16 research outputs found
Towards an Efficient Discovery of the Topological Representative Subgraphs
With the emergence of graph databases, the task of frequent subgraph
discovery has been extensively addressed. Although the proposed approaches in
the literature have made this task feasible, the number of discovered frequent
subgraphs is still very high to be efficiently used in any further exploration.
Feature selection for graph data is a way to reduce the high number of frequent
subgraphs based on exact or approximate structural similarity. However, current
structural similarity strategies are not efficient enough in many real-world
applications, besides, the combinatorial nature of graphs makes it
computationally very costly. In order to select a smaller yet structurally
irredundant set of subgraphs, we propose a novel approach that mines the top-k
topological representative subgraphs among the frequent ones. Our approach
allows detecting hidden structural similarities that existing approaches are
unable to detect such as the density or the diameter of the subgraph. In
addition, it can be easily extended using any user defined structural or
topological attributes depending on the sought properties. Empirical studies on
real and synthetic graph datasets show that our approach is fast and scalable
ProtNN: Fast and Accurate Nearest Neighbor Protein Function Prediction based on Graph Embedding in Structural and Topological Space
Studying the function of proteins is important for understanding the
molecular mechanisms of life. The number of publicly available protein
structures has increasingly become extremely large. Still, the determination of
the function of a protein structure remains a difficult, costly, and time
consuming task. The difficulties are often due to the essential role of spatial
and topological structures in the determination of protein functions in living
cells. In this paper, we propose ProtNN, a novel approach for protein function
prediction. Given an unannotated protein structure and a set of annotated
proteins, ProtNN finds the nearest neighbor annotated structures based on
protein-graph pairwise similarities. Given a query protein, ProtNN finds the
nearest neighbor reference proteins based on a graph representation model and a
pairwise similarity between vector embedding of both query and reference
protein-graphs in structural and topological spaces. ProtNN assigns to the
query protein the function with the highest number of votes across the set of k
nearest neighbor reference proteins, where k is a user-defined parameter.
Experimental evaluation demonstrates that ProtNN is able to accurately classify
several datasets in an extremely fast runtime compared to state-of-the-art
approaches. We further show that ProtNN is able to scale up to a whole PDB
dataset in a single-process mode with no parallelization, with a gain of
thousands order of magnitude of runtime compared to state-of-the-art
approaches
Predicting Graph Categories from Structural Properties
Complex networks are often categorized according to the underlying phenomena that they represent such as molecular interactions, re-tweets, and brain activity. In this work, we investigate the problem of predicting the category (domain) of arbitrary networks. This includes complex networks from different domains as well as synthetically generated graphs from five different network models. A classification accuracy of 96.6% is achieved using a random forest classifier with both real and synthetic networks. This work makes two important findings. First, our results indicate that complex networks from various domains have distinct structural properties that allow us to predict with high accuracy the category of a new previously unseen network. Second, synthetic graphs are trivial to classify as the classification model can predict with near-certainty the network model used to generate it. Overall, the results demonstrate that networks drawn from different domains (and network models) are trivial to distinguish using only a handful of simple structural properties
Significant Subgraph Mining with Multiple Testing Correction
The problem of finding itemsets that are statistically significantly enriched
in a class of transactions is complicated by the need to correct for multiple
hypothesis testing. Pruning untestable hypotheses was recently proposed as a
strategy for this task of significant itemset mining. It was shown to lead to
greater statistical power, the discovery of more truly significant itemsets,
than the standard Bonferroni correction on real-world datasets. An open
question, however, is whether this strategy of excluding untestable hypotheses
also leads to greater statistical power in subgraph mining, in which the number
of hypotheses is much larger than in itemset mining. Here we answer this
question by an empirical investigation on eight popular graph benchmark
datasets. We propose a new efficient search strategy, which always returns the
same solution as the state-of-the-art approach and is approximately two orders
of magnitude faster. Moreover, we exploit the dependence between subgraphs by
considering the effective number of tests and thereby further increase the
statistical power.Comment: 18 pages, 5 figure, accepted to the 2015 SIAM International
Conference on Data Mining (SDM15
PersLay: A Neural Network Layer for Persistence Diagrams and New Graph Topological Signatures
Persistence diagrams, the most common descriptors of Topological Data
Analysis, encode topological properties of data and have already proved pivotal
in many different applications of data science. However, since the (metric)
space of persistence diagrams is not Hilbert, they end up being difficult
inputs for most Machine Learning techniques. To address this concern, several
vectorization methods have been put forward that embed persistence diagrams
into either finite-dimensional Euclidean space or (implicit) infinite
dimensional Hilbert space with kernels. In this work, we focus on persistence
diagrams built on top of graphs. Relying on extended persistence theory and the
so-called heat kernel signature, we show how graphs can be encoded by
(extended) persistence diagrams in a provably stable way. We then propose a
general and versatile framework for learning vectorizations of persistence
diagrams, which encompasses most of the vectorization techniques used in the
literature. We finally showcase the experimental strength of our setup by
achieving competitive scores on classification tasks on real-life graph
datasets
EEG sleep stages identification based on weighted undirected complex networks
Sleep scoring is important in sleep research because any errors in the scoring of the patient's sleep electroencephalography (EEG) recordings can cause serious problems such as incorrect diagnosis, medication errors, and misinterpretations of patient's EEG recordings. The aim of this research is to develop a new automatic method for EEG sleep stages classification based on a statistical model and weighted brain networks.
Methods
each EEG segment is partitioned into a number of blocks using a sliding window technique. A set of statistical features are extracted from each block. As a result, a vector of features is obtained to represent each EEG segment. Then, the vector of features is mapped into a weighted undirected network. Different structural and spectral attributes of the networks are extracted and forwarded to a least square support vector machine (LS-SVM) classifier. At the same time the network's attributes are also thoroughly investigated. It is found that the network's characteristics vary with their sleep stages. Each sleep stage is best represented using the key features of their networks.
Results
In this paper, the proposed method is evaluated using two datasets acquired from different channels of EEG (Pz-Oz and C3-A2) according to the R&K and the AASM without pre-processing the original EEG data. The obtained results by the LS-SVM are compared with those by Naïve, k-nearest and a multi-class-SVM. The proposed method is also compared with other benchmark sleep stages classification methods. The comparison results demonstrate that the proposed method has an advantage in scoring sleep stages based on single channel EEG signals.
Conclusions
An average accuracy of 96.74% is obtained with the C3-A2 channel according to the AASM standard, and 96% with the Pz-Oz channel based on the R&K standard