Pub Date : 2016-05-24DOI: 10.4108/EAI.3-12-2015.2262498
Xinhua Zhang, Garrett T. Kenyon
Sparse coding is a widely-used technique for learning an overcomplete basis set from unlabeled image data. We hypothesize that as the size of the image patch spanned by each basis vector increases, the resulting dictionary should encompass a broader range of spatial scales, including more features that better discriminate between object classes. Previous efforts to measure the effects of patch size on image classification performance were confounded by the difficulty of maintaining a given level of overcompleteness as the patch size is increased. Here, we employ a type of deconvolutional network in which overcompleteness is independent of patch size. Based on image classification results on the CIFAR10 database, we find that optimizing our deconvolutional network for sparse reconstruction leads to improved classification performance as a function of the number of training epochs. Different from previous reports, we find that enforcing a certain degree of sparsity improves classification performance. We also find that classification performance improves as both the number of learned features (dictionary size) and the size of the image patch spanned by each feature (patch size) are increased, ultimately the best published results for sparse autoencoders
{"title":"A Deconvolutional Strategy for Implementing Large Patch Sizes Supports Improved Image Classification","authors":"Xinhua Zhang, Garrett T. Kenyon","doi":"10.4108/EAI.3-12-2015.2262498","DOIUrl":"https://doi.org/10.4108/EAI.3-12-2015.2262498","url":null,"abstract":"Sparse coding is a widely-used technique for learning an overcomplete basis set from unlabeled image data. We hypothesize that as the size of the image patch spanned by each basis vector increases, the resulting dictionary should encompass a broader range of spatial scales, including more features that better discriminate between object classes. Previous efforts to measure the effects of patch size on image classification performance were confounded by the difficulty of maintaining a given level of overcompleteness as the patch size is increased. Here, we employ a type of deconvolutional network in which overcompleteness is independent of patch size. Based on image classification results on the CIFAR10 database, we find that optimizing our deconvolutional network for sparse reconstruction leads to improved classification performance as a function of the number of training epochs. Different from previous reports, we find that enforcing a certain degree of sparsity improves classification performance. We also find that classification performance improves as both the number of learned features (dictionary size) and the size of the image patch spanned by each feature (patch size) are increased, ultimately the best published results for sparse autoencoders","PeriodicalId":415083,"journal":{"name":"International Conference on Bio-inspired Information and Communications Technologies","volume":"45 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":"115252567","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.3-12-2015.2262458
Naoki Kanatani, H. Kojima, K. Oiwa
Experimental systems have long been demanded for the study of collective motion often observed in biology (a flock of birds, a shoal of fish, cell migrations during development etc). In vitro motility assays commonly used in biophysical studies on protein-motors now fulfill the demand described above. Using the in vitro motility assays, we report collective motion and vortex emergence of microtubules (MTs) driven by some subspecies of axonemal dyneins and find that under some experimental conditions, the collective motion of MTs can display nematic order, millimeter-scale meandering streams or millimeter-scale vortices. To explore the conditions causing such phase-shifts, we examine the effects of mechanical properties of dyneins on the pattern formation.
{"title":"Dynamic Alignment and Millimeter-scale Vortex Formation of Microtubules Driven by Different Types of Dynein","authors":"Naoki Kanatani, H. Kojima, K. Oiwa","doi":"10.4108/EAI.3-12-2015.2262458","DOIUrl":"https://doi.org/10.4108/EAI.3-12-2015.2262458","url":null,"abstract":"Experimental systems have long been demanded for the study of collective motion often observed in biology (a flock of birds, a shoal of fish, cell migrations during development etc). In vitro motility assays commonly used in biophysical studies on protein-motors now fulfill the demand described above. Using the in vitro motility assays, we report collective motion and vortex emergence of microtubules (MTs) driven by some subspecies of axonemal dyneins and find that under some experimental conditions, the collective motion of MTs can display nematic order, millimeter-scale meandering streams or millimeter-scale vortices. To explore the conditions causing such phase-shifts, we examine the effects of mechanical properties of dyneins on the pattern formation.","PeriodicalId":415083,"journal":{"name":"International Conference on Bio-inspired Information and Communications Technologies","volume":"38 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":"128278732","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.3-12-2015.2262523
A. Mamuye, E. Merelli, L. Tesei
In this paper we introduce a shape language for representing RNA secondary structures in a non-standard, non-linear way. The main motivation is to propose a new interpretation of RNA folding as a self-adaptability process, within the S[B] paradigm, towards a minimum free energy configuration. An RNA secondary structure is decomposed first by distinguishing between pseudoknot free and pseudonotted sub-structures. For pseudoknot free sub-structures a proper formal language is defined. To address the representation of pseudoknotted sub-structures the crucial aspects of RNA irreducible shapes and their associated automatic groups are introduced.
{"title":"Towards a Shape Language for Interpreting RNA Folding","authors":"A. Mamuye, E. Merelli, L. Tesei","doi":"10.4108/EAI.3-12-2015.2262523","DOIUrl":"https://doi.org/10.4108/EAI.3-12-2015.2262523","url":null,"abstract":"In this paper we introduce a shape language for representing RNA secondary structures in a non-standard, non-linear way. The main motivation is to propose a new interpretation of RNA folding as a self-adaptability process, within the S[B] paradigm, towards a minimum free energy configuration. \u0000 \u0000An RNA secondary structure is decomposed first by distinguishing between pseudoknot free and pseudonotted sub-structures. For pseudoknot free sub-structures a proper formal language is defined. To address the representation of pseudoknotted sub-structures the crucial aspects of RNA irreducible shapes and their associated automatic groups are introduced.","PeriodicalId":415083,"journal":{"name":"International Conference on Bio-inspired Information and Communications Technologies","volume":"19 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":"122930771","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.3-12-2015.2262398
M. Bär, M. Hauser, Sergio Alonso Muñoz, M. Radszuweit, H. Engel
We consider one prominent example for an active biological fluid, namely the cytoplasm of the true slime mold Physarum polycephalum. We model the cytoskeleton as a solid matrix that together with the cytosol as interstitial fluid constitutes an active poroelastic material and reproduce a large variety of experimentally observed mechanochemical wave forms, e. g. spirals, turbulence, target waves.
{"title":"Dynamics of Physarum Microdroplets - an Example for Mechanochemical Pattern Formation in Active Biological Matter","authors":"M. Bär, M. Hauser, Sergio Alonso Muñoz, M. Radszuweit, H. Engel","doi":"10.4108/EAI.3-12-2015.2262398","DOIUrl":"https://doi.org/10.4108/EAI.3-12-2015.2262398","url":null,"abstract":"We consider one prominent example for an active biological fluid, namely the cytoplasm of the true slime mold Physarum polycephalum. We model the cytoskeleton as a solid matrix that together with the cytosol as interstitial fluid constitutes an active poroelastic material and reproduce a large variety of experimentally observed mechanochemical wave forms, e. g. spirals, turbulence, target waves.","PeriodicalId":415083,"journal":{"name":"International Conference on Bio-inspired Information and Communications Technologies","volume":"82 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":"122314645","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.3-12-2015.2262451
Benjamin J. Dubin-Thaler
The BioBus mobile science lab has helped unlock the scientific potential of thousands of low-income students and their teachers by giving them the chance to hunt for and record movies of amoebae using research microscopes with research scientists. This extended abstract summarizes an invited presentation delivered at PhysNet 2015.
{"title":"Learning with amoeba aboard the BioBus","authors":"Benjamin J. Dubin-Thaler","doi":"10.4108/EAI.3-12-2015.2262451","DOIUrl":"https://doi.org/10.4108/EAI.3-12-2015.2262451","url":null,"abstract":"The BioBus mobile science lab has helped unlock the scientific potential of thousands of low-income students and their teachers by giving them the chance to hunt for and record movies of amoebae using research microscopes with research scientists. This extended abstract summarizes an invited presentation delivered at PhysNet 2015.","PeriodicalId":415083,"journal":{"name":"International Conference on Bio-inspired Information and Communications Technologies","volume":"20 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":"132051869","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.3-12-2015.2262585
R. Pidaparti, Somenath Das, P. Ghosh
Self-assembly is a ubiquitous, naturally occurring, robust process in many living organisms. Microtubule, a self-organization system assembles itself into functional units by attaching to cellular structures. Modeling microtubule self-organization is of interest as microtubule forms a network of protein filaments that is critical to many processes in eukaryotic cells. In this paper, we developed a modeling algorithm starting from alpha and beta tubulins as basic building block in the self-organization of microtubule. The developed algorithm and the necessary steps are described in detail. The preliminary results obtained from the model demonstrate that a stable self-organization conformation is possible for a microtubule.
{"title":"An Algorithm for stable Microtubule Curvature Conformation","authors":"R. Pidaparti, Somenath Das, P. Ghosh","doi":"10.4108/EAI.3-12-2015.2262585","DOIUrl":"https://doi.org/10.4108/EAI.3-12-2015.2262585","url":null,"abstract":"Self-assembly is a ubiquitous, naturally occurring, robust process in many living organisms. Microtubule, a self-organization system assembles itself into functional units by attaching to cellular structures. Modeling microtubule self-organization is of interest as microtubule forms a network of protein filaments that is critical to many processes in eukaryotic cells. In this paper, we developed a modeling algorithm starting from alpha and beta tubulins as basic building block in the self-organization of microtubule. The developed algorithm and the necessary steps are described in detail. The preliminary results obtained from the model demonstrate that a stable self-organization conformation is possible for a microtubule.","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":"130217303","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.3-12-2015.2262416
Y. Yajima, T. Hoshino, N. Kondo
{"title":"Three-dimensional imaging of structural development in the fruiting body of field-collected true slime molds","authors":"Y. Yajima, T. Hoshino, N. Kondo","doi":"10.4108/EAI.3-12-2015.2262416","DOIUrl":"https://doi.org/10.4108/EAI.3-12-2015.2262416","url":null,"abstract":"","PeriodicalId":415083,"journal":{"name":"International Conference on Bio-inspired Information and Communications Technologies","volume":"87 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":"126307936","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 : 2015-11-04DOI: 10.4108/EAI.3-12-2015.2262453
Kevin J. Emmett, Benjamin Schweinhart, R. Rabadán
The three dimensional structure of DNA in the nucleus (chromatin) plays an important role in many cellular processes. Recent experimental advances have led to high-throughput methods of capturing information about chromatin conformation on genome-wide scales. New models are needed to quantitatively interpret this data at a global scale. Here we introduce the use of tools from topological data analysis to study chromatin conformation. We use persistent homology to identify and characterize conserved loops and voids in contact map data and identify scales of interaction. We demonstrate the utility of the approach on simulated data and then look data from both a bacterial genome and a human cell line. We identify substantial multiscale topology in these datasets.
{"title":"Multiscale Topology of Chromatin Folding","authors":"Kevin J. Emmett, Benjamin Schweinhart, R. Rabadán","doi":"10.4108/EAI.3-12-2015.2262453","DOIUrl":"https://doi.org/10.4108/EAI.3-12-2015.2262453","url":null,"abstract":"The three dimensional structure of DNA in the nucleus (chromatin) plays an important role in many cellular processes. Recent experimental advances have led to high-throughput methods of capturing information about chromatin conformation on genome-wide scales. New models are needed to quantitatively interpret this data at a global scale. Here we introduce the use of tools from topological data analysis to study chromatin conformation. We use persistent homology to identify and characterize conserved loops and voids in contact map data and identify scales of interaction. We demonstrate the utility of the approach on simulated data and then look data from both a bacterial genome and a human cell line. We identify substantial multiscale topology in these datasets.","PeriodicalId":415083,"journal":{"name":"International Conference on Bio-inspired Information and Communications Technologies","volume":"53 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130470322","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 : 2015-11-04DOI: 10.4108/EAI.3-12-2015.2262454
Kevin J. Emmett, R. Rabadán
Reticulate evolutionary processes result in phylogenetic histories that cannot be modeled using a tree topology. Here, we apply methods from topological data analysis to molecular sequence data with reticulations. Using a simple example, we demonstrate the correspondence between nontrivial higher homology and reticulate evolution. We discuss the sensitivity of the standard filtration and show cases where reticulate evolution can fail to be detected. We introduce an extension of the standard framework and define the median complex as a construction to recover signal of the frequency and scale of reticulate evolution by inferring and imputing putative ancestral states. Finally, we apply our methods to two datasets from phylogenetics. Our work expands on earlier ideas of using topology to extract important evolutionary features from genomic data.
{"title":"Quantifying Reticulation in Phylogenetic Complexes Using Homology","authors":"Kevin J. Emmett, R. Rabadán","doi":"10.4108/EAI.3-12-2015.2262454","DOIUrl":"https://doi.org/10.4108/EAI.3-12-2015.2262454","url":null,"abstract":"Reticulate evolutionary processes result in phylogenetic histories that cannot be modeled using a tree topology. Here, we apply methods from topological data analysis to molecular sequence data with reticulations. Using a simple example, we demonstrate the correspondence between nontrivial higher homology and reticulate evolution. We discuss the sensitivity of the standard filtration and show cases where reticulate evolution can fail to be detected. We introduce an extension of the standard framework and define the median complex as a construction to recover signal of the frequency and scale of reticulate evolution by inferring and imputing putative ancestral states. Finally, we apply our methods to two datasets from phylogenetics. Our work expands on earlier ideas of using topology to extract important evolutionary features from genomic data.","PeriodicalId":415083,"journal":{"name":"International Conference on Bio-inspired Information and Communications Technologies","volume":"14 1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127157170","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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