Sequence Weights - Semantic Scholar
... simply removing or ignoring sequences that are more than % identical to some sequence already included. Advantages: Very fast and simple. Duplicating a sequence does not alter results. Disadvantages: No definition of what is being optimized. Dependent on order in which sequences are considered. Som ...
... simply removing or ignoring sequences that are more than % identical to some sequence already included. Advantages: Very fast and simple. Duplicating a sequence does not alter results. Disadvantages: No definition of what is being optimized. Dependent on order in which sequences are considered. Som ...
Statistical Genetics
... genetics provoking new developments in statistical theory. In fact some modern parameter search procedures (“genetic algorithms”), which could be used in any field of statistical application, even rely on the principles of genetics. The first genetic principles were formulated by the Austrian monk, ...
... genetics provoking new developments in statistical theory. In fact some modern parameter search procedures (“genetic algorithms”), which could be used in any field of statistical application, even rely on the principles of genetics. The first genetic principles were formulated by the Austrian monk, ...
Neural agents can evolve to reproduce sequences
... neural networks, which enables them to produce large neural networks from comparatively small genomes. Examples of such methods include HyperNEAT, NEATfields and Compressed Network Complexity Search (Stanley et al., 2009; Inden et al., 2012; Gomez et al., 2012). These methods enhance the scalability ...
... neural networks, which enables them to produce large neural networks from comparatively small genomes. Examples of such methods include HyperNEAT, NEATfields and Compressed Network Complexity Search (Stanley et al., 2009; Inden et al., 2012; Gomez et al., 2012). These methods enhance the scalability ...
Lecture 6: May 31, 2007 6.1 Introduction to Classification 6.2
... Accuracy The accuracy of a classifier can be evaluated using a test set with known class derivation for every item. The classification error can be tested using varying schemes, which will be discussed in 6.7.1. Transparency Some classification functions are very clear (for example a threshold funct ...
... Accuracy The accuracy of a classifier can be evaluated using a test set with known class derivation for every item. The classification error can be tested using varying schemes, which will be discussed in 6.7.1. Transparency Some classification functions are very clear (for example a threshold funct ...
Document
... Comparing DNA and protein based phylogenies can be useful – Different genes - e.g. 18S rRNA versus EF-2 protein – Protein encoding gene - codons versus amino acids ...
... Comparing DNA and protein based phylogenies can be useful – Different genes - e.g. 18S rRNA versus EF-2 protein – Protein encoding gene - codons versus amino acids ...
history
... generation time of 25 years resulted in a TMRCA of 7,325-39,900 years ago. Averaging over all of our best models, the mean TMRCA is 513 generations ago or about 12,825 years ago. The 95% confidence intervals for all of the best models produced ages for the MRCA of the 9-repeat allele, that range fro ...
... generation time of 25 years resulted in a TMRCA of 7,325-39,900 years ago. Averaging over all of our best models, the mean TMRCA is 513 generations ago or about 12,825 years ago. The 95% confidence intervals for all of the best models produced ages for the MRCA of the 9-repeat allele, that range fro ...
Forest Genetics and Productivity: The Role of Seed Source Control
... temperatures seem to occur every few years. Drought years, although infrequent, can be successive and, depending on drought severity, rewatered trees may or may not return to normal. Cold hardiness and drought resistance are only a few characteristics necessary for growth and survival. It is importa ...
... temperatures seem to occur every few years. Drought years, although infrequent, can be successive and, depending on drought severity, rewatered trees may or may not return to normal. Cold hardiness and drought resistance are only a few characteristics necessary for growth and survival. It is importa ...
Nuclear Gene Trees and the Phylogenetic Relationships of the
... Phylogenetic relationships of mangabeys within the Old World monkey tribe Papionini are inferred from analyses of nuclear DNA sequences from five unlinked loci. The following conclusions are strongly supported, based on congruence among trees derived for the five separate gene regions: (1) mangabeys ...
... Phylogenetic relationships of mangabeys within the Old World monkey tribe Papionini are inferred from analyses of nuclear DNA sequences from five unlinked loci. The following conclusions are strongly supported, based on congruence among trees derived for the five separate gene regions: (1) mangabeys ...
Speeding up the Consensus Clustering methodology for microarray
... • Missing results for G-Gap, GAP, WCSS,FOM and CLEST on 7 data sets - Normal, Novartis, PBM, St. Jude, Gaussian 3, 5 and 6. • There are known algorithms for computing the “knee” of a curve (known as the L-shape algorithm), it seems that no such algorithm was tested here. ...
... • Missing results for G-Gap, GAP, WCSS,FOM and CLEST on 7 data sets - Normal, Novartis, PBM, St. Jude, Gaussian 3, 5 and 6. • There are known algorithms for computing the “knee” of a curve (known as the L-shape algorithm), it seems that no such algorithm was tested here. ...
Massachusetts Institute of Technology
... b. What is the time to the most recent common ancestor? Write it down. c. Repeat (a) and (b) 5 times (by pressing recalc). How does the time to first coalescence and time to most recent common ancestor vary? 2. Repeat with n= 10 and n=20 sequences. What are the times to the first coalescence and the ...
... b. What is the time to the most recent common ancestor? Write it down. c. Repeat (a) and (b) 5 times (by pressing recalc). How does the time to first coalescence and time to most recent common ancestor vary? 2. Repeat with n= 10 and n=20 sequences. What are the times to the first coalescence and the ...
PPTX - UT Computer Science
... profiling. These methods only classify fragments that are assigned to their marker genes. They will fail to classify some fragments. ...
... profiling. These methods only classify fragments that are assigned to their marker genes. They will fail to classify some fragments. ...
Generative Choreography using Deep Learning
... Can a computer create meaningful choreographies? With its potential to expand and facilitate artistic expression, this question has been explored since the start of the computer age. For answering it, a good starting point is to identify the different levels that go into a choreographic work. A chor ...
... Can a computer create meaningful choreographies? With its potential to expand and facilitate artistic expression, this question has been explored since the start of the computer age. For answering it, a good starting point is to identify the different levels that go into a choreographic work. A chor ...
J-Express Pro Practicals 2
... “Ok” and then “Close”. 5. Resize the window to make it bigger 6. Different things may happen when you select some samples in this window. To zoom in on some samples (square symbols), click on the “Framecontents To PCA” button before dragging a frame around the samples (click and drag the mouse aroun ...
... “Ok” and then “Close”. 5. Resize the window to make it bigger 6. Different things may happen when you select some samples in this window. To zoom in on some samples (square symbols), click on the “Framecontents To PCA” button before dragging a frame around the samples (click and drag the mouse aroun ...
What is a Database
... • A field is a single piece of information; • a record is one complete set of fields • a file is a collection of records. For example, a telephone book is analogous to a file. It contains a list of records, each of which consists of three fields: name, address, and ...
... • A field is a single piece of information; • a record is one complete set of fields • a file is a collection of records. For example, a telephone book is analogous to a file. It contains a list of records, each of which consists of three fields: name, address, and ...
Data Mining in Bioinformatics using Weka
... Weka’s clustering algorithms. These include k-means, mixtures of normal distributions with diagonal co-variance matrices estimated using EM, and a heuristic incremental hierarchical clustering scheme. Cluster assignments can be visualized and compared to actual clusters defined by one of the attribu ...
... Weka’s clustering algorithms. These include k-means, mixtures of normal distributions with diagonal co-variance matrices estimated using EM, and a heuristic incremental hierarchical clustering scheme. Cluster assignments can be visualized and compared to actual clusters defined by one of the attribu ...
Integrated analysis of regulatory and metabolic networks
... almost doubled the number of gene expression discrepancies that could be explained through regulatory cascades derived from the data. • The predictions of growth rates of TF deletion strains made by the iMH805/837 model were in good agreement with experimentally measured growth rates for most TF/car ...
... almost doubled the number of gene expression discrepancies that could be explained through regulatory cascades derived from the data. • The predictions of growth rates of TF deletion strains made by the iMH805/837 model were in good agreement with experimentally measured growth rates for most TF/car ...
Molecular Phylogenetic Analysis Among Bryophytes and
... (Nta, (Osa, Zma))), 135,000 trees were examined for their approximate likelihoods under the JTT-F model (Jones, Taylor, and Thornton 1992) with the ‘‘-e’’ option, and the best 3,000 trees were extracted. The likelihood of each of those 3,000 trees was evaluated. Local bootstrap probability was estim ...
... (Nta, (Osa, Zma))), 135,000 trees were examined for their approximate likelihoods under the JTT-F model (Jones, Taylor, and Thornton 1992) with the ‘‘-e’’ option, and the best 3,000 trees were extracted. The likelihood of each of those 3,000 trees was evaluated. Local bootstrap probability was estim ...
The optimization of feed forward neural networks structure using
... Ioan Ileană, Corina Rotar, Arpad Incze - The optimization of feed forward neural networks structure using genetic algorithms dimension implies the establishment of the layer number, neuron number in each layer and interconnections between neurons. At the time being, there are no formal methods for ...
... Ioan Ileană, Corina Rotar, Arpad Incze - The optimization of feed forward neural networks structure using genetic algorithms dimension implies the establishment of the layer number, neuron number in each layer and interconnections between neurons. At the time being, there are no formal methods for ...
Ray-tracing Method for Estimating Radio Propagation Using Genetic
... We propose a GA ray-tracing method which applies a genetic algorithm to ray tracing in order to complete the large-scale computation of estimating radio propagation in a practical amount of time. We describe the GA ray-tracing method as well as a demonstration of its effectiveness through numerical ...
... We propose a GA ray-tracing method which applies a genetic algorithm to ray tracing in order to complete the large-scale computation of estimating radio propagation in a practical amount of time. We describe the GA ray-tracing method as well as a demonstration of its effectiveness through numerical ...
Gene expression
... population is derived from the best individuals of that pool. To guarantee that the population contains each solution only once duplicates are eliminated. The recombination operator is a modified uniform crossover, similar to the uniform crossover for binary strings . To preserve the number of clust ...
... population is derived from the best individuals of that pool. To guarantee that the population contains each solution only once duplicates are eliminated. The recombination operator is a modified uniform crossover, similar to the uniform crossover for binary strings . To preserve the number of clust ...
MSWord
... of microarray gene expression datasets (Culhane et al., 2003). CIA is a multivariate method that identifies trends or co-relationships in multiple datasets which contain the same samples. That is either the rows or the columns of a matrix must be "matchable". CIA can be applied to datasets where the ...
... of microarray gene expression datasets (Culhane et al., 2003). CIA is a multivariate method that identifies trends or co-relationships in multiple datasets which contain the same samples. That is either the rows or the columns of a matrix must be "matchable". CIA can be applied to datasets where the ...
Interactive Visual Analysis of Gene Expression Data
... Multiple data types. Ability to see patterns across different types of data, including networks, pathways, sequences, tabular data, images, 3-D, text. Multiple modes of interaction, including static visualizations, interactive “what-if” visual analyses, multiple time slices, dynamic data. Interactiv ...
... Multiple data types. Ability to see patterns across different types of data, including networks, pathways, sequences, tabular data, images, 3-D, text. Multiple modes of interaction, including static visualizations, interactive “what-if” visual analyses, multiple time slices, dynamic data. Interactiv ...
Human Ovarian carcinoma microarray data analysis based on Support Vector
... select the significant genes, but after all, the data is nonlinear. The statistics difference is not significant and the complexity of classification feature is low. After a series of comparison, we found out that RBF kernel function is the best option for most of the data analysis, because it combi ...
... select the significant genes, but after all, the data is nonlinear. The statistics difference is not significant and the complexity of classification feature is low. After a series of comparison, we found out that RBF kernel function is the best option for most of the data analysis, because it combi ...
Supplemental Material S1
... efficiency parameters. The wiring cost reaches 1 when all possible n (n-1)/2 undirected connections are present (this assumes the higher cost of a single edge is 1). Otherwise, the cost will be defined by values lower than 1. Prior to proceeding with the description of the weighting methods, it is f ...
... efficiency parameters. The wiring cost reaches 1 when all possible n (n-1)/2 undirected connections are present (this assumes the higher cost of a single edge is 1). Otherwise, the cost will be defined by values lower than 1. Prior to proceeding with the description of the weighting methods, it is f ...
Applying Semantic and Network Methods in AOP Knowledge Discovery
... • Generation of literature supported association networks • More open-ended association finding and visualization • Random-Walk methods • Most recent research at IU ...
... • Generation of literature supported association networks • More open-ended association finding and visualization • Random-Walk methods • Most recent research at IU ...