognostic or diagnostic tests that can be applied at an individual patient level. Many neuropsychiatric diseases are due to a combination of alterations that occur in a human brain rather than the result of localized lesions. While there is hope that newer imaging technologies such as functional and anatomic connectivity MRI or molecular imaging may offer breakthroughs, the single biomarkers that are discovered using these datasets are limited by their inability to capture the heterogeneity and complexity of most multifactorial brain disorders. Recently, complex biomarkers have been explored to address this limitation using neuroimaging data. In this manuscript we consider the nature of complex biomarkers being investigated in the recent literature and present techniques to find such biomarkers that have been developed in related areas of data mining, statistics, machine learning and bioinformatics