13 Result(s)
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Article
Open AccessProtein function prediction through multi-view multi-label latent tensor reconstruction
In last two decades, the use of high-throughput sequencing technologies has accelerated the pace of discovery of proteins. However, due to the time and resource limitations of rigorous experimental functional ...
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Article
Open AccessLearning symmetry-aware atom map** in chemical reactions through deep graph matching
Accurate atom map**, which establishes correspondences between atoms in reactants and products, is a crucial step in analyzing chemical reactions. In this paper, we present a novel end-to-end approach that f...
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Article
Open AccessCritical Assessment of Small Molecule Identification 2016: automated methods
The fourth round of the Critical Assessment of Small Molecule Identification (CASMI) Contest (www.casmi-contest.org) was held in 2016, with two new cat...
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Article
Open AccessSelected proceedings of Machine Learning in Systems Biology: MLSB 2016
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Chapter and Conference Paper
Reconstructing Gapless Ancestral Metabolic Networks
We present a method for inferring the structure of ancestral metabolic networks directly from the networks of observed species and their phylogenetic tree. In particular, we aim to minimize the number of mutat...
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Chapter and Conference Paper
Multi-task Drug Bioactivity Classification with Graph Labeling Ensembles
We present a new method for drug bioactivity classification based on learning an ensemble of multi-task classifiers. As the base classifiers of the ensemble we use Max-Margin Conditional Random Field (MMCRF) m...
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Chapter and Conference Paper
Structured Output Prediction of Novel Enzyme Function with Reaction Kernels
Enzyme function prediction is an important problem in post-genomic bioinformatics, needed for reconstruction of metabolic networks of organisms. Currently there are two general methods for solving the problem:...
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Chapter and Conference Paper
Structured Output Prediction of Anti-cancer Drug Activity
We present a structured output prediction approach for classifying potential anti-cancer drugs. Our QSAR model takes as input a description of a molecule and predicts the activity against a set of cancer cell ...
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Article
Open AccessInferring branching pathways in genome-scale metabolic networks
A central problem in computational metabolic modelling is how to find biochemically plausible pathways between metabolites in a metabolic network. Two general, complementary frameworks have been utilized to fi...
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Article
Open AccessAn analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments
Metabolic fluxes provide invaluable insight on the integrated response of a cell to environmental stimuli or genetic modifications. Current computational methods for estimating the metabolic fluxes from 13C isoto...
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Article
Open AccessInformation Theoretic Methods for Bioinformatics
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Chapter and Conference Paper
A Computational Method for Reconstructing Gapless Metabolic Networks
We propose a computational method for reconstructing metabolic networks. The method utilizes optimization techniques and graph traversal algorithms to discover a set of biochemical reactions that is most likel...
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Article
Open AccessProbabilistic modeling and machine learning in structural and systems biology
This supplement contains extended versions of a selected subset of papers presented at the workshop PMSB 2007, Probabilistic Modeling and Machine Learning in Structural and Systems Biology, Tuusula, Finland, f...
