Bolstering is an error estimation technique that provides a less biased estimation than resubstitution. While a general bolstering model exists for continuous classification spaces, discrete classifiers present a more complex framework. The paper proposes a bolstering model for discrete classification based on a convolution kernel applied to conditional probabilities. This approach could help infer genetic regulatory functions from microarray data by deducing transcriptional states of genes based on other genes' states.
The urinary system produces, stores, and eliminates urine and includes the kidneys, ureters, bladder, and urethra. It was described along with abbreviations for chronic renal failure (CRF), urinary tract infection (UTI), and urine culture (UC). CRF is the progressive loss of renal function over time that can be detected by increased creatinine or urine protein. A UTI is a bacterial infection of the urinary tract that is more common in women and often treated with antibiotics. A UC is a test to detect bacteria in urine and determine antibiotic sensitivity to diagnose and treat a UTI.
The document discusses various technology companies and their use of social media. It provides details on the social media presence and activities of companies like Round Arch, Design Kitchen, Adaptive Path, Headspring, Springbox, T3, Frog, and Razorfish. It then discusses how Quotient could start using social media by first creating a blog and presence on Facebook and Twitter to share company and technology news. It suggests designating employees to maintain different social media activities and working collaboratively to launch and maintain their social media.
This document discusses sex-linked and X-linked inheritance patterns. It provides information on pedigree analysis and the four main inheritance patterns: autosomal recessive, autosomal dominant, X-linked recessive, and X-linked dominant. For X-linked traits, it notes that males are typically affected for recessive traits since they do not have a second X chromosome to provide the working gene. It provides examples of color blindness and hemophilia to illustrate X-linked recessive inheritance and how traits can skip generations and be passed from carrier mothers to affected sons.
There was heavy rain in Taipei City on December 19th. People in Taipei wore heavy clothes, raincoats, and umbrellas due to the cold and rainy weather. In Miaoli County, the weather was bitterly cold without any rain. Residents dressed in thick sweaters, socks, and mittens to stay warm.
Este documento describe un estudio presentado en el 2o Congreso Argentino de Bioinformática y Biología Computacional en la Universidad Católica de Córdoba entre el 11 y 13 de mayo de 2011. El estudio desarrolló nuevos descriptores y un modelo QSPR utilizando redes neuronales artificiales para predecir la temperatura de transición vítrea molar de polímeros. El modelo se basó en cuatro descriptores relacionados con las áreas superficiales y enlaces rotatorios de las cadenas laterales y principales de la unidad repetitiva promedio
Este documento describe las actividades de la Unidad de Bioinformática del INTA en Argentina. En 3 oraciones o menos:
La Unidad de Bioinformática del INTA ha realizado estudios genómicos limitados en girasol y ha desarrollado herramientas bioinformáticas para analizar secuencias moleculares. Han colaborado con otras instituciones para crear una base de datos y han formado recursos humanos a través de cursos y pasantías para aplicar tecnología informática a preguntas biológicas. El objetivo es responder preguntas biol
This document analyzes the sequence and functional evolution of the E7 protein in papillomaviruses using 210 natural sequences. It finds that:
1) The intrinsically disordered N-terminal domain (E7N) and globular C-terminal domain (E7C) are both highly conserved, despite E7N lacking a stable structure.
2) Key linear motifs in E7N, like the LxCxE Rb-binding site and CKII phosphorylation site, have coevolved and suggest a functional relationship.
3) The C-terminal domain is also highly conserved, retaining zinc-binding cysteines and residues important for dimerization and interactions with cellular targets.
The urinary system produces, stores, and eliminates urine and includes the kidneys, ureters, bladder, and urethra. It was described along with abbreviations for chronic renal failure (CRF), urinary tract infection (UTI), and urine culture (UC). CRF is the progressive loss of renal function over time that can be detected by increased creatinine or urine protein. A UTI is a bacterial infection of the urinary tract that is more common in women and often treated with antibiotics. A UC is a test to detect bacteria in urine and determine antibiotic sensitivity to diagnose and treat a UTI.
The document discusses various technology companies and their use of social media. It provides details on the social media presence and activities of companies like Round Arch, Design Kitchen, Adaptive Path, Headspring, Springbox, T3, Frog, and Razorfish. It then discusses how Quotient could start using social media by first creating a blog and presence on Facebook and Twitter to share company and technology news. It suggests designating employees to maintain different social media activities and working collaboratively to launch and maintain their social media.
This document discusses sex-linked and X-linked inheritance patterns. It provides information on pedigree analysis and the four main inheritance patterns: autosomal recessive, autosomal dominant, X-linked recessive, and X-linked dominant. For X-linked traits, it notes that males are typically affected for recessive traits since they do not have a second X chromosome to provide the working gene. It provides examples of color blindness and hemophilia to illustrate X-linked recessive inheritance and how traits can skip generations and be passed from carrier mothers to affected sons.
There was heavy rain in Taipei City on December 19th. People in Taipei wore heavy clothes, raincoats, and umbrellas due to the cold and rainy weather. In Miaoli County, the weather was bitterly cold without any rain. Residents dressed in thick sweaters, socks, and mittens to stay warm.
Este documento describe un estudio presentado en el 2o Congreso Argentino de Bioinformática y Biología Computacional en la Universidad Católica de Córdoba entre el 11 y 13 de mayo de 2011. El estudio desarrolló nuevos descriptores y un modelo QSPR utilizando redes neuronales artificiales para predecir la temperatura de transición vítrea molar de polímeros. El modelo se basó en cuatro descriptores relacionados con las áreas superficiales y enlaces rotatorios de las cadenas laterales y principales de la unidad repetitiva promedio
Este documento describe las actividades de la Unidad de Bioinformática del INTA en Argentina. En 3 oraciones o menos:
La Unidad de Bioinformática del INTA ha realizado estudios genómicos limitados en girasol y ha desarrollado herramientas bioinformáticas para analizar secuencias moleculares. Han colaborado con otras instituciones para crear una base de datos y han formado recursos humanos a través de cursos y pasantías para aplicar tecnología informática a preguntas biológicas. El objetivo es responder preguntas biol
This document analyzes the sequence and functional evolution of the E7 protein in papillomaviruses using 210 natural sequences. It finds that:
1) The intrinsically disordered N-terminal domain (E7N) and globular C-terminal domain (E7C) are both highly conserved, despite E7N lacking a stable structure.
2) Key linear motifs in E7N, like the LxCxE Rb-binding site and CKII phosphorylation site, have coevolved and suggest a functional relationship.
3) The C-terminal domain is also highly conserved, retaining zinc-binding cysteines and residues important for dimerization and interactions with cellular targets.
The algorithm discovers novel functional linear motifs within sets of unaligned protein sequences using a greedy approach. It identifies overrepresented short sequences or "motifs" that may mediate protein-protein interactions. The algorithm is tested on known motifs from databases, showing it can correctly identify several known motifs. As a case study, the algorithm extracts a putative nucleolar localization motif present in nucleolar proteins including the N-terminus of protein MAGE-B2, explaining its nucleolar localization.
Este documento describe un modelo estocástico para la regulación de la expresión génica que incluye múltiples sitios de unión para factores de transcripción en el sistema regulatorio cis. El modelo predice que la cooperatividad y el nivel de ruido aumentan con la energía de interacción entre los factores de transcripción. El modelo también distingue entre dos mecanismos de unión cooperativa que resultan en diferentes niveles de ruido aunque la expresión media sea la misma. El documento analiza el diagrama de fases para determinar las regiones donde
This document describes a computational study that aimed to predict heparin binding sites on glyceraldehyde-3-phosphate dehydrogenase (GAPDH) using molecular docking simulations. The researchers developed a docking protocol that successfully identified heparin binding sites on other proteins. Applying this protocol, they predicted that positively charged residues on GAPDH interact with the negatively charged sulfate and carboxylate groups on heparin. The results provide insight into how protein-glycosaminoglycan interactions may contribute to amyloid formation associated with neurodegenerative diseases.
This document summarizes a study that analyzed three major evolutionary signals in protein sequences: conservation, specificity determining positions (SDPs), and coevolution between residues. These signals result from different evolutionary mechanisms and have been used by bioinformatics methods to predict functionally important sites. The study evaluated several methods for predicting conserved residues, SDPs, and coevolving positions using a dataset of 434 protein families. It found that the methods capture different information and identify different top-scoring residues. Conservation and mutual information scores performed best at detecting catalytic residues, but combining scores could improve predictions. SDP prediction remains challenging due to limited data and methods detecting conserved residues may miss SDPs until more sequences are available.
The document discusses predicting peptide interactions with MHC molecules to identify epitopes for vaccine design and diagnosis. It notes the challenges of identifying epitopes within pathogen genomes and accounting for human HLA diversity. It presents data on experimentally validating bioinformatics predictions of peptide-MHC binding, and discusses strategies for covering common HLA alleles based on clustering and representative alleles from different supertypes.
The document describes research to design degenerate primers to amplify a segment of the putative ACE-1 transcription factor gene in Peniophora sp. using bioinformatics tools. Researchers identified a conserved copper-fist DNA binding domain in the ACE-1 protein sequence of Phanerochaete chrysosporium that is about 50 amino acids long and 80-90% similar to other sequences. Degenerate primers targeting this conserved region were designed and analyzed in silico. The results suggest the conserved domain is likely important for function and differences are due to synonymous substitutions, supporting using online tools to accelerate molecular biology research.
Este documento describe el modelado tridimensional de la proteína P35 de Toxoplasma gondii y la predicción de sus epitopes. Los autores modelaron la estructura de P35 usando programas de modelado y evaluaron la calidad del modelo. Luego predijeron los epitopes lineales y estructurales de P35 usando programas de predicción de epitopes. La mayoría de las regiones antigénicas predichas se encuentran en la región media y N-terminal de la proteína. Actualmente están evaluando experimentalmente estas regiones como posibles antígenos
The document discusses balancing data for phenotype classification based on SNPs. It explains that training data often has imbalanced class distributions that do not reflect real-world proportions, affecting classifier design. Techniques are presented to balance discrete SNP data artificially by changing marginal distributions while keeping conditional distributions unchanged. This produces a classifier independent of sample proportions and more robust to incorrect prior assumptions. Balancing allows generating the same optimal classifier from any sample sizes.
The document proposes a new algorithm for gene selection that uses hierarchical clustering and the Silhouette index. Hierarchical clustering is used to group genes with similar expression into clusters. The Silhouette index measures how tightly grouped and separated clusters are. The algorithm ranks gene subsets based on their Silhouette index scores and selects the subsets with the highest scores, providing sets of genes with very similar expression patterns.
Biopython is a set of freely available Python tools for bioinformatics and molecular biology. It provides features like parsing bioinformatics files into Python structures, a sequence class to store sequences and features, and interfaces to popular bioinformatics programs. Biopython can be used to address common bioinformatics problems like sequence manipulation, searching for primers, and running BLAST searches. The current version is 1.53 from December 2009 and future plans include updating the multiple sequence alignment object and adding a Bio.Phylo module.
El documento resume los conceptos de estabilidad termodinámica y cinética en proteínas de dos y tres estados. Explica que la estabilidad termodinámica se refiere a la diferencia de energía libre entre los estados plegado y desplegado, mientras que la estabilidad cinética se refiere a las tasas de plegamiento y desplegamiento. Los estudios de mutaciones en múltiples proteínas muestran que el plegamiento se ve afectado negativamente pero el desplegamiento y la estabilidad general se ven afectados
El documento describe métodos para el análisis de vicarianza, un enfoque de biogeografía histórica que utiliza información geográfica directamente en lugar de áreas predefinidas. Se presentan algoritmos para representar distribuciones geográficas como árboles cuadrados y optimizar reconstrucciones biogeográficas mediante criterios que minimizan nodos no vicariantes. También se discuten heurísticas como "subida de colina" para encontrar soluciones óptimas en árboles grandes.
Threats to mobile devices are more prevalent and increasing in scope and complexity. Users of mobile devices desire to take full advantage of the features
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- These are slides of the talk given at IEEE International Conference on Software Testing Verification and Validation Workshop, ICSTW 2022.
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This document describes a computational study that aimed to predict heparin binding sites on glyceraldehyde-3-phosphate dehydrogenase (GAPDH) using molecular docking simulations. The researchers developed a docking protocol that successfully identified heparin binding sites on other proteins. Applying this protocol, they predicted that positively charged residues on GAPDH interact with the negatively charged sulfate and carboxylate groups on heparin. The results provide insight into how protein-glycosaminoglycan interactions may contribute to amyloid formation associated with neurodegenerative diseases.
This document summarizes a study that analyzed three major evolutionary signals in protein sequences: conservation, specificity determining positions (SDPs), and coevolution between residues. These signals result from different evolutionary mechanisms and have been used by bioinformatics methods to predict functionally important sites. The study evaluated several methods for predicting conserved residues, SDPs, and coevolving positions using a dataset of 434 protein families. It found that the methods capture different information and identify different top-scoring residues. Conservation and mutual information scores performed best at detecting catalytic residues, but combining scores could improve predictions. SDP prediction remains challenging due to limited data and methods detecting conserved residues may miss SDPs until more sequences are available.
The document discusses predicting peptide interactions with MHC molecules to identify epitopes for vaccine design and diagnosis. It notes the challenges of identifying epitopes within pathogen genomes and accounting for human HLA diversity. It presents data on experimentally validating bioinformatics predictions of peptide-MHC binding, and discusses strategies for covering common HLA alleles based on clustering and representative alleles from different supertypes.
The document describes research to design degenerate primers to amplify a segment of the putative ACE-1 transcription factor gene in Peniophora sp. using bioinformatics tools. Researchers identified a conserved copper-fist DNA binding domain in the ACE-1 protein sequence of Phanerochaete chrysosporium that is about 50 amino acids long and 80-90% similar to other sequences. Degenerate primers targeting this conserved region were designed and analyzed in silico. The results suggest the conserved domain is likely important for function and differences are due to synonymous substitutions, supporting using online tools to accelerate molecular biology research.
Este documento describe el modelado tridimensional de la proteína P35 de Toxoplasma gondii y la predicción de sus epitopes. Los autores modelaron la estructura de P35 usando programas de modelado y evaluaron la calidad del modelo. Luego predijeron los epitopes lineales y estructurales de P35 usando programas de predicción de epitopes. La mayoría de las regiones antigénicas predichas se encuentran en la región media y N-terminal de la proteína. Actualmente están evaluando experimentalmente estas regiones como posibles antígenos
The document discusses balancing data for phenotype classification based on SNPs. It explains that training data often has imbalanced class distributions that do not reflect real-world proportions, affecting classifier design. Techniques are presented to balance discrete SNP data artificially by changing marginal distributions while keeping conditional distributions unchanged. This produces a classifier independent of sample proportions and more robust to incorrect prior assumptions. Balancing allows generating the same optimal classifier from any sample sizes.
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El documento resume los conceptos de estabilidad termodinámica y cinética en proteínas de dos y tres estados. Explica que la estabilidad termodinámica se refiere a la diferencia de energía libre entre los estados plegado y desplegado, mientras que la estabilidad cinética se refiere a las tasas de plegamiento y desplegamiento. Los estudios de mutaciones en múltiples proteínas muestran que el plegamiento se ve afectado negativamente pero el desplegamiento y la estabilidad general se ven afectados
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Bolstered error estimation for discrete classifier applied to genomic signal processing
1. Marcel Brun1, Virginia Ballarín1
1Laboratorio de Procesos y Medición de Señales, Facultad de Ingeniería, UNMdP
mbrun@fi.mdp.edu.ar
Introduction
Introduction
Bolstering is a error estimation technique that provides a less biased estimation than resubstitution, avoiding the large variability of leave-one-out and cross
validation [Braga & Dougherty 2004]. AT this moment a general model for Bolstering was provided for continuous classification spaces, like Rn, where the concept of
expanding the sample points by a circular kernel is conceptually clear, and works very well in practice [Sima & Braga 2005]. In the other hand, discrete classifiers, like
the ones used for image processing and genomic signal processing, present a more complex framework for the design of Bolstered error estimation. In this work we
define a model for Bolstering based on a convolution kernel on both conditional probabilities.
BRCA2 = 1 BRCA1 = 0
Discrete Classification in Genomics: Can we deduce Microarray Data
the transcriptional state of a gene, or a phenotypical
feature, based on the transcriptional state of other
Frequencies Decision
genes? Data Collecting x1x2x3 0 1 x1x2x3 ψ
Gene Gene Gene 3 Status 000 0 14 000 1
1 2
001 2 6 001 1
1 0 1 1
“If gene X1 is active and gene X2 is 010 3 2 010 0
suppressed, gene Y would be 1 0 0 1
011 5 1 011 0
activated”
0 1 1 0
Can we infer regulatory genetic 100 0 3 100 1
function from the cDNA 1 0 1 1
101 7 2 101 0
microarray data,
for both known and unknown 1 0 1 0 110 3 1
R EL-B
110 0
R CH1
B CL3
FR A1
IAP -1
A TF3
functions?
Cell-line Condition … … … … 111 15 1 111 0
ML-1 IR -1 1 1 1 1 1
ML-1 MMS 0 0 0 0 1 0
Molt4 IR -1 0 0 1 1 0
Molt4 MMS 0 0 1 0 1 0
Continuous Bolstering: Bolstered SR IR -1 0 0 1 1 1 Automatic Design: Statistical analysis of the
SR MMS 0 0 0 0 1 0
resubstitution for linear classification, assuming A549 IR 0 0 0 0 0 0 relationship between the index (target) and the status of
A549 MMS 0 0 0 0 1 0
uniform circular bolstering kernels. The A549 UV 0 0 0 0 1 0 the genes of interest (predictors) define the optimal
MCF7 IR -1 0 1 1 0 0
bolstered MCF7
MCF7
MMS
UV
0
0
0
0
1
1
0
1
1
1
0
0
binary classifier. Resubstitution error is estimated by
resubstitution error is the sum of all RKO
RKO MMS
IR 0
0
1
0
0
0
1
0
1
1
1
0
probability of wrong classification (values in red). In this
contributions (shaded areas) divided by the example is 9/65=13.8%
number of points. Resubstitution estimator is usually low biased!!
Discrete Bolstering
Discrete Bolstering
Discrete Bolstering: Bolstered resubstitution error estimation for discrete classification, using a lattice bolstering kernel. The bolstered count for each
configuration is based on the weighted sum of its original value and the ones of its neighbors. In this example, the assigned class for configuration 010
changes from Positive to Negative because of the new counting.
Before Bolstering: estimated error = 0.138 After Bolstering: estimated error = 0.223
1 111
Bolstering
15 111 12 111 1.1 111
0.1
3 110 7 5 011 1 110 2 101 1 011 3.9 110 6.6 5.5 011 1.3 110 2.4 1.6 011
101 101 101
0.7
0 100 3 010 2 001 3 100 2 010 6 001 1 100 2.9 010 2.6 001 3.8 100 3 010 5.9 001
0.1 0.1
0 000 14 000 0.5 000 10.9 000
Number of positive Samples for Number of negative Samples Convolution Kernel Result of convolution for Result of convolution for
each observed configuration for each observed configuration
positive samples negative samples
(35 observations) (30 observations)
Results
Results Conclusions
Conclusions
3 variables simulated data (geometric spatial distribution) with convolution • Discrete Bolstering can be defined in function of convolution kernels, like in the
kernel varying as function of a parameter a. continuous case.
• Convolution of both conditional probabilities induce changes in the amount of error
computed for the estimated classifier.
Convolution Kernels Estimated Error as function of the Bolstering Kernel
• The increase/decrease in the estimated error can be made to change continuously as
0.7
N = 3, M = 58 function of a Kernel Size parameter a.
• Usually there is an optimal a which makes the bolstered error estimator similar to the
0.6
true error of the estimated classifier.
0.5
• Future works is directed to the choose the optimal Kernel parameter a for specific
situations.
Bayes Error 0.282
Estimated Error
0.4 True error 0.301
1
LOO error 0.293
Resub error 0.224 References
References
0.9 Bolstered (Best b = 0.05)
0.8
0.3 Bolstered 0.302
Diff Oper (Best Diff = 0.01) • Ulisses Braga-Neto, Edward Dougherty, “Bolstered error estimation”, Pattern Recognition, 37, pp. 1267-1281, 2004.
0.7
0.6 • Braga-Neto, U., and Dougherty, E. R., "Classification," Genomic Signal Processing and Statistics, eds. Dougherty, E. R., Shmulevich, I. ,
Kernel Value
0.5
0.2 Chen, J., and Wang, Z. J., EURASIP Book Series on Signal Processing and Communication, Hindawi Publishing Corporation, 2005.
0.4
• Choudhary A, Brun M, Hua J, Lowey J, Suh E, Dougherty ER., “Genetic test bed for feature selection”, Bioinformatics. 2006 Apr 1;22(7):837-
0.3
42. Epub 2006 Jan 20.
0.2
0.1
0.1
• Chao Sima, Ulisses Braga-Neto and Edward R. Dougherty, “Superior feature-set ranking for small samples using bolstered error estimation”,
0
Bioinformatics, 21 (7), pp 1046–1054, 2005
0 0.5 1 1.5 2 2.5 3
Distance
0
−4 −3 −2 −1 0 1 2 3 4 • Phillip Stafford and Marcel Brun, “Three methods for optimization of cross-laboratory and cross-platform microarray expression data”, Nucleic
Parameter b Acids Research, 2007, 1–16
• Qian Xu, Jianping Hua, Ulisses Braga-Neto, Zixiang Xiong, Edward Suh, Edward R. Dougherty, Ph.D., “Confidence Intervals for the True
Classification Error Conditioned on the Estimated Error”, Technology in Cancer Research and Treatment, Volume 5, Number 6, December
(2006)