scholarly journals Integrating Multiple Interaction Networks for Gene Function Inference

Molecules ◽  
2018 ◽  
Vol 24 (1) ◽  
pp. 30 ◽  
Author(s):  
Jingpu Zhang ◽  
Lei Deng
Keyword(s):  
State Of The Art ◽  
Interaction Networks ◽  
Dimensional Representation ◽  
Functional Interaction ◽  
High Throughput Data ◽  
Multiple Networks ◽  
The Past ◽  
Proteomic Data ◽  
Multiple Interaction ◽  
Low Dimensional

In the past few decades, the number and variety of genomic and proteomic data available have increased dramatically. Molecular or functional interaction networks are usually constructed according to high-throughput data and the topological structure of these interaction networks provide a wealth of information for inferring the function of genes or proteins. It is a widely used way to mine functional information of genes or proteins by analyzing the association networks. However, it remains still an urgent but unresolved challenge how to combine multiple heterogeneous networks to achieve more accurate predictions. In this paper, we present a method named ReprsentConcat to improve function inference by integrating multiple interaction networks. The low-dimensional representation of each node in each network is extracted, then these representations from multiple networks are concatenated and fed to gcForest, which augment feature vectors by cascading and automatically determines the number of cascade levels. We experimentally compare ReprsentConcat with a state-of-the-art method, showing that it achieves competitive results on the datasets of yeast and human. Moreover, it is robust to the hyperparameters including the number of dimensions.

scholarly journals Neurobiological successor features for spatial navigation

2019 ◽  
Author(s):  
William de Cothi ◽  
Caswell Barry
Keyword(s):  
Grid Cell ◽  
Biological Data ◽  
Basis Set ◽  
Grid Cells ◽  
Dimensional Representation ◽  
Boundary Vector ◽  
Good Account ◽  
Cell Firing ◽  
Low Dimensional ◽  
Environmental Geometry

AbstractThe hippocampus has long been observed to encode a representation of an animal’s position in space. Recent evidence suggests that the nature of this representation is somewhat predictive and can be modelled by learning a successor representation (SR) between distinct positions in an environment. However, this discretisation of space is subjective making it difficult to formulate predictions about how some environmental manipulations should impact the hippocampal representation. Here we present a model of place and grid cell firing as a consequence of learning a SR from a basis set of known neurobiological features – boundary vector cells (BVCs). The model describes place cell firing as the successor features of the SR, with grid cells forming a low-dimensional representation of these successor features. We show that the place and grid cells generated using the BVC-SR model provide a good account of biological data for a variety of environmental manipulations, including dimensional stretches, barrier insertions, and the influence of environmental geometry on the hippocampal representation of space.

scholarly journals An Incremental Version of L-MVU for the Feature Extraction of MI-EEG

2019 ◽  
Vol 2019 ◽  
pp. 1-19
Author(s):  
Mingai Li ◽  
Hongwei Xi ◽  
Xiaoqing Zhu
Keyword(s):  
Feature Extraction ◽  
Extraction Method ◽  
Average Energy ◽  
High Dimensional ◽  
Dimensional Representation ◽  
Feature Extraction Method ◽  
Sample Data ◽  
Out Of Sample ◽  
Nonlinear Features ◽  
Low Dimensional

Due to the nonlinear and high-dimensional characteristics of motor imagery electroencephalography (MI-EEG), it can be challenging to get high online accuracy. As a nonlinear dimension reduction method, landmark maximum variance unfolding (L-MVU) can completely retain the nonlinear features of MI-EEG. However, L-MVU still requires considerable computation costs for out-of-sample data. An incremental version of L-MVU (denoted as IL-MVU) is proposed in this paper. The low-dimensional representation of the training data is generated by L-MVU. For each out-of-sample data, its nearest neighbors will be found in the high-dimensional training samples and the corresponding reconstruction weight matrix be calculated to generate its low-dimensional representation as well. IL-MVU is further combined with the dual-tree complex wavelet transform (DTCWT), which develops a hybrid feature extraction method (named as IL-MD). IL-MVU is applied to extract the nonlinear features of the specific subband signals, which are reconstructed by DTCWT and have the obvious event-related synchronization/event-related desynchronization phenomenon. The average energy features of α and β waves are calculated simultaneously. The two types of features are fused and are evaluated by a linear discriminant analysis classifier. Based on the two public datasets with 12 subjects, extensive experiments were conducted. The average recognition accuracies of 10-fold cross-validation are 92.50% on Dataset 3b and 88.13% on Dataset 2b, and they gain at least 1.43% and 3.45% improvement, respectively, compared to existing methods. The experimental results show that IL-MD can extract more accurate features with relatively lower consumption cost, and it also has better feature visualization and self-adaptive characteristics to subjects. The t-test results and Kappa values suggest the proposed feature extraction method reaches statistical significance and has high consistency in classification.

EEG Connectivity Analysis Using Denoising Autoencoders for the Detection of Dyslexia

2020 ◽  
Vol 30 (07) ◽  
pp. 2050037
Author(s):  
Francisco J. Martinez-Murcia ◽  
Andres Ortiz ◽  
Juan Manuel Gorriz ◽  
Javier Ramirez ◽  
Pedro Javier Lopez-Abarejo ◽  
...  
Keyword(s):  
Primary Auditory Cortex ◽  
Cognitive Tasks ◽  
Connectivity Analysis ◽  
Dimensional Representation ◽  
Denoising Autoencoder ◽  
Classification Analysis ◽  
Temporal Sampling ◽  
Reading Efficiency ◽  
Eeg Connectivity ◽  
Low Dimensional

The Temporal Sampling Framework (TSF) theorizes that the characteristic phonological difficulties of dyslexia are caused by an atypical oscillatory sampling at one or more temporal rates. The LEEDUCA study conducted a series of Electroencephalography (EEG) experiments on children listening to amplitude modulated (AM) noise with slow-rythmic prosodic (0.5–1[Formula: see text]Hz), syllabic (4–8[Formula: see text]Hz) or the phoneme (12–40[Formula: see text]Hz) rates, aimed at detecting differences in perception of oscillatory sampling that could be associated with dyslexia. The purpose of this work is to check whether these differences exist and how they are related to children’s performance in different language and cognitive tasks commonly used to detect dyslexia. To this purpose, temporal and spectral inter-channel EEG connectivity was estimated, and a denoising autoencoder (DAE) was trained to learn a low-dimensional representation of the connectivity matrices. This representation was studied via correlation and classification analysis, which revealed ability in detecting dyslexic subjects with an accuracy higher than 0.8, and balanced accuracy around 0.7. Some features of the DAE representation were significantly correlated ([Formula: see text]) with children’s performance in language and cognitive tasks of the phonological hypothesis category such as phonological awareness and rapid symbolic naming, as well as reading efficiency and reading comprehension. Finally, a deeper analysis of the adjacency matrix revealed a reduced bilateral connection between electrodes of the temporal lobe (roughly the primary auditory cortex) in DD subjects, as well as an increased connectivity of the F7 electrode, placed roughly on Broca’s area. These results pave the way for a complementary assessment of dyslexia using more objective methodologies such as EEG.

scholarly journals Tracking Full-Body Motion of Multiple Fish with Midline Subspace Constrained Multicue Optimization

2019 ◽  
Vol 2019 ◽  
pp. 1-7
Author(s):  
Xiang Liu ◽  
Pei Ru Zhu ◽  
Ye Liu ◽  
Jing Wen Zhao
Keyword(s):  
Objective Function ◽  
Complex Shape ◽  
The Body ◽  
Body Motion ◽  
Sources Of Information ◽  
Dimensional Representation ◽  
Multiple Sources ◽  
Optimization Framework ◽  
Low Dimensional ◽  
Full Body

Capturing the body motion of fish has been gaining considerable attention from scientists of various fields. In this paper, we propose a method which is able to track the full-body motion of multiple fish with frequent interactions. We firstly propose to model the midline subspace of a fish body which gives a compact low-dimensional representation of the complex shape and motion. Then we propose a particle swarm-based optimization framework whose objective function takes into account multiple sources of information. The proposed multicue objective function is able to describe the details of fish appearance and is also effective through mutual occlusions. Excessive experimental results have demonstrated the effectiveness and robustness of the proposed method.

scholarly journals GLEE: Geometric Laplacian Eigenmap Embedding

2020 ◽  
Vol 8 (2) ◽  
Author(s):  
Leo Torres ◽  
Kevin S Chan ◽  
Tina Eliassi-Rad
Keyword(s):  
Link Prediction ◽  
Graph Embedding ◽  
Laplacian Matrix ◽  
Dimensional Representation ◽  
Laplacian Eigenmaps ◽  
New Approach ◽  
Graph Reconstruction ◽  
Node Similarity ◽  
Distance Minimization ◽  
Low Dimensional

Abstract Graph embedding seeks to build a low-dimensional representation of a graph $G$. This low-dimensional representation is then used for various downstream tasks. One popular approach is Laplacian Eigenmaps (LE), which constructs a graph embedding based on the spectral properties of the Laplacian matrix of $G$. The intuition behind it, and many other embedding techniques, is that the embedding of a graph must respect node similarity: similar nodes must have embeddings that are close to one another. Here, we dispose of this distance-minimization assumption. Instead, we use the Laplacian matrix to find an embedding with geometric properties instead of spectral ones, by leveraging the so-called simplex geometry of $G$. We introduce a new approach, Geometric Laplacian Eigenmap Embedding, and demonstrate that it outperforms various other techniques (including LE) in the tasks of graph reconstruction and link prediction.

scholarly journals Combined Reinforcement Learning via Abstract Representations

2019 ◽  
Vol 33 ◽  
pp. 3582-3589 ◽  
Author(s):  
Vincent Francois-Lavet ◽  
Yoshua Bengio ◽  
Doina Precup ◽  
Joelle Pineau
Keyword(s):  
Reinforcement Learning ◽  
State Space ◽  
Transfer Learning ◽  
Computationally Efficient ◽  
Dimensional Representation ◽  
Learning Methods ◽  
Model Free ◽  
Abstract Representations ◽  
Low Dimensional ◽  
New Strategies

In the quest for efficient and robust reinforcement learning methods, both model-free and model-based approaches offer advantages. In this paper we propose a new way of explicitly bridging both approaches via a shared low-dimensional learned encoding of the environment, meant to capture summarizing abstractions. We show that the modularity brought by this approach leads to good generalization while being computationally efficient, with planning happening in a smaller latent state space. In addition, this approach recovers a sufficient low-dimensional representation of the environment, which opens up new strategies for interpretable AI, exploration and transfer learning.

Correspondence Analysis: Graphical Representation of Categorical Data in Marketing Research

1986 ◽  
Vol 23 (3) ◽  
pp. 213-227 ◽  
Author(s):  
Donna L. Hoffman ◽  
George R. Franke
Keyword(s):  
Correspondence Analysis ◽  
Categorical Data ◽  
Graphical Representation ◽  
Dimensional Space ◽  
Soft Drink ◽  
Marketing Research ◽  
Data Matrix ◽  
Soft Drink Consumption ◽  
Analysis Technique ◽  
Low Dimensional

Correspondence analysis is an exploratory data analysis technique for the graphical display of contingency tables and multivariate categorical data. Its history can be traced back at least 50 years under a variety of names, but it has received little attention in the marketing literature. Correspondence analysis scales the rows and columns of a rectangular data matrix in corresponding units so that each can be displayed graphically in the same low-dimensional space. The authors present the theory behind the method, illustrate its use and interpretation with an example representing soft drink consumption, and discuss its relationship to other approaches that jointly represent the rows and columns of a rectangular data matrix.

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