Pub Date : 2016-05-24DOI: 10.4108/EAI.3-12-2015.2262441
A. Parker, H. Bridge, G. Coullon
The spatial distribution of signals from magnetic resonance imaging (MRI) using measures of Blood Oxygen Level Dependent (BOLD) activations presents a fundamental limit on the ability of MRI to resolve the neural signals from the brain. Here we show that the multiple samples of low-level BOLD activity comprise a form of neural “imaging dust” with distinct spatial characteristics. We apply the distance-dependent measurement of variance to spatial maps of BOLD signals to deliver a new approach to estimating the empirical point-spread function (PSF) of MRI. We show that these new estimates are similar to earlier measures of the PSF of high field 7-T imaging, but deliver the advantage that they are specific to each individual tested in a single scanning session. We explore various potential applications of this approach.
{"title":"Spatial scale of correlated signals in 7T BOLD imaging","authors":"A. Parker, H. Bridge, G. Coullon","doi":"10.4108/EAI.3-12-2015.2262441","DOIUrl":"https://doi.org/10.4108/EAI.3-12-2015.2262441","url":null,"abstract":"The spatial distribution of signals from magnetic resonance imaging (MRI) using measures of Blood Oxygen Level Dependent (BOLD) activations presents a fundamental limit on the ability of MRI to resolve the neural signals from the brain. Here we show that the multiple samples of low-level BOLD activity comprise a form of neural “imaging dust” with distinct spatial characteristics. We apply the distance-dependent measurement of variance to spatial maps of BOLD signals to deliver a new approach to estimating the empirical point-spread function (PSF) of MRI. We show that these new estimates are similar to earlier measures of the PSF of high field 7-T imaging, but deliver the advantage that they are specific to each individual tested in a single scanning session. We explore various potential applications of this approach.","PeriodicalId":415083,"journal":{"name":"International Conference on Bio-inspired Information and Communications Technologies","volume":"25 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127527467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-05-24DOI: 10.4108/EAI.3-12-2015.2262350
Aydin Saribudak, Yiyu Dong, J. Hsieh, M. U. Uyar
In this paper, we analyze digitized images of Hematoxylin-Eosin (H&E) slides equipped with tumorous tissues from patient derived xenograft models to build our bio-inspired computation method, namely Personalized Relevance Parameterization of Spatial Randomness (PReP-SR). Applying spatial pattern analysis techniques of quadrat counts, kernel estimation and nearest neighbor functions to the images of the H&E samples, slide-specific features are extracted to examine the hypothesis that existence of dependency of nuclei positions possesses information of individual tumor characteristics. These features are then used as inputs to PReP-SR to compute tumor growth parameters for exponential-linear model. Differential evolution algorithms are developed for tumor growth parameter computations, where a candidate vector in a population consists of size selection indices for spatial evaluation and weight coefficients for spatial features and their correlations. Using leave-one-out-cross-validation method, we showed that, for a set of H&E slides from kidney cancer patient derived xenograft models, PReP-SR generates personalized model parameters with an average error rate of 13.58%. The promising results indicate that bio-inspired computation techniques may be useful to construct mathematical models with patient specific growth parameters in clinical systems.
{"title":"Bio-inspired Computation Approach for Tumor Growth with Spatial Randomness Analysis of Kidney Cancer Xenograft Pathology Slides","authors":"Aydin Saribudak, Yiyu Dong, J. Hsieh, M. U. Uyar","doi":"10.4108/EAI.3-12-2015.2262350","DOIUrl":"https://doi.org/10.4108/EAI.3-12-2015.2262350","url":null,"abstract":"In this paper, we analyze digitized images of Hematoxylin-Eosin \u0000 \u0000(H&E) slides equipped with tumorous tissues from patient derived xenograft models to build our bio-inspired computation method, namely Personalized Relevance Parameterization of Spatial Randomness (PReP-SR). Applying spatial pattern analysis techniques of quadrat counts, kernel estimation and nearest neighbor functions to the images of the H&E samples, slide-specific features are extracted to examine the hypothesis that existence of dependency of nuclei positions possesses information of individual tumor characteristics. \u0000 \u0000These features are then used as inputs to PReP-SR to compute tumor growth parameters for exponential-linear model. Differential evolution \u0000 \u0000algorithms are developed for tumor growth parameter computations, where a candidate vector in a population consists of size selection indices for spatial evaluation and weight coefficients for spatial features and their correlations. Using leave-one-out-cross-validation method, we showed that, for a set of H&E slides from kidney cancer patient derived xenograft models, PReP-SR generates \u0000 \u0000personalized model parameters with an average error rate of \u0000 \u000013.58%. The promising results indicate that bio-inspired computation techniques may be useful to construct mathematical models with patient specific growth parameters in clinical systems.","PeriodicalId":415083,"journal":{"name":"International Conference on Bio-inspired Information and Communications Technologies","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129712043","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-05-24DOI: 10.4108/EAI.3-12-2015.2262486
Dean A. Pospisil, Anitha Pasupathy, W. Bair
Hierarchical neural nets are currently the highest performing general purpose image recognition computer algorithms. Their design is loosely inspired by the neural architecture of the ventral visual pathway in the primate brain, which is believed to underlie the perception of form and the ability to recognize objects. The exact tuning of artificial neural units within an HNN, however, is not prescribed from known biology, but is trained using a performance-based learning algorithm. In evaluating whether HNNs are ripe for further bio-inspired performance improvements, it is of interest to test whether the response properties in the intermediate layers of the HNN approximate those of the ventral visual stream. We therefore characterized units within a popular HNN with a set of visual stimuli that has been employed by neurophysiologists to successfully characterize the shape-tuning properties of neurons in the intermediate visual cortical area V4 of the ventral stream. We found that the tuning and fits of a small but significant number of units in the HNN were strikingly similar to those of some V4 neurons for our simple set of test shapes. There tended to be more such units in the deeper layers of the HNN. We discuss implications of our results to the encoding of curvature in the primate brain and propose ways to further characterize V4-like shape tuning in HNNs.
{"title":"Comparing the brain's representation of shape to that of a deep convolutional neural network","authors":"Dean A. Pospisil, Anitha Pasupathy, W. Bair","doi":"10.4108/EAI.3-12-2015.2262486","DOIUrl":"https://doi.org/10.4108/EAI.3-12-2015.2262486","url":null,"abstract":"Hierarchical neural nets are currently the highest performing \u0000 \u0000general purpose image recognition computer algorithms. Their \u0000 \u0000design is loosely inspired by the neural architecture of the ventral \u0000 \u0000visual pathway in the primate brain, which is believed to underlie \u0000 \u0000the perception of form and the ability to recognize objects. The \u0000 \u0000exact tuning of artificial neural units within an HNN, however, is \u0000 \u0000not prescribed from known biology, but is trained using a \u0000 \u0000performance-based learning algorithm. In evaluating whether \u0000 \u0000HNNs are ripe for further bio-inspired performance \u0000 \u0000improvements, it is of interest to test whether the response \u0000 \u0000properties in the intermediate layers of the HNN approximate \u0000 \u0000those of the ventral visual stream. We therefore characterized \u0000 \u0000units within a popular HNN with a set of visual stimuli that has \u0000 \u0000been employed by neurophysiologists to successfully characterize \u0000 \u0000the shape-tuning properties of neurons in the intermediate visual \u0000 \u0000cortical area V4 of the ventral stream. We found that the tuning \u0000 \u0000and fits of a small but significant number of units in the HNN \u0000 \u0000were strikingly similar to those of some V4 neurons for our simple \u0000 \u0000set of test shapes. There tended to be more such units in the \u0000 \u0000deeper layers of the HNN. We discuss implications of our results \u0000 \u0000to the encoding of curvature in the primate brain and propose \u0000 \u0000ways to further characterize V4-like shape tuning in HNNs.","PeriodicalId":415083,"journal":{"name":"International Conference on Bio-inspired Information and Communications Technologies","volume":"46 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129596556","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-05-24DOI: 10.4108/EAI.3-12-2015.2262391
Seongho Kim, Joohyoung Lee
A practical and powerful approach for stable isotope labeling is stable isotope labeling by amino acids in cell culture (SILAC). A key advantage of SILAC is the ability to detecting simultaneously the isotopically labeled peptides in a single instrument run and so guarantees relative quantitation for a large number of peptides without introducing any variation caused by separate experiments. In this work, we introduce a new quantitative approach to dealing with SILAC protein-level summary using classification-based methodologies. Unlike existing methods, our approach depends mainly on the protein ratio summary and is not restricted only to the proteins with two or more peptide hits. In particular, our approach uses Gaussian mixture model and a stochastic, metaheuristic global optimization algorithm, particle swarm optimization (PSO), to avoid either a premature of convergence or being stuck in a local optimum. Our simulation studies show that the proposed method performs the best in terms of F1 score.
{"title":"A Classification-based Quantitative Approach for SILAC Data","authors":"Seongho Kim, Joohyoung Lee","doi":"10.4108/EAI.3-12-2015.2262391","DOIUrl":"https://doi.org/10.4108/EAI.3-12-2015.2262391","url":null,"abstract":"A practical and powerful approach for stable isotope labeling is stable isotope labeling by amino acids in cell culture (SILAC). A key advantage of SILAC is the ability to detecting simultaneously the isotopically labeled peptides in a single instrument run and so guarantees relative quantitation for a large number of peptides without introducing any variation caused by separate experiments. In this work, we introduce a new quantitative approach to dealing with SILAC protein-level summary using classification-based methodologies. Unlike existing methods, our approach depends mainly \u0000 \u0000on the protein ratio summary and is not restricted only to \u0000 \u0000the proteins with two or more peptide hits. In particular, \u0000 \u0000our approach uses Gaussian mixture model and a stochastic, metaheuristic global optimization algorithm, particle swarm \u0000 \u0000optimization (PSO), to avoid either a premature of convergence or being stuck in a local optimum. Our simulation studies show that the proposed method performs the best in terms of F1 score.","PeriodicalId":415083,"journal":{"name":"International Conference on Bio-inspired Information and Communications Technologies","volume":"50 1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128928520","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-05-24DOI: 10.4108/EAI.3-12-2015.2262521
Shun Zhang, R. Guy, Juan Carlos del Alamo
In this work, we jointly measure the intracellular flow, traction stresses and free intracellular calcium level in physarum microplasmodium during amoeboid locomotion. Our mea- surements relates, for the first time, the intracellular mass transportation, the forces applied on the substrate and the signal of [Ca2+]i with high resolution in both time and space.
{"title":"Coordinations of Intracellular Flow, Calcium Signal and Cellular Contraction in Migrating Physarum","authors":"Shun Zhang, R. Guy, Juan Carlos del Alamo","doi":"10.4108/EAI.3-12-2015.2262521","DOIUrl":"https://doi.org/10.4108/EAI.3-12-2015.2262521","url":null,"abstract":"In this work, we jointly measure the intracellular flow, traction stresses and free intracellular calcium level in physarum microplasmodium during amoeboid locomotion. Our mea- surements relates, for the first time, the intracellular mass transportation, the forces applied on the substrate and the signal of [Ca2+]i with high resolution in both time and space.","PeriodicalId":415083,"journal":{"name":"International Conference on Bio-inspired Information and Communications Technologies","volume":"423 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123144844","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-05-24DOI: 10.4108/EAI.3-12-2015.2262531
M. Haupt, M. Hauser
The slime mold Physarum polycephalum forms an extended network used for transportation of protoplasm through the cell. Although the flow is always laminar, protoplasmic particles are efficiently distributed within the cell. To elucidate how mixing is achieved in such a microfluidic system, we performed PIV experiments and follow tracers in the flow fields. This work was presented at PhysNet 2015
{"title":"Efficient mixing of protoplasm in tubular network of the slime mould Physarum polycephalum","authors":"M. Haupt, M. Hauser","doi":"10.4108/EAI.3-12-2015.2262531","DOIUrl":"https://doi.org/10.4108/EAI.3-12-2015.2262531","url":null,"abstract":"The slime mold Physarum polycephalum forms an extended network used for transportation of protoplasm through the cell. Although the flow is always laminar, protoplasmic particles are efficiently distributed within the cell. To elucidate how mixing is achieved in such a microfluidic system, we performed PIV experiments and follow tracers in the flow fields. This work was presented at PhysNet 2015","PeriodicalId":415083,"journal":{"name":"International Conference on Bio-inspired Information and Communications Technologies","volume":"35 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114353281","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-05-24DOI: 10.4108/EAI.3-12-2015.2262394
W. Marwan
In this paper, we describe a Systems Genetics approach to the sporulation control network in Physarum polycephalum based on the time-resolved analysis of signaling events in individual plasmodial cells.
{"title":"A Systems Genetics Approach to the Sporulation Control Network in Physarum polycephalum","authors":"W. Marwan","doi":"10.4108/EAI.3-12-2015.2262394","DOIUrl":"https://doi.org/10.4108/EAI.3-12-2015.2262394","url":null,"abstract":"In this paper, we describe a Systems Genetics approach to the sporulation control network in Physarum polycephalum based on the time-resolved analysis of signaling events in individual plasmodial cells.","PeriodicalId":415083,"journal":{"name":"International Conference on Bio-inspired Information and Communications Technologies","volume":"110 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124696875","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-05-24DOI: 10.4108/EAI.3-12-2015.2262570
Youngjae Kim, Jung-Ryun Lee, Ji-Young Jung, Eutteum Kong, Uiseong You, Chanjae Lee, Hyun-Ho Choi, Jaesung Park, Myoung-hun Han, Bongsoo Roh, Chanyi Park, Mijeong Hoh, Hyungseok Choi
Recently, researches on resource allocation algorithms operating in a distributed way are widely conducted because of the increasing number of network nodes and the rapidly changing the network environment. In this paper, we propose new biologically inspired TDMA-based resource allocation scheme operating in a distributed manner in multi-hop networks. In this paper, we define a frame structure for the proposed algorithm and firing message structure which is a reference for resource allocation and propose the related operating procedures. Through simulation evaluations, it is shown that proposed algorithm works well in multi-hop networks.
{"title":"Bio-inspired Resource Allocation for Multi-hop Networks","authors":"Youngjae Kim, Jung-Ryun Lee, Ji-Young Jung, Eutteum Kong, Uiseong You, Chanjae Lee, Hyun-Ho Choi, Jaesung Park, Myoung-hun Han, Bongsoo Roh, Chanyi Park, Mijeong Hoh, Hyungseok Choi","doi":"10.4108/EAI.3-12-2015.2262570","DOIUrl":"https://doi.org/10.4108/EAI.3-12-2015.2262570","url":null,"abstract":"Recently, researches on resource allocation algorithms operating \u0000 \u0000in a distributed way are widely conducted because \u0000 \u0000of the increasing number of network nodes and the rapidly \u0000 \u0000changing the network environment. In this paper, we propose \u0000 \u0000new biologically inspired TDMA-based resource allocation \u0000 \u0000scheme operating in a distributed manner in multi-hop \u0000 \u0000networks. In this paper, we define a frame structure for the \u0000 \u0000proposed algorithm and firing message structure which is \u0000 \u0000a reference for resource allocation and propose the related \u0000 \u0000operating procedures. Through simulation evaluations, it \u0000 \u0000is shown that proposed algorithm works well in multi-hop \u0000 \u0000networks.","PeriodicalId":415083,"journal":{"name":"International Conference on Bio-inspired Information and Communications Technologies","volume":"130 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116692668","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-05-24DOI: 10.4108/EAI.3-12-2015.2262474
Owen L. Lewis, R. Guy
{"title":"Investigation of peristaltic pumping as a cellular motility mechanism","authors":"Owen L. Lewis, R. Guy","doi":"10.4108/EAI.3-12-2015.2262474","DOIUrl":"https://doi.org/10.4108/EAI.3-12-2015.2262474","url":null,"abstract":"","PeriodicalId":415083,"journal":{"name":"International Conference on Bio-inspired Information and Communications Technologies","volume":"03 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129459912","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-05-24DOI: 10.4108/EAI.3-12-2015.2262423
Stewart Heitmann, B. Ermentrout
The majority of neurons in primary visual cortex respond preferentially to moving bars of light with a specific orientation and direction of motion. The directional selectivity of those neurons implies that their responses cannot be achieved with separate spatial and temporal neural processes. How cortical neurons achieve non-separable space-time responses is still a mystery. We present a mathematical model of visual cortex in which neurons are predisposed to traveling waves of activity in a given anatomical direction. Those neurons resonate vigorously with moving stimuli that have a similar space-time signature to the intrinsic traveling wave. Yet they are quiescent to stimulus motion in the opposite direction. The model demonstrates how direction-selectivity can arise from the spatiotemporal properties of intrinsic cortical activity without resort to explicit time delays.
{"title":"Propagating Waves as a Cortical Mechanism of Direction-Selectivity in V1 Motion Cells","authors":"Stewart Heitmann, B. Ermentrout","doi":"10.4108/EAI.3-12-2015.2262423","DOIUrl":"https://doi.org/10.4108/EAI.3-12-2015.2262423","url":null,"abstract":"The majority of neurons in primary visual cortex respond preferentially to moving bars of light with a specific orientation and direction of motion. The directional selectivity of those neurons implies that their responses cannot be achieved with separate spatial and temporal neural processes. How cortical neurons achieve non-separable space-time responses is still a mystery. We present a mathematical model of visual cortex in which neurons are predisposed to traveling waves of activity in a given anatomical direction. Those neurons resonate vigorously with moving stimuli that have a similar space-time signature to the intrinsic traveling wave. Yet they are quiescent to stimulus motion in the opposite direction. The model demonstrates how direction-selectivity can arise from the spatiotemporal properties of intrinsic cortical activity without resort to explicit time delays.","PeriodicalId":415083,"journal":{"name":"International Conference on Bio-inspired Information and Communications Technologies","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115028472","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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