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Algorithms for computational biology : 8th international conference, AlCoB 2021 Missoula, MT, USA, June 7-11, 2021 proceedings / / Carlos Martin-Vide, Miguel A. Vega-Rodriguez, Travis Wheeler, editors
| Algorithms for computational biology : 8th international conference, AlCoB 2021 Missoula, MT, USA, June 7-11, 2021 proceedings / / Carlos Martin-Vide, Miguel A. Vega-Rodriguez, Travis Wheeler, editors |
| Pubbl/distr/stampa | Cham, Switzerland : , : Springer, , [2021] |
| Descrizione fisica | 1 online resource (177 pages) |
| Disciplina | 570.285 |
| Collana | Lecture Notes in Computer Science |
| Soggetto topico |
Computational biology
Algorithms |
| ISBN | 3-030-74432-9 |
| Formato | Materiale a stampa  |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Intro -- Preface -- Organization -- Contents -- Biological Dynamical Systems and Other Biological Processes -- Learning Molecular Classes from Small Numbers of Positive Examples Using Graph Grammars -- 1 Introduction -- 2 Related Work -- 3 Learning the Graph Grammar -- 3.1 Learning a Graph-Grammar -- 4 Experiments -- 4.1 Comparison to Machine Learning on SMILES -- 4.2 Comparison to Standard Machine Learning Using Graph-Grammar Rules as Features -- 5 Conclusion -- References -- Can We Replace Reads by Numeric Signatures? Lyndon Fingerprints as Representations of Sequencing Reads for Machine Learning -- 1 Introduction -- 2 Lyndon Factorizations and Overlapping Reads -- 3 Probabilistic Behaviour of Fingerprints -- 4 Methodology and Experiments -- 4.1 Fingerprint-Based Approach -- 4.2 k-Finger-Based Approach -- 5 Discussion -- References -- Exploiting Variable Sparsity in Computing Equilibria of Biological Dynamical Systems by Triangular Decomposition -- 1 Introduction -- 2 Preliminaries -- 2.1 Autonomous Biological Dynamical Systems and Their Equilibria -- 2.2 Polynomial Sets and Associated Graphs -- 2.3 Triangular Sets and Sparse Triangular Decomposition -- 3 Variable Sparsity in Biological Dynamical Systems -- 3.1 Original Variable Sparsity -- 3.2 Variable Sparsity After Chordal Completion -- 4 Sparse Triangular Decomposition for Computing Equilibria -- 5 Concluding Remarks -- References -- A Recovery Algorithm and Pooling Designs for One-Stage Noisy Group Testing Under the Probabilistic Framework -- 1 Introduction -- 2 Methods -- 2.1 Noisy Group Testing Under the Probabilistic Framework -- 2.2 A Group Testing Protocol -- 2.3 Recovery Algorithm -- 3 Results -- 3.1 Performance of the Recovery Algorithm -- 3.2 Pooling Matrices -- 4 Discussion -- References -- Phylogenetics -- Novel Phylogenetic Network Distances Based on Cherry Picking.
1 Introduction -- 2 Preliminaries -- 2.1 Network Definitions -- 2.2 Cherry Operations -- 3 Distances Based on Cherry-Picking Sequences -- 4 Computing the Tail Distance Between Two Trees -- 4.1 Computing an LR-MAST -- 5 NP-hardness of dtail Between a Tree and a Network -- 6 Discussion and Future Work -- 1 Proof of Lemma 1 (Page 6) -- 2 Proof of Theorems in Sect.3 (Theorem 2 Page 7, Theroem 3 Page 8, Theorem 4 Page 8, Theorem 5 Page 8) -- 3 Proof of Lemma 6, 7 and Theorem 8 (Page 9) -- 4 LR-MAST Algorithm, and Associated Theorem (Page 9) -- 5 Proof of Theorem 10 (Page 12) and Theorem 11 (Page 12) -- References -- Best Match Graphs with Binary Trees -- 1 Introduction -- 2 Best Match Graphs -- 3 Binary Trees Explaining a BMG in Near Cubic Time -- 4 The Binary-Refinable Tree of a BMG -- 5 Simulation Results -- 6 Concluding Remarks -- References -- Scalable and Accurate Phylogenetic Placement Using pplacer-XR -- 1 Introduction -- 2 pplacer-XR -- 3 Experimental Study Design -- 4 Results -- 4.1 Query Placement Accuracy -- 4.2 Time Analysis -- 5 Conclusions -- References -- Comparing Methods for Species Tree Estimation with Gene Duplication and Loss -- 1 Introduction -- 2 Experimental Design -- 3 Results -- 4 Discussion and Conclusion -- References -- Sequence Alignment and Genome Rearrangement -- Reversal Distance on Genomes with Different Gene Content and Intergenic Regions Information -- 1 Introduction -- 2 Background -- 3 Labeled Intergenic Breakpoint Graph -- 4 3-Approximation Algorithm -- 5 Conclusions -- References -- Reversals Distance Considering Flexible Intergenic Regions Sizes -- 1 Introduction -- 2 Definitions -- 2.1 Flexible Weighted Cycle Graph -- 3 Results -- 3.1 Lower Bound -- 3.2 Approximation Algorithm -- 4 Conclusion -- References -- Improved DNA-versus-Protein Homology Search for Protein Fossils -- 1 Introduction -- 2 Methods. 2.1 Alignment Elements -- 2.2 Scoring Scheme -- 2.3 Finding a Maximum-Score Local Alignment -- 2.4 Probability Model -- 2.5 Sum over All Alignments Passing Through (i,j) -- 2.6 Significance Calculation -- 2.7 Seed-and-Extend Heuristic -- 2.8 Fitting Substitution and Gap Parameters to Sequence Data -- 3 Results -- 3.1 Software -- 3.2 Parameter Fitting -- 3.3 Significance Calculation and Simple Sequences -- 3.4 Comparison to Blastx -- 3.5 Discovery of Missing TE Orders in the Human Genome -- 4 Discussion -- References -- The Maximum Weight Trace Alignment Merging Problem -- 1 Introduction -- 2 Maximum Weight Trace Alignment Merging -- 3 Graph Clustering Merger (GCM) -- 4 Experimental Study -- 5 Results -- 6 Conclusions -- References -- Author Index. |
| Record Nr. | UNISA-996464503403316 |
| Cham, Switzerland : , : Springer, , [2021] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. di Salerno | ||
| ||
Algorithms for computational biology : 8th international conference, AlCoB 2021 Missoula, MT, USA, June 7-11, 2021 proceedings / / Carlos Martin-Vide, Miguel A. Vega-Rodriguez, Travis Wheeler, editors
| Algorithms for computational biology : 8th international conference, AlCoB 2021 Missoula, MT, USA, June 7-11, 2021 proceedings / / Carlos Martin-Vide, Miguel A. Vega-Rodriguez, Travis Wheeler, editors |
| Pubbl/distr/stampa | Cham, Switzerland : , : Springer, , [2021] |
| Descrizione fisica | 1 online resource (177 pages) |
| Disciplina | 570.285 |
| Collana | Lecture Notes in Computer Science |
| Soggetto topico |
Computational biology
Algorithms |
| ISBN | 3-030-74432-9 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Intro -- Preface -- Organization -- Contents -- Biological Dynamical Systems and Other Biological Processes -- Learning Molecular Classes from Small Numbers of Positive Examples Using Graph Grammars -- 1 Introduction -- 2 Related Work -- 3 Learning the Graph Grammar -- 3.1 Learning a Graph-Grammar -- 4 Experiments -- 4.1 Comparison to Machine Learning on SMILES -- 4.2 Comparison to Standard Machine Learning Using Graph-Grammar Rules as Features -- 5 Conclusion -- References -- Can We Replace Reads by Numeric Signatures? Lyndon Fingerprints as Representations of Sequencing Reads for Machine Learning -- 1 Introduction -- 2 Lyndon Factorizations and Overlapping Reads -- 3 Probabilistic Behaviour of Fingerprints -- 4 Methodology and Experiments -- 4.1 Fingerprint-Based Approach -- 4.2 k-Finger-Based Approach -- 5 Discussion -- References -- Exploiting Variable Sparsity in Computing Equilibria of Biological Dynamical Systems by Triangular Decomposition -- 1 Introduction -- 2 Preliminaries -- 2.1 Autonomous Biological Dynamical Systems and Their Equilibria -- 2.2 Polynomial Sets and Associated Graphs -- 2.3 Triangular Sets and Sparse Triangular Decomposition -- 3 Variable Sparsity in Biological Dynamical Systems -- 3.1 Original Variable Sparsity -- 3.2 Variable Sparsity After Chordal Completion -- 4 Sparse Triangular Decomposition for Computing Equilibria -- 5 Concluding Remarks -- References -- A Recovery Algorithm and Pooling Designs for One-Stage Noisy Group Testing Under the Probabilistic Framework -- 1 Introduction -- 2 Methods -- 2.1 Noisy Group Testing Under the Probabilistic Framework -- 2.2 A Group Testing Protocol -- 2.3 Recovery Algorithm -- 3 Results -- 3.1 Performance of the Recovery Algorithm -- 3.2 Pooling Matrices -- 4 Discussion -- References -- Phylogenetics -- Novel Phylogenetic Network Distances Based on Cherry Picking.
1 Introduction -- 2 Preliminaries -- 2.1 Network Definitions -- 2.2 Cherry Operations -- 3 Distances Based on Cherry-Picking Sequences -- 4 Computing the Tail Distance Between Two Trees -- 4.1 Computing an LR-MAST -- 5 NP-hardness of dtail Between a Tree and a Network -- 6 Discussion and Future Work -- 1 Proof of Lemma 1 (Page 6) -- 2 Proof of Theorems in Sect.3 (Theorem 2 Page 7, Theroem 3 Page 8, Theorem 4 Page 8, Theorem 5 Page 8) -- 3 Proof of Lemma 6, 7 and Theorem 8 (Page 9) -- 4 LR-MAST Algorithm, and Associated Theorem (Page 9) -- 5 Proof of Theorem 10 (Page 12) and Theorem 11 (Page 12) -- References -- Best Match Graphs with Binary Trees -- 1 Introduction -- 2 Best Match Graphs -- 3 Binary Trees Explaining a BMG in Near Cubic Time -- 4 The Binary-Refinable Tree of a BMG -- 5 Simulation Results -- 6 Concluding Remarks -- References -- Scalable and Accurate Phylogenetic Placement Using pplacer-XR -- 1 Introduction -- 2 pplacer-XR -- 3 Experimental Study Design -- 4 Results -- 4.1 Query Placement Accuracy -- 4.2 Time Analysis -- 5 Conclusions -- References -- Comparing Methods for Species Tree Estimation with Gene Duplication and Loss -- 1 Introduction -- 2 Experimental Design -- 3 Results -- 4 Discussion and Conclusion -- References -- Sequence Alignment and Genome Rearrangement -- Reversal Distance on Genomes with Different Gene Content and Intergenic Regions Information -- 1 Introduction -- 2 Background -- 3 Labeled Intergenic Breakpoint Graph -- 4 3-Approximation Algorithm -- 5 Conclusions -- References -- Reversals Distance Considering Flexible Intergenic Regions Sizes -- 1 Introduction -- 2 Definitions -- 2.1 Flexible Weighted Cycle Graph -- 3 Results -- 3.1 Lower Bound -- 3.2 Approximation Algorithm -- 4 Conclusion -- References -- Improved DNA-versus-Protein Homology Search for Protein Fossils -- 1 Introduction -- 2 Methods. 2.1 Alignment Elements -- 2.2 Scoring Scheme -- 2.3 Finding a Maximum-Score Local Alignment -- 2.4 Probability Model -- 2.5 Sum over All Alignments Passing Through (i,j) -- 2.6 Significance Calculation -- 2.7 Seed-and-Extend Heuristic -- 2.8 Fitting Substitution and Gap Parameters to Sequence Data -- 3 Results -- 3.1 Software -- 3.2 Parameter Fitting -- 3.3 Significance Calculation and Simple Sequences -- 3.4 Comparison to Blastx -- 3.5 Discovery of Missing TE Orders in the Human Genome -- 4 Discussion -- References -- The Maximum Weight Trace Alignment Merging Problem -- 1 Introduction -- 2 Maximum Weight Trace Alignment Merging -- 3 Graph Clustering Merger (GCM) -- 4 Experimental Study -- 5 Results -- 6 Conclusions -- References -- Author Index. |
| Record Nr. | UNINA-9910484962603321 |
| Cham, Switzerland : , : Springer, , [2021] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Algorithms for Computational Biology [[electronic resource] ] : 7th International Conference, AlCoB 2020, Missoula, MT, USA, April 13–15, 2020, Proceedings / / edited by Carlos Martín-Vide, Miguel A. Vega-Rodríguez, Travis Wheeler
| Algorithms for Computational Biology [[electronic resource] ] : 7th International Conference, AlCoB 2020, Missoula, MT, USA, April 13–15, 2020, Proceedings / / edited by Carlos Martín-Vide, Miguel A. Vega-Rodríguez, Travis Wheeler |
| Edizione | [1st ed. 2020.] |
| Pubbl/distr/stampa | Cham : , : Springer International Publishing : , : Imprint : Springer, , 2020 |
| Descrizione fisica | 1 online resource (XVIII, 199 p. 111 illus., 34 illus. in color.) |
| Disciplina | 570.285 |
| Collana | Lecture Notes in Bioinformatics |
| Soggetto topico |
Bioinformatics
Artificial intelligence Algorithms Computer organization Computers Software engineering Computational Biology/Bioinformatics Artificial Intelligence Algorithm Analysis and Problem Complexity Computer Systems Organization and Communication Networks Information Systems and Communication Service Software Engineering/Programming and Operating Systems |
| ISBN | 3-030-42266-6 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Genomics -- Parallel Generalized Su x Tree Construction for Genomic Data -- A 3.5-Approximation Algorithm for Sorting by Intergenic Transpositions -- Heuristics for Reversal Distance between Genomes with Duplicated Genes -- Extending Maximal Perfect Haplotype Blocks to the Realm of Pangenomics -- Gaps and Runs in Syntenic Alignments -- Phylogenetics -- Comparing Integer Linear Programming to SAT-Solving for Hard Problems in Computational and Systems Biology -- Combining Networks Using Cherry Picking Sequences -- Linear Time Algorithm for Tree-Child Network Containment -- PathOGiST: A Novel Method for Clustering Pathogen Isolates by Combining Multiple Genotyping Signals -- TreeSolve: Rapid Error-Correction of Microbial Gene Trees -- RNA-Seq and Other Biological Processes -- Time Series Adjustment Enhancement of Hierarchical Modeling of Arabidopsis Thaliana Gene Interactions -- BESTox: A Convolutional Neural Network Regression Model Based on Binary-Encoded SMILES for Acute Oral Toxicity Prediction of Chemical Compounds -- Stratified Test Alleviates Batch Effects in Single-Cell Data -- A Topological Data Analysis Approach on Predicting Phenotypes from Gene Expression Data -- BOAssembler: A Bayesian Optimization Framework to Improve RNA-Seq Assembly Performance. |
| Record Nr. | UNISA-996418204403316 |
| Cham : , : Springer International Publishing : , : Imprint : Springer, , 2020 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. di Salerno | ||
| ||
Algorithms for Computational Biology : 7th International Conference, AlCoB 2020, Missoula, MT, USA, April 13–15, 2020, Proceedings / / edited by Carlos Martín-Vide, Miguel A. Vega-Rodríguez, Travis Wheeler
| Algorithms for Computational Biology : 7th International Conference, AlCoB 2020, Missoula, MT, USA, April 13–15, 2020, Proceedings / / edited by Carlos Martín-Vide, Miguel A. Vega-Rodríguez, Travis Wheeler |
| Edizione | [1st ed. 2020.] |
| Pubbl/distr/stampa | Cham : , : Springer International Publishing : , : Imprint : Springer, , 2020 |
| Descrizione fisica | 1 online resource (XVIII, 199 p. 111 illus., 34 illus. in color.) |
| Disciplina | 570.285 |
| Collana | Lecture Notes in Bioinformatics |
| Soggetto topico |
Bioinformatics
Artificial intelligence Algorithms Computer organization Computers Software engineering Computational Biology/Bioinformatics Artificial Intelligence Algorithm Analysis and Problem Complexity Computer Systems Organization and Communication Networks Information Systems and Communication Service Software Engineering/Programming and Operating Systems |
| ISBN | 3-030-42266-6 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Genomics -- Parallel Generalized Su x Tree Construction for Genomic Data -- A 3.5-Approximation Algorithm for Sorting by Intergenic Transpositions -- Heuristics for Reversal Distance between Genomes with Duplicated Genes -- Extending Maximal Perfect Haplotype Blocks to the Realm of Pangenomics -- Gaps and Runs in Syntenic Alignments -- Phylogenetics -- Comparing Integer Linear Programming to SAT-Solving for Hard Problems in Computational and Systems Biology -- Combining Networks Using Cherry Picking Sequences -- Linear Time Algorithm for Tree-Child Network Containment -- PathOGiST: A Novel Method for Clustering Pathogen Isolates by Combining Multiple Genotyping Signals -- TreeSolve: Rapid Error-Correction of Microbial Gene Trees -- RNA-Seq and Other Biological Processes -- Time Series Adjustment Enhancement of Hierarchical Modeling of Arabidopsis Thaliana Gene Interactions -- BESTox: A Convolutional Neural Network Regression Model Based on Binary-Encoded SMILES for Acute Oral Toxicity Prediction of Chemical Compounds -- Stratified Test Alleviates Batch Effects in Single-Cell Data -- A Topological Data Analysis Approach on Predicting Phenotypes from Gene Expression Data -- BOAssembler: A Bayesian Optimization Framework to Improve RNA-Seq Assembly Performance. |
| Record Nr. | UNINA-9910409680003321 |
| Cham : , : Springer International Publishing : , : Imprint : Springer, , 2020 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||