Abstract Feature selection is critical in data mining and knowledge discovery. Previously, a feat... more Abstract Feature selection is critical in data mining and knowledge discovery. Previously, a feature selection technique known as the wrapper model was shown e ective for decision trees induction. However, it is prohibitively expensive when applied to real-world neural net data mining characterized by large volumes of data and many attribute choices. Our approach incorporates the wrapper model with a weight based heuristic metric called ANNIGMA which allows the wrapper model feature selection feasible for neural nets.
Abstract Utilization of the World Wide Web can be boosted if we can explore the “deep Web” and in... more Abstract Utilization of the World Wide Web can be boosted if we can explore the “deep Web” and integrate information from various Web sites together. However, to automate deep Web exploration and data integration requires custom-made software to accommodate the differences among Web sites, and thus is error-prone and time-consuming. This paper defines a language called Web Navigation Description
Abstract Predicting an individual customer's likelihood of purchasing a specific item forms the b... more Abstract Predicting an individual customer's likelihood of purchasing a specific item forms the basis of many marketing activities, such as personalized shopping recommendation. Collaborative filtering and association rule mining can be applied to this problem, but in retail supermarkets, the problem becomes particularly challenging because of the sparsity and skewness of transaction data.
Abstract: SIMS provides intelligent access to heterogeneous, distributed information sources, whi... more Abstract: SIMS provides intelligent access to heterogeneous, distributed information sources, while insulating human users and application programs from the need to be aware of the location of the sources, their query languages, organization, size, etc. This manual explains how to bring up a SIMS information server in a new domain.
Abstract Integrating a large number of Web information sources may significantly increase the uti... more Abstract Integrating a large number of Web information sources may significantly increase the utility of the World-Wide Web. A promising solution to the integration is through the use of a Web Information mediator that provides seamless, transparent access for the clients. Information mediators need wrappers to access a Web source as a structured database, but building wrappers by hand is impractical.
Background Previously, gene normalization (GN) systems are mostly focused on disambiguation using... more Background Previously, gene normalization (GN) systems are mostly focused on disambiguation using contextual information. An effective gene mention tagger is deemed unnecessary because the subsequent steps will filter out false positives and high recall is sufficient. However, unlike similar tasks in the past BioCreative challenges, the BioCreative III GN task is particularly challenging because it is not species-specific.
Previously, Bottou and LeCun [1] established that the second-order stochastic gradient descent (S... more Previously, Bottou and LeCun [1] established that the second-order stochastic gradient descent (SGD) method can potentially achieve generalization performance as well as empirical optimum in a single pass through the training examples. However, second-order SGD requires computing the inverse of the Hessian matrix of the loss function, which is usually prohibitively expensive. Recently, we invented a new second-order SGD method, called Periodic Stepsize Adaptation (PSA).
Abstract It has been established that the second-order stochastic gradient descent (2SGD) method ... more Abstract It has been established that the second-order stochastic gradient descent (2SGD) method can potentially achieve generalization performance as well as empirical optimum in a single pass (ie, epoch) through the training examples. However, 2SGD requires computing the inverse of the Hessian matrix of the loss function, which is prohibitively expensive.
Abstract Accurate phenotype mapping will play an important role in facilitating Phenome-Wide Asso... more Abstract Accurate phenotype mapping will play an important role in facilitating Phenome-Wide Association Studies (PheWAS), and potentially in other phenomics based studies. The Phe-WAS approach investigates the association between genetic variation and an extensive range of phenotypes in a high-throughput manner to better understand the impact of genetic variations on multiple phenotypes.
Background Decades of genome-wide association studies (GWAS) have accumulated large volumes of ge... more Background Decades of genome-wide association studies (GWAS) have accumulated large volumes of genomic data that can potentially be reused to increase statistical power of new studies, but different genotyping platforms with different marker sets have been used as biotechnology has evolved, preventing pooling and comparability of old and new data. For example, to pool together data collected by 550K chips with newer data collected by 900K chips, we will need to impute missing loci.
ABSTRACT Recommendation has achieved successful results in many applications. However, for superm... more ABSTRACT Recommendation has achieved successful results in many applications. However, for supermarkets, since the transaction data is extremely skewed in the sense that a large portion of sales is concentrated in a small number of hot seller items, collaborative filtering recommenders usually recommend hot sellers while rarely recommend cold sellers. But recommenders are supposed to provide better campaigns for cold sellers to increase sales.
Abstract Many genetic epidemiological studies of human diseases have multiple variables related t... more Abstract Many genetic epidemiological studies of human diseases have multiple variables related to any given phenotype, resulting from different definitions and multiple measurements or subsets of data. Manually mapping and harmonizing these phenotypes is a timeconsuming process that may still miss the most appropriate variables. Previously, a supervised learning algorithm was proposed for this problem. That algorithm learns to determine whether a pair of phenotypes is in the same class.
In gene mention tagging task (GM) of BioCreative II (2007) challenge, we had built a system based... more In gene mention tagging task (GM) of BioCreative II (2007) challenge, we had built a system based on bi-directional parsing models of Conditional Random Fields (CRFs), achieved a F-score of 86.83 [2] on GM test corpus and ranked second among twenty-one participants. After which, we improved its performance to a F-score of 88.3 by integrating high dimensional bi-directional parsing models (up to 6 models)[1].
Abstract Using a phenome-wide association study (PheWAS) approach, we comprehensively tested gene... more Abstract Using a phenome-wide association study (PheWAS) approach, we comprehensively tested genetic variants for association with phenotypes available for 70,061 study participants in the Population Architecture using Genomics and Epidemiology (PAGE) network. Our aim was to better characterize the genetic architecture of complex traits and identify novel pleiotropic relationships.
Abstract Although there exist many high-performing text-mining tools to address literature biocur... more Abstract Although there exist many high-performing text-mining tools to address literature biocuration (populating biomedical databases from the published literature), the challenge of delivering effective computational support for curation of large-scale biomedical databases is still unsolved. We describe a community-driven solution (the SciKnowMine Project) implemented using the Unstructured Information Management Architecture (UIMA) framework.
Background Recombinant protein production is a useful biotechnology to produce a large quantity o... more Background Recombinant protein production is a useful biotechnology to produce a large quantity of highly soluble proteins. Currently, the most widely used production system is to fuse a target protein into different vectors in Escherichia coli (E. coli). However, the production efficacy of different vectors varies for different target proteins. Trial-and-error is still the common practice to find out the efficacy of a vector for a given target protein.
1.1 Purpose ezTrial provides users with a web-based clinical trial management service, which is s... more 1.1 Purpose ezTrial provides users with a web-based clinical trial management service, which is simple to operate and can be conveniently accessed from the internet. The service provides the function of creating and designing multiple clinical trials with predefined study plans, and is able to integrate customized phase assignment rules within each trial.
Abstract Previously, algorithms for training conditional random fields were derived from the seco... more Abstract Previously, algorithms for training conditional random fields were derived from the second-order Taylor expansion of the log-likelihood of the training data and the key issue is to approximate the Hessian matrix, which usually requires O (n2) computations per iteration.
Abstract Many algorithms have been developed to identify important nodes in a complex network, in... more Abstract Many algorithms have been developed to identify important nodes in a complex network, including various centrality metrics and Page Rank, but most fail to consider the dynamic nature of the network. They therefore suffer from recency bias and fail to recognize important new nodes that have not had as much time to accumulate links as their older counterparts. This paper describes the Effective Contagion Matrix (ECM), a solution to address recency bias in the analysis of dynamic complex networks.
Abstract Feature selection is critical in data mining and knowledge discovery. Previously, a feat... more Abstract Feature selection is critical in data mining and knowledge discovery. Previously, a feature selection technique known as the wrapper model was shown e ective for decision trees induction. However, it is prohibitively expensive when applied to real-world neural net data mining characterized by large volumes of data and many attribute choices. Our approach incorporates the wrapper model with a weight based heuristic metric called ANNIGMA which allows the wrapper model feature selection feasible for neural nets.
Abstract Utilization of the World Wide Web can be boosted if we can explore the “deep Web” and in... more Abstract Utilization of the World Wide Web can be boosted if we can explore the “deep Web” and integrate information from various Web sites together. However, to automate deep Web exploration and data integration requires custom-made software to accommodate the differences among Web sites, and thus is error-prone and time-consuming. This paper defines a language called Web Navigation Description
Abstract Predicting an individual customer's likelihood of purchasing a specific item forms the b... more Abstract Predicting an individual customer's likelihood of purchasing a specific item forms the basis of many marketing activities, such as personalized shopping recommendation. Collaborative filtering and association rule mining can be applied to this problem, but in retail supermarkets, the problem becomes particularly challenging because of the sparsity and skewness of transaction data.
Abstract: SIMS provides intelligent access to heterogeneous, distributed information sources, whi... more Abstract: SIMS provides intelligent access to heterogeneous, distributed information sources, while insulating human users and application programs from the need to be aware of the location of the sources, their query languages, organization, size, etc. This manual explains how to bring up a SIMS information server in a new domain.
Abstract Integrating a large number of Web information sources may significantly increase the uti... more Abstract Integrating a large number of Web information sources may significantly increase the utility of the World-Wide Web. A promising solution to the integration is through the use of a Web Information mediator that provides seamless, transparent access for the clients. Information mediators need wrappers to access a Web source as a structured database, but building wrappers by hand is impractical.
Background Previously, gene normalization (GN) systems are mostly focused on disambiguation using... more Background Previously, gene normalization (GN) systems are mostly focused on disambiguation using contextual information. An effective gene mention tagger is deemed unnecessary because the subsequent steps will filter out false positives and high recall is sufficient. However, unlike similar tasks in the past BioCreative challenges, the BioCreative III GN task is particularly challenging because it is not species-specific.
Previously, Bottou and LeCun [1] established that the second-order stochastic gradient descent (S... more Previously, Bottou and LeCun [1] established that the second-order stochastic gradient descent (SGD) method can potentially achieve generalization performance as well as empirical optimum in a single pass through the training examples. However, second-order SGD requires computing the inverse of the Hessian matrix of the loss function, which is usually prohibitively expensive. Recently, we invented a new second-order SGD method, called Periodic Stepsize Adaptation (PSA).
Abstract It has been established that the second-order stochastic gradient descent (2SGD) method ... more Abstract It has been established that the second-order stochastic gradient descent (2SGD) method can potentially achieve generalization performance as well as empirical optimum in a single pass (ie, epoch) through the training examples. However, 2SGD requires computing the inverse of the Hessian matrix of the loss function, which is prohibitively expensive.
Abstract Accurate phenotype mapping will play an important role in facilitating Phenome-Wide Asso... more Abstract Accurate phenotype mapping will play an important role in facilitating Phenome-Wide Association Studies (PheWAS), and potentially in other phenomics based studies. The Phe-WAS approach investigates the association between genetic variation and an extensive range of phenotypes in a high-throughput manner to better understand the impact of genetic variations on multiple phenotypes.
Background Decades of genome-wide association studies (GWAS) have accumulated large volumes of ge... more Background Decades of genome-wide association studies (GWAS) have accumulated large volumes of genomic data that can potentially be reused to increase statistical power of new studies, but different genotyping platforms with different marker sets have been used as biotechnology has evolved, preventing pooling and comparability of old and new data. For example, to pool together data collected by 550K chips with newer data collected by 900K chips, we will need to impute missing loci.
ABSTRACT Recommendation has achieved successful results in many applications. However, for superm... more ABSTRACT Recommendation has achieved successful results in many applications. However, for supermarkets, since the transaction data is extremely skewed in the sense that a large portion of sales is concentrated in a small number of hot seller items, collaborative filtering recommenders usually recommend hot sellers while rarely recommend cold sellers. But recommenders are supposed to provide better campaigns for cold sellers to increase sales.
Abstract Many genetic epidemiological studies of human diseases have multiple variables related t... more Abstract Many genetic epidemiological studies of human diseases have multiple variables related to any given phenotype, resulting from different definitions and multiple measurements or subsets of data. Manually mapping and harmonizing these phenotypes is a timeconsuming process that may still miss the most appropriate variables. Previously, a supervised learning algorithm was proposed for this problem. That algorithm learns to determine whether a pair of phenotypes is in the same class.
In gene mention tagging task (GM) of BioCreative II (2007) challenge, we had built a system based... more In gene mention tagging task (GM) of BioCreative II (2007) challenge, we had built a system based on bi-directional parsing models of Conditional Random Fields (CRFs), achieved a F-score of 86.83 [2] on GM test corpus and ranked second among twenty-one participants. After which, we improved its performance to a F-score of 88.3 by integrating high dimensional bi-directional parsing models (up to 6 models)[1].
Abstract Using a phenome-wide association study (PheWAS) approach, we comprehensively tested gene... more Abstract Using a phenome-wide association study (PheWAS) approach, we comprehensively tested genetic variants for association with phenotypes available for 70,061 study participants in the Population Architecture using Genomics and Epidemiology (PAGE) network. Our aim was to better characterize the genetic architecture of complex traits and identify novel pleiotropic relationships.
Abstract Although there exist many high-performing text-mining tools to address literature biocur... more Abstract Although there exist many high-performing text-mining tools to address literature biocuration (populating biomedical databases from the published literature), the challenge of delivering effective computational support for curation of large-scale biomedical databases is still unsolved. We describe a community-driven solution (the SciKnowMine Project) implemented using the Unstructured Information Management Architecture (UIMA) framework.
Background Recombinant protein production is a useful biotechnology to produce a large quantity o... more Background Recombinant protein production is a useful biotechnology to produce a large quantity of highly soluble proteins. Currently, the most widely used production system is to fuse a target protein into different vectors in Escherichia coli (E. coli). However, the production efficacy of different vectors varies for different target proteins. Trial-and-error is still the common practice to find out the efficacy of a vector for a given target protein.
1.1 Purpose ezTrial provides users with a web-based clinical trial management service, which is s... more 1.1 Purpose ezTrial provides users with a web-based clinical trial management service, which is simple to operate and can be conveniently accessed from the internet. The service provides the function of creating and designing multiple clinical trials with predefined study plans, and is able to integrate customized phase assignment rules within each trial.
Abstract Previously, algorithms for training conditional random fields were derived from the seco... more Abstract Previously, algorithms for training conditional random fields were derived from the second-order Taylor expansion of the log-likelihood of the training data and the key issue is to approximate the Hessian matrix, which usually requires O (n2) computations per iteration.
Abstract Many algorithms have been developed to identify important nodes in a complex network, in... more Abstract Many algorithms have been developed to identify important nodes in a complex network, including various centrality metrics and Page Rank, but most fail to consider the dynamic nature of the network. They therefore suffer from recency bias and fail to recognize important new nodes that have not had as much time to accumulate links as their older counterparts. This paper describes the Effective Contagion Matrix (ECM), a solution to address recency bias in the analysis of dynamic complex networks.
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Papers by Chun-Nan Hsu