scholarly journals Comprehensive analysis of behavioral dynamics in the protochordate Ciona intestinalis

2021 ◽  
Author(s):  
Athira Athira ◽  
Daniel Dondorp ◽  
Jerneja Rudolf ◽  
Olivia Peytral ◽  
Marios Chatzigeorgiou
Keyword(s):  
Light Stimulus ◽  
Dimensional Space ◽  
Ciona Intestinalis ◽  
Building Blocks ◽  
Behavioral Repertoire ◽  
Behavioral Differences ◽  
Behavioral Dynamics ◽  
Spatio Temporal ◽  
Low Dimensional ◽  
Locomotor Behaviors

Locomotion is broadly conserved in the animal kingdom, yet our understanding of how complex locomotor behaviors are generated and have evolved is relatively limited by the lack of an accurate description of their structural organization. Here we take a neuroethological approach to break down the motor behavioral repertoire of one of our nearest invertebrate relative, the protochordate Ciona intestinalis, into basic building blocks. Using machine vision, we track thousands of swimming larvae to obtain a feature-rich description of larval swimming and show that most of the postural variance can be captured by six basic shapes, which we term Eigencionas. Using multiple complementary approaches, we built representations of the larval behavioral dynamics and systematically reveal the global structure of behavior. By employing matrix profiling and subsequence time-series clustering, we reveal that Ciona swimming is rich in stereotyped behavioral motifs. Combining pharmacological inhibition of bioamine signaling with Hidden Markov Model we discover underlying behavioral states including multiple modes of roaming and dwelling. Finally, performing a spatio-temporal embedding of the postural features onto a behavioral space provides insight into the behavioral repertoire by project it to a low-dimensional space and highlights subtle light stimulus evoked behavioral differences. Taken together, Ciona larvae generate their spontaneous swimming and visuomotor behavioral repertoire by altering both their motor modules and transitions between, which are amenable to pharmacological perturbations, facilitating future functional and mechanistic investigations.

Online Long-Term Object Tracking Based on Compressed Haar-Like Features via Sparse Representation

2014 ◽  
Vol 989-994 ◽  
pp. 1610-1614
Author(s):  
Ming Zhao ◽  
Lu Ping Wang ◽  
Lu Ping Zhang
Keyword(s):  
Sparse Representation ◽  
Target Location ◽  
Model Updating ◽  
Dimensional Space ◽  
Reconstruction Error ◽  
Illumination Changes ◽  
Spatio Temporal ◽  
Low Dimensional ◽  
Scale Variation

Online long-term tracking is a challenging problem as data streams change over time. In this paper, sparse representation has been applied to visual tracking by finding the most correct sample with minimal reconstruction error using compressed Haar-like features. However, most sparse representation tracking algorithm introduce l1 regularization into the PCA reconstruction using samples directly, which leads to complexity computation and can not adapt to occlusion, rotation and change in size. Our model updating not only uses the samples from the training set, but also generates the warped versions (include scale variation, rotation, occlusion and illumination changes) for the previous tracking result. Also, we do not use the samples in models for sparse representation directly, but the Haar-like features instead which are compressed in a very low-dimensional space. In addition, we use a robust and fast algorithm which exploits the spatio-temporal context for predicting the target location in the next frame. This step will lead to the reduction of the searching range by the detector. We demonstrate the proposed method is able to track objects well under pose and scale variation, rotation, occlusion and illumination with great real-time performance on challenging image sequences.

scholarly journals GRep: Gene Set Representation via Gaussian Embedding

2019 ◽  
Author(s):  
Sheng Wang ◽  
Emily Flynn ◽  
Russ B. Altman
Keyword(s):  
Gaussian Distribution ◽  
Protein Complexes ◽  
Dimensional Space ◽  
Single Point ◽  
Building Blocks ◽  
Multivariate Gaussian Distribution ◽  
Gene Set ◽  
Gene Sets ◽  
Multivariate Gaussian ◽  
Low Dimensional

ABSTRACTMolecular interaction networks are our basis for understanding functional interdependencies among genes. Network embedding approaches analyze these complicated networks by representing genes as low-dimensional vectors based on the network topology. These low-dimensional vectors have recently become the building blocks for a larger number of systems biology applications. Despite the success of embedding genes in this way, it remains unclear how to effectively represent gene sets, such as protein complexes and signaling pathways. The direct adaptation of existing gene embedding approaches to gene sets cannot model the diverse functions of genes in a set. Here, we propose GRep, a novel gene set embedding approach, which represents each gene set as a multivariate Gaussian distribution rather than a single point in the low-dimensional space. The diversity of genes in a set, or the uncertainty of their contribution to a particular function, is modeled by the covariance matrix of the multivariate Gaussian distribution. By doing so, GRep produces a highly informative and compact gene set representation. Using our representation, we analyze two major pharmacogenomics studies and observe substantial improvement in drug target identification from expression-derived gene sets. Overall, the GRep framework provides a novel representation of gene sets that can be used as input features to off-the-shelf machine learning classifiers for gene set analysis.

scholarly journals Cwebs beyond three loops in multiparton amplitudes

2021 ◽  
Vol 2021 (3) ◽  
Author(s):  
Neelima Agarwal ◽  
Lorenzo Magnea ◽  
Sourav Pal ◽  
Anurag Tripathi
Keyword(s):  
Gauge Theories ◽  
Anomalous Dimension ◽  
Wilson Line ◽  
Building Blocks ◽  
Feynman Diagrams ◽  
Loop Order ◽  
Abelian Gauge ◽  
Sum Rule ◽  
Combinatorial Properties ◽  
Low Dimensional

Abstract Correlators of Wilson-line operators in non-abelian gauge theories are known to exponentiate, and their logarithms can be organised in terms of collections of Feynman diagrams called webs. In [1] we introduced the concept of Cweb, or correlator web, which is a set of skeleton diagrams built with connected gluon correlators, and we computed the mixing matrices for all Cwebs connecting four or five Wilson lines at four loops. Here we complete the evaluation of four-loop mixing matrices, presenting the results for all Cwebs connecting two and three Wilson lines. We observe that the conjuctured column sum rule is obeyed by all the mixing matrices that appear at four-loops. We also show how low-dimensional mixing matrices can be uniquely determined from their known combinatorial properties, and provide some all-order results for selected classes of mixing matrices. Our results complete the required colour building blocks for the calculation of the soft anomalous dimension matrix at four-loop order.

scholarly journals A Generative-Discriminative Framework that Integrates Imaging, Genetic, and Diagnosis into Coupled Low Dimensional Space

NeuroImage ◽  
2021 ◽  
pp. 118200
Author(s):  
Sayan Ghosal ◽  
Qiang Chen ◽  
Giulio Pergola ◽  
Aaron L. Goldman ◽  
William Ulrich ◽  
...  
Keyword(s):  
Dimensional Space ◽  
Low Dimensional

scholarly journals Artifacts in Simultaneous hdEEG/fMRI Imaging: A Nonlinear Dimensionality Reduction Approach

Sensors ◽  
2019 ◽  
Vol 19 (20) ◽  
pp. 4454 ◽  
Author(s):  
Marek Piorecky ◽  
Vlastimil Koudelka ◽  
Jan Strobl ◽  
Martin Brunovsky ◽  
Vladimir Krajca
Keyword(s):  
Data Structure ◽  
Spatial Clustering ◽  
Dimensional Space ◽  
Head Movements ◽  
Nonlinear Dimensionality Reduction ◽  
Space Resolution ◽  
Additional Information ◽  
Nonlinear Dimension ◽  
The Time Domain ◽  
Low Dimensional

Simultaneous recordings of electroencephalogram (EEG) and functional magnetic resonance imaging (fMRI) are at the forefront of technologies of interest to physicians and scientists because they combine the benefits of both modalities—better time resolution (hdEEG) and space resolution (fMRI). However, EEG measurements in the scanner contain an electromagnetic field that is induced in leads as a result of gradient switching slight head movements and vibrations, and it is corrupted by changes in the measured potential because of the Hall phenomenon. The aim of this study is to design and test a methodology for inspecting hidden EEG structures with respect to artifacts. We propose a top-down strategy to obtain additional information that is not visible in a single recording. The time-domain independent component analysis algorithm was employed to obtain independent components and spatial weights. A nonlinear dimension reduction technique t-distributed stochastic neighbor embedding was used to create low-dimensional space, which was then partitioned using the density-based spatial clustering of applications with noise (DBSCAN). The relationships between the found data structure and the used criteria were investigated. As a result, we were able to extract information from the data structure regarding electrooculographic, electrocardiographic, electromyographic and gradient artifacts. This new methodology could facilitate the identification of artifacts and their residues from simultaneous EEG in fMRI.

scholarly journals Optimizing the structure and movement of a robotic bat with biological kinematic synergies

2018 ◽  
Vol 37 (10) ◽  
pp. 1233-1252 ◽  
Author(s):  
Jonathan Hoff ◽  
Alireza Ramezani ◽  
Soon-Jo Chung ◽  
Seth Hutchinson
Keyword(s):  
Principal Component Analysis ◽  
Topological Structure ◽  
Degrees Of Freedom ◽  
Dimensional Space ◽  
Principal Component ◽  
Biologically Inspired ◽  
Wing Kinematics ◽  
Wing Motion ◽  
Kinematic Synergies ◽  
Low Dimensional

In this article, we present methods to optimize the design and flight characteristics of a biologically inspired bat-like robot. In previous, work we have designed the topological structure for the wing kinematics of this robot; here we present methods to optimize the geometry of this structure, and to compute actuator trajectories such that its wingbeat pattern closely matches biological counterparts. Our approach is motivated by recent studies on biological bat flight that have shown that the salient aspects of wing motion can be accurately represented in a low-dimensional space. Although bats have over 40 degrees of freedom (DoFs), our robot possesses several biologically meaningful morphing specializations. We use principal component analysis (PCA) to characterize the two most dominant modes of biological bat flight kinematics, and we optimize our robot’s parametric kinematics to mimic these. The method yields a robot that is reduced from five degrees of actuation (DoAs) to just three, and that actively folds its wings within a wingbeat period. As a result of mimicking synergies, the robot produces an average net lift improvesment of 89% over the same robot when its wings cannot fold.

Reduced $$k$$ k -means clustering with MCA in a low-dimensional space

2014 ◽  
Vol 30 (2) ◽  
pp. 463-475 ◽  
Author(s):  
Masaki Mitsuhiro ◽  
Hiroshi Yadohisa
Keyword(s):  
Dimensional Space ◽  
Low Dimensional

scholarly journals Season- and Trend-aware Symbolic Approximation for Accurate and Efficient Time Series Matching

2021 ◽  
Author(s):  
Lars Kegel ◽  
Claudio Hartmann ◽  
Maik Thiele ◽  
Wolfgang Lehner
Keyword(s):  
Time Series ◽  
State Of The Art ◽  
Dimensional Space ◽  
Symbolic Aggregate Approximation ◽  
Current State ◽  
Optimal Representation ◽  
Symbolic Approximation ◽  
Low Dimensional ◽  
Deterministic Behavior ◽  
Support Time

AbstractProcessing and analyzing time series datasets have become a central issue in many domains requiring data management systems to support time series as a native data type. A core access primitive of time series is matching, which requires efficient algorithms on-top of appropriate representations like the symbolic aggregate approximation (SAX) representing the current state of the art. This technique reduces a time series to a low-dimensional space by segmenting it and discretizing each segment into a small symbolic alphabet. Unfortunately, SAX ignores the deterministic behavior of time series such as cyclical repeating patterns or a trend component affecting all segments, which may lead to a sub-optimal representation accuracy. We therefore introduce a novel season- and a trend-aware symbolic approximation and demonstrate an improved representation accuracy without increasing the memory footprint. Most importantly, our techniques also enable a more efficient time series matching by providing a match up to three orders of magnitude faster than SAX.

scholarly journals Neuroimaging: into the Multiverse

2020 ◽  
Author(s):  
Jessica Dafflon ◽  
Pedro F. Da Costa ◽  
František Váša ◽  
Ricardo Pio Monti ◽  
Danilo Bzdok ◽  
...  
Keyword(s):  
Active Learning ◽  
Statistical Power ◽  
Predictive Power ◽  
Dimensional Space ◽  
Graph Theoretic ◽  
Processing Pipeline ◽  
Regression Approach ◽  
Low Dimensional ◽  
Sequential Analyses ◽  
Processing Steps

AbstractFor most neuroimaging questions the huge range of possible analytic choices leads to the possibility that conclusions from any single analytic approach may be misleading. Examples of possible choices include the motion regression approach used and smoothing and threshold factors applied during the processing pipeline. Although it is possible to perform a multiverse analysis that evaluates all possible analytic choices, this can be computationally challenging and repeated sequential analyses on the same data can compromise inferential and predictive power. Here, we establish how active learning on a low-dimensional space that captures the inter-relationships between analysis approaches can be used to efficiently approximate the whole multiverse of analyses. This approach balances the benefits of a multiverse analysis without the accompanying cost to statistical power, computational power and the integrity of inferences. We illustrate this approach with a functional MRI dataset of functional connectivity across adolescence, demonstrating how a multiverse of graph theoretic and simple pre-processing steps can be efficiently navigated using active learning. Our study shows how this approach can identify the subset of analysis techniques (i.e., pipelines) which are best able to predict participants’ ages, as well as allowing the performance of different approaches to be quantified.

scholarly journals Network Embedding via a Bi-Mode and Deep Neural Network Model

2017 ◽  
Author(s):  
Yang Fang ◽  
Xiang Zhao ◽  
Zhen Tan
Keyword(s):  
Neural Network ◽  
Deep Neural Network ◽  
Semantic Information ◽  
Dimensional Space ◽  
Relation Extraction ◽  
Network Embedding ◽  
Structure Information ◽  
Second Mode ◽  
Real World Datasets ◽  
Low Dimensional

Network Embedding (NE) is an important method to learn the representations of network via a low-dimensional space. Conventional NE models focus on capturing the structure information and semantic information of vertices while neglecting such information for edges. In this work, we propose a novel NE model named BimoNet to capture both the structure and semantic information of edges. BimoNet is composed of two parts, i.e., the bi-mode embedding part and the deep neural network part. For bi-mode embedding part, the first mode named add-mode is used to express the entity-shared features of edges and the second mode named subtract-mode is employed to represent the entity-specific features of edges. These features actually reflect the semantic information. For deep neural network part, we firstly regard the edges in a network as nodes, and the vertices as links, which will not change the overall structure of the whole network. Then we take the nodes' adjacent matrix as the input of the deep neural network as it can obtain similar representations for nodes with similar structure. Afterwards, by jointly optimizing the objective function of these two parts, BimoNet could preserve both the semantic and structure information of edges. In experiments, we evaluate BimoNet on three real-world datasets and task of relation extraction, and BimoNet is demonstrated to outperform state-of-the-art baseline models consistently and significantly.

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