1,261 research outputs found
Some results on more flexible versions of Graph Motif
The problems studied in this paper originate from Graph Motif, a problem
introduced in 2006 in the context of biological networks. Informally speaking,
it consists in deciding if a multiset of colors occurs in a connected subgraph
of a vertex-colored graph. Due to the high rate of noise in the biological
data, more flexible definitions of the problem have been outlined. We present
in this paper two inapproximability results for two different optimization
variants of Graph Motif: one where the size of the solution is maximized, the
other when the number of substitutions of colors to obtain the motif from the
solution is minimized. We also study a decision version of Graph Motif where
the connectivity constraint is replaced by the well known notion of graph
modularity. While the problem remains NP-complete, it allows algorithms in FPT
for biologically relevant parameterizations
Contextual Motifs: Increasing the Utility of Motifs using Contextual Data
Motifs are a powerful tool for analyzing physiological waveform data.
Standard motif methods, however, ignore important contextual information (e.g.,
what the patient was doing at the time the data were collected). We hypothesize
that these additional contextual data could increase the utility of motifs.
Thus, we propose an extension to motifs, contextual motifs, that incorporates
context. Recognizing that, oftentimes, context may be unobserved or
unavailable, we focus on methods to jointly infer motifs and context. Applied
to both simulated and real physiological data, our proposed approach improves
upon existing motif methods in terms of the discriminative utility of the
discovered motifs. In particular, we discovered contextual motifs in continuous
glucose monitor (CGM) data collected from patients with type 1 diabetes.
Compared to their contextless counterparts, these contextual motifs led to
better predictions of hypo- and hyperglycemic events. Our results suggest that
even when inferred, context is useful in both a long- and short-term prediction
horizon when processing and interpreting physiological waveform data.Comment: 10 pages, 7 figures, accepted for oral presentation at KDD '1
Detecting communities of triangles in complex networks using spectral optimization
The study of the sub-structure of complex networks is of major importance to
relate topology and functionality. Many efforts have been devoted to the
analysis of the modular structure of networks using the quality function known
as modularity. However, generally speaking, the relation between topological
modules and functional groups is still unknown, and depends on the semantic of
the links. Sometimes, we know in advance that many connections are transitive
and, as a consequence, triangles have a specific meaning. Here we propose the
study of the modular structure of networks considering triangles as the
building blocks of modules. The method generalizes the standard modularity and
uses spectral optimization to find its maximum. We compare the partitions
obtained with those resulting from the optimization of the standard modularity
in several real networks. The results show that the information reported by the
analysis of modules of triangles complements the information of the classical
modularity analysis.Comment: Computer Communications (in press
The Partial Evaluation Approach to Information Personalization
Information personalization refers to the automatic adjustment of information
content, structure, and presentation tailored to an individual user. By
reducing information overload and customizing information access,
personalization systems have emerged as an important segment of the Internet
economy. This paper presents a systematic modeling methodology - PIPE
(`Personalization is Partial Evaluation') - for personalization.
Personalization systems are designed and implemented in PIPE by modeling an
information-seeking interaction in a programmatic representation. The
representation supports the description of information-seeking activities as
partial information and their subsequent realization by partial evaluation, a
technique for specializing programs. We describe the modeling methodology at a
conceptual level and outline representational choices. We present two
application case studies that use PIPE for personalizing web sites and describe
how PIPE suggests a novel evaluation criterion for information system designs.
Finally, we mention several fundamental implications of adopting the PIPE model
for personalization and when it is (and is not) applicable.Comment: Comprehensive overview of the PIPE model for personalizatio
Predicting Genetic Regulatory Response Using Classification
We present a novel classification-based method for learning to predict gene
regulatory response. Our approach is motivated by the hypothesis that in simple
organisms such as Saccharomyces cerevisiae, we can learn a decision rule for
predicting whether a gene is up- or down-regulated in a particular experiment
based on (1) the presence of binding site subsequences (``motifs'') in the
gene's regulatory region and (2) the expression levels of regulators such as
transcription factors in the experiment (``parents''). Thus our learning task
integrates two qualitatively different data sources: genome-wide cDNA
microarray data across multiple perturbation and mutant experiments along with
motif profile data from regulatory sequences. We convert the regression task of
predicting real-valued gene expression measurement to a classification task of
predicting +1 and -1 labels, corresponding to up- and down-regulation beyond
the levels of biological and measurement noise in microarray measurements. The
learning algorithm employed is boosting with a margin-based generalization of
decision trees, alternating decision trees. This large-margin classifier is
sufficiently flexible to allow complex logical functions, yet sufficiently
simple to give insight into the combinatorial mechanisms of gene regulation. We
observe encouraging prediction accuracy on experiments based on the Gasch S.
cerevisiae dataset, and we show that we can accurately predict up- and
down-regulation on held-out experiments. Our method thus provides predictive
hypotheses, suggests biological experiments, and provides interpretable insight
into the structure of genetic regulatory networks.Comment: 8 pages, 4 figures, presented at Twelfth International Conference on
Intelligent Systems for Molecular Biology (ISMB 2004), supplemental website:
http://www.cs.columbia.edu/compbio/geneclas
Comparative genomic analysis of novel Acinetobacter symbionts : A combined systems biology and genomics approach
Acknowledgements This work was supported by University of Delhi, Department of Science and Technology- Promotion of University Research and Scientific Excellence (DST-PURSE). V.G., S.H. and U.S. gratefully acknowledge the Council for Scientific and Industrial Research (CSIR), University Grant Commission (UGC) and Department of Biotechnology (DBT) for providing research fellowship.Peer reviewedPublisher PD
ImageJ2: ImageJ for the next generation of scientific image data
ImageJ is an image analysis program extensively used in the biological
sciences and beyond. Due to its ease of use, recordable macro language, and
extensible plug-in architecture, ImageJ enjoys contributions from
non-programmers, amateur programmers, and professional developers alike.
Enabling such a diversity of contributors has resulted in a large community
that spans the biological and physical sciences. However, a rapidly growing
user base, diverging plugin suites, and technical limitations have revealed a
clear need for a concerted software engineering effort to support emerging
imaging paradigms, to ensure the software's ability to handle the requirements
of modern science. Due to these new and emerging challenges in scientific
imaging, ImageJ is at a critical development crossroads.
We present ImageJ2, a total redesign of ImageJ offering a host of new
functionality. It separates concerns, fully decoupling the data model from the
user interface. It emphasizes integration with external applications to
maximize interoperability. Its robust new plugin framework allows everything
from image formats, to scripting languages, to visualization to be extended by
the community. The redesigned data model supports arbitrarily large,
N-dimensional datasets, which are increasingly common in modern image
acquisition. Despite the scope of these changes, backwards compatibility is
maintained such that this new functionality can be seamlessly integrated with
the classic ImageJ interface, allowing users and developers to migrate to these
new methods at their own pace. ImageJ2 provides a framework engineered for
flexibility, intended to support these requirements as well as accommodate
future needs
- …