Michael Leung - Academia.edu (original) (raw)

Papers by Michael Leung

Journal of the American College of Cardiology, 2014

Background: Second generation 320-row CT Angiography (CTA) is associated with improved temporal r... more Background: Second generation 320-row CT Angiography (CTA) is associated with improved temporal resolution (135ms). We hypothesised that this advance might enable cardiac imaging in patients with high heart rates (HR) without impacting on diagnostic accuracy.

Journal of Econometrics, 2022

SSRN Electronic Journal, 2021

Since network data commonly consists of observations on a single large network, researchers often... more Since network data commonly consists of observations on a single large network, researchers often partition the network into clusters in order to apply cluster-robust inference methods. All existing such methods require clusters to be asymptotically independent. We prove that for this requirement to hold, under certain conditions, it is necessary and sufficient for clusters to have low conductance, the ratio of edge boundary size to volume, which yields a measure of cluster quality. We show in simulations that, for important classes of networks lacking low-conductance clusters, cluster-robust methods can exhibit substantial size distortion. To assess the existence of low-conductance clusters and construct them, we draw on results in spectral graph theory showing a close connection between conductance and the spectrum of the graph Laplacian. Based on these results, we propose to use the spectrum to compute the number of low-conductance clusters and spectral clustering to compute the clusters. We illustrate our results and proposed methods in simulations and empirical applications.

SSRN Electronic Journal, 2019

This paper studies causal inference in randomized experiments under network interference. Most of... more This paper studies causal inference in randomized experiments under network interference. Most of the literature assumes a model of interference under which treatments assigned to alters beyond a certain network distance from the ego have no effect on the ego's response. However, many models of social interactions do not satisfy this assumption. This paper proposes a substantially weaker model of "approximate neighborhood interference" (ANI), under which treatments assigned to alters further from the ego have a smaller, but potentially nonzero, impact on the ego's response. We show that ANI is satisfied in well-known models of social interactions. We also prove that, under ANI, standard inverse-probability weighting estimators can consistently estimate useful exposure effects and are asymptotically normal under asymptotics taking the network size large. For inference, we consider a network HAC variance estimator. Under a finite population model, we show the estimator is biased but that the bias can be interpreted as the variance of unit-level exposure effects. This generalizes Neyman's well-known result on conservative variance estimation to settings with interference.

SSRN Electronic Journal, 2019

SSRN Electronic Journal, 2019

Die Dokumente auf EconStor dürfen zu eigenen wissenschaftlichen Zwecken und zum Privatgebrauch ge... more Die Dokumente auf EconStor dürfen zu eigenen wissenschaftlichen Zwecken und zum Privatgebrauch gespeichert und kopiert werden. Sie dürfen die Dokumente nicht für öffentliche oder kommerzielle Zwecke vervielfältigen, öffentlich ausstellen, öffentlich zugänglich machen, vertreiben oder anderweitig nutzen. Sofern die Verfasser die Dokumente unter Open-Content-Lizenzen (insbesondere CC-Lizenzen) zur Verfügung gestellt haben sollten, gelten abweichend von diesen Nutzungsbedingungen die in der dort genannten Lizenz gewährten Nutzungsrechte. Terms of use: Documents in EconStor may be saved and copied for your personal and scholarly purposes. You are not to copy documents for public or commercial purposes, to exhibit the documents publicly, to make them publicly available on the internet, or to distribute or otherwise use the documents in public.

SSRN Electronic Journal, 2019

We develop a methodology for proving central limit theorems in network models with strategic inte... more We develop a methodology for proving central limit theorems in network models with strategic interactions and homophilous agents. We consider an asymptotic framework in which the size of the network tends to infinity, which is useful for inference in the typical setting in which the sample consists of a single large network. In the presence of strategic interactions, network moments are generally complex functions of network components, where a node's component consists of all alters to which it is directly or indirectly connected. We find that a modification of "exponential stabilization" conditions from the stochastic geometry literature provides a useful formulation of weak dependence for moments of this type. Our first contribution is to prove a CLT for a large class of network moments satisfying stabilization and a moment condition. Our second contribution is a methodology for deriving primitive sufficient conditions for stabilization using results in branching process theory. We apply the methodology to static and dynamic models of network formation and discuss how it can be used more broadly.

SSRN Electronic Journal, 2017

We develop inference procedures robust to general forms of weak dependence. The procedures utiliz... more We develop inference procedures robust to general forms of weak dependence. The procedures utilize test statistics constructed by resampling in a manner that does not depend on the unknown correlation structure of the data. We prove that the statistics are asymptotically normal under the weak requirement that the target parameter can be consistently estimated at the parametric rate. This holds for regular estimators under many well-known forms of weak dependence and justifies the claim of dependence-robustness. We consider applications to settings with unknown or complicated forms of dependence, with various forms of network dependence as leading examples. We develop tests for both moment equalities and inequalities.

SSRN Electronic Journal, 2018

This paper studies inference on finite-population average and local average treatment effects und... more This paper studies inference on finite-population average and local average treatment effects under limited overlap, meaning that some strata have a small proportion of treated or untreated units. We model limited overlap in an asymptotic framework, sending the propensity score to zero (or one) with the sample size. We derive the asymptotic distribution of analogue estimators of the treatment effects under two common randomization schemes: conditionally independent and stratified block randomization. Under either scheme, the limit distribution is the same and conventional standard error formulas remain asymptotically valid, but the rate of convergence is slower the faster the propensity score degenerates. The practical import of these results is twofold. When overlap is limited, standard methods can perform poorly in smaller samples, as asymptotic approximations are inadequate owing to the slower rate of convergence. However, in larger samples, standard methods can work quite well even when the propensity score is small.

International Journal of Fatigue, 2018

The ability to perform accurate remnant life predictions is crucial to ensure the integrity of en... more The ability to perform accurate remnant life predictions is crucial to ensure the integrity of engineering components that experience fatigue loading during operation. This is conventionally done with periodic inspections, where results from non-destructive evaluation and estimation of the operating conditions are obtained to perform remnant life predictions using empirical crack growth laws. However, remnant life predictions made with this approach are very sensitive to their input parameters; uncertainty in each parameter would aggregate and result in great uncertainty in the final prediction. Recent technological advances have made permanently installed monitoring systems increasingly viable, making it possible to obtain and monitor trends in damage growth rate. It is proposed that the rate of damage growth can be used to more accurately and confidently gauge the integrity of an engineering component and perform remnant life predictions using the Failure Forecast Method. A statistical analysis of an example fatigue crack growth test was performed to compare the uncertainties of the remnant life predictions made using the conventional inspection approach, which utilises nominally-known operating conditions and empirical crack growth laws, and the proposed rate-based monitoring approach. Results show that the remnant life predictions made using the Failure Forecast Method produce significantly more accurate and confident predictions compared to the inspection approach. The Failure Forecast Method can also be adapted to accommodate load changes. An example fatigue test with a 20% load reduction after a period of crack growth was performed and the life predictions made with inspection data at the time of the load change and monitoring data up to that point were compared. Again it was shown that the uncertainty in the life prediction with the Failure Forecast Method using the monitoring data was lower than that with the inspection approach, but the improvement was smaller than in the constant load case because data on the load change and the Paris law exponent were required, thus increasing the uncertainty. The study has shown that the frequent data obtained from permanently installed monitoring systems provides new opportunities in remnant life estimates and potentially opens the way to increasing the intervals between outages and reducing design conservatism.

Scientific reports, Jan 5, 2018

Intraoperative image-guided surgical navigation for craniospinal procedures has significantly imp... more Intraoperative image-guided surgical navigation for craniospinal procedures has significantly improved accuracy by providing an avenue for the surgeon to visualize underlying internal structures corresponding to the exposed surface anatomy. Despite the obvious benefits of surgical navigation, surgeon adoption remains relatively low due to long setup and registration times, steep learning curves, and workflow disruptions. We introduce an experimental navigation system utilizing optical topographical imaging (OTI) to acquire the 3D surface anatomy of the surgical cavity, enabling visualization of internal structures relative to exposed surface anatomy from registered preoperative images. Our OTI approach includes near instantaneous and accurate optical measurement of >250,000 surface points, computed at >52,000 points-per-second for considerably faster patient registration than commercially available benchmark systems without compromising spatial accuracy. Our experience of 171 ...

Pediatric surgery international, Jan 26, 2017

Short segment Hirschsprung's disease (HSCR) carries a better prognosis than long segment dise... more Short segment Hirschsprung's disease (HSCR) carries a better prognosis than long segment disease, but the definition of short is controversial. The objective of this study is to determine anatomically the extent of disease involvement that would be associated with a better functional outcome. This is a retrospective multicenter (n = 3) study with patients (≥ 3 years) who had transanal pullthrough operation done for aganglionosis limited to the recto-sigmoid colon were reviewed. The extent of disease involvement and bowel resection was retrieved by reviewing the operative records as well as histopathological reports of the resected specimens. Clinical assessment was performed according to the criteria of a seven-itemed bowel function score (BFS) (maximum score = 20). Manometric assessment was performed with anorectal manometry. The study period started from 2003 to 45 patients were studied with median age at assessment = 52.0 months and operation = 3.0 months. The disease involve...

Processing of transcripts at the 3’-end involves cleavage at a polyadenylation site followed by t... more Processing of transcripts at the 3’-end involves cleavage at a polyadenylation site followed by the addition of a poly(A)-tail. By selecting which polyadenylation site is cleaved, alternative polyadenylation enables genes to produce transcript isoforms with different 3’-ends. To facilitate the identification and treatment of disease-causing mutations that affect polyadenylation and to understand the underlying regulatory processes, a computational model that can accurately predict polyadenylation patterns based on genomic features is desirable. Previous works have focused on identifying candidate polyadenylation sites and classifying sites which may be tissue-specific. What is lacking is a predictive model of the underlying mechanism of site selection, competition, and processing efficiency in a tissue-specific manner. We develop a deep learning model that trains on 3’-end sequencing data and predicts tissue-specific site selection among competing polyadenylation sites in the 3’ unt...

Proceedings of the IEEE, 2016

This paper provides an introduction to machine learning tasks that are relevant to important prob... more This paper provides an introduction to machine learning tasks that are relevant to important problems in genomic medicine.

Heart, Lung and Circulation, 2015

Journal of Biomedical Optics, 2015

Vitrification is an increasingly popular method of embryo cryopreservation that is used in assist... more Vitrification is an increasingly popular method of embryo cryopreservation that is used in assisted reproductive technology. Although vitrification has high post-thaw survival rates compared to other freezing techniques, its long-term effects on embryo development are still poorly understood. We demonstrate an application of full-field optical coherence tomography (FF-OCT) to visualize the effects of vitrification on live single-cell (2 pronuclear) mouse embryos without harmful labels. Using FF-OCT, we observed that vitrification causes a significant increase in the aggregation of structures within the embryo cytoplasm, consistent with reports in literature based on fluorescence techniques. We quantify the degree of aggregation with an objective metric, the cytoplasmic aggregation (CA) score, and observe a high degree of correlation between the CA scores of FF-OCT images of embryos and of fluorescence images of their mitochondria. Our results indicate that FF-OCT shows promise as a label-free assessment of the effects of vitrification on embryo mitochondria distribution. The CA score provides a quantitative metric to describe the degree to which embryos have been affected by vitrification and could aid clinicians in selecting embryos for transfer.

Bioinformatics (Oxford, England), Jan 15, 2014

Alternative splicing (AS) is a regulated process that directs the generation of different transcr... more Alternative splicing (AS) is a regulated process that directs the generation of different transcripts from single genes. A computational model that can accurately predict splicing patterns based on genomic features and cellular context is highly desirable, both in understanding this widespread phenomenon, and in exploring the effects of genetic variations on AS. Using a deep neural network, we developed a model inferred from mouse RNA-Seq data that can predict splicing patterns in individual tissues and differences in splicing patterns across tissues. Our architecture uses hidden variables that jointly represent features in genomic sequences and tissue types when making predictions. A graphics processing unit was used to greatly reduce the training time of our models with millions of parameters. We show that the deep architecture surpasses the performance of the previous Bayesian method for predicting AS patterns. With the proper optimization procedure and selection of hyperparamete...

Canadian family physician Médecin de famille canadien, 2002

PLoS ONE, 2012

This study examined the dissociable neural effects of a ¯na ¯pa ¯nasati (focused-attention medita... more This study examined the dissociable neural effects of a ¯na ¯pa ¯nasati (focused-attention meditation, FAM) and metta ¯(lovingkindness meditation, LKM) on BOLD signals during cognitive (continuous performance test, CPT) and affective (emotionprocessing task, EPT, in which participants viewed affective pictures) processing. Twenty-two male Chinese expert meditators (11 FAM experts, 11 LKM experts) and 22 male Chinese novice meditators (11 FAM novices, 11 LKM novices) had their brain activity monitored by a 3T MRI scanner while performing the cognitive and affective tasks in both meditation and baseline states. We examined the interaction between state (meditation vs. baseline) and expertise (expert vs. novice) separately during LKM and FAM, using a conjunction approach to reveal common regions sensitive to the expert meditative state. Additionally, exclusive masking techniques revealed distinct interactions between state and group during LKM and FAM. Specifically, we demonstrated that the practice of FAM was associated with expertise-related behavioral improvements and neural activation differences in attention task performance. However, the effect of state LKM meditation did not carry over to attention task performance. On the other hand, both FAM and LKM practice appeared to affect the neural responses to affective pictures. For viewing sad faces, the regions activated for FAM practitioners were consistent with attention-related processing; whereas responses of LKM experts to sad pictures were more in line with differentiating emotional contagion from compassion/emotional regulation processes. Our findings provide the first report of distinct neural activity associated with forms of meditation during sustained attention and emotion processing.

Journal of the American College of Cardiology, 2014

Background: Second generation 320-row CT Angiography (CTA) is associated with improved temporal r... more Background: Second generation 320-row CT Angiography (CTA) is associated with improved temporal resolution (135ms). We hypothesised that this advance might enable cardiac imaging in patients with high heart rates (HR) without impacting on diagnostic accuracy.

Journal of Econometrics, 2022

SSRN Electronic Journal, 2021

Since network data commonly consists of observations on a single large network, researchers often... more Since network data commonly consists of observations on a single large network, researchers often partition the network into clusters in order to apply cluster-robust inference methods. All existing such methods require clusters to be asymptotically independent. We prove that for this requirement to hold, under certain conditions, it is necessary and sufficient for clusters to have low conductance, the ratio of edge boundary size to volume, which yields a measure of cluster quality. We show in simulations that, for important classes of networks lacking low-conductance clusters, cluster-robust methods can exhibit substantial size distortion. To assess the existence of low-conductance clusters and construct them, we draw on results in spectral graph theory showing a close connection between conductance and the spectrum of the graph Laplacian. Based on these results, we propose to use the spectrum to compute the number of low-conductance clusters and spectral clustering to compute the clusters. We illustrate our results and proposed methods in simulations and empirical applications.

SSRN Electronic Journal, 2019

This paper studies causal inference in randomized experiments under network interference. Most of... more This paper studies causal inference in randomized experiments under network interference. Most of the literature assumes a model of interference under which treatments assigned to alters beyond a certain network distance from the ego have no effect on the ego's response. However, many models of social interactions do not satisfy this assumption. This paper proposes a substantially weaker model of "approximate neighborhood interference" (ANI), under which treatments assigned to alters further from the ego have a smaller, but potentially nonzero, impact on the ego's response. We show that ANI is satisfied in well-known models of social interactions. We also prove that, under ANI, standard inverse-probability weighting estimators can consistently estimate useful exposure effects and are asymptotically normal under asymptotics taking the network size large. For inference, we consider a network HAC variance estimator. Under a finite population model, we show the estimator is biased but that the bias can be interpreted as the variance of unit-level exposure effects. This generalizes Neyman's well-known result on conservative variance estimation to settings with interference.

SSRN Electronic Journal, 2019

SSRN Electronic Journal, 2019

Die Dokumente auf EconStor dürfen zu eigenen wissenschaftlichen Zwecken und zum Privatgebrauch ge... more Die Dokumente auf EconStor dürfen zu eigenen wissenschaftlichen Zwecken und zum Privatgebrauch gespeichert und kopiert werden. Sie dürfen die Dokumente nicht für öffentliche oder kommerzielle Zwecke vervielfältigen, öffentlich ausstellen, öffentlich zugänglich machen, vertreiben oder anderweitig nutzen. Sofern die Verfasser die Dokumente unter Open-Content-Lizenzen (insbesondere CC-Lizenzen) zur Verfügung gestellt haben sollten, gelten abweichend von diesen Nutzungsbedingungen die in der dort genannten Lizenz gewährten Nutzungsrechte. Terms of use: Documents in EconStor may be saved and copied for your personal and scholarly purposes. You are not to copy documents for public or commercial purposes, to exhibit the documents publicly, to make them publicly available on the internet, or to distribute or otherwise use the documents in public.

SSRN Electronic Journal, 2019

We develop a methodology for proving central limit theorems in network models with strategic inte... more We develop a methodology for proving central limit theorems in network models with strategic interactions and homophilous agents. We consider an asymptotic framework in which the size of the network tends to infinity, which is useful for inference in the typical setting in which the sample consists of a single large network. In the presence of strategic interactions, network moments are generally complex functions of network components, where a node's component consists of all alters to which it is directly or indirectly connected. We find that a modification of "exponential stabilization" conditions from the stochastic geometry literature provides a useful formulation of weak dependence for moments of this type. Our first contribution is to prove a CLT for a large class of network moments satisfying stabilization and a moment condition. Our second contribution is a methodology for deriving primitive sufficient conditions for stabilization using results in branching process theory. We apply the methodology to static and dynamic models of network formation and discuss how it can be used more broadly.

SSRN Electronic Journal, 2017

We develop inference procedures robust to general forms of weak dependence. The procedures utiliz... more We develop inference procedures robust to general forms of weak dependence. The procedures utilize test statistics constructed by resampling in a manner that does not depend on the unknown correlation structure of the data. We prove that the statistics are asymptotically normal under the weak requirement that the target parameter can be consistently estimated at the parametric rate. This holds for regular estimators under many well-known forms of weak dependence and justifies the claim of dependence-robustness. We consider applications to settings with unknown or complicated forms of dependence, with various forms of network dependence as leading examples. We develop tests for both moment equalities and inequalities.

SSRN Electronic Journal, 2018

This paper studies inference on finite-population average and local average treatment effects und... more This paper studies inference on finite-population average and local average treatment effects under limited overlap, meaning that some strata have a small proportion of treated or untreated units. We model limited overlap in an asymptotic framework, sending the propensity score to zero (or one) with the sample size. We derive the asymptotic distribution of analogue estimators of the treatment effects under two common randomization schemes: conditionally independent and stratified block randomization. Under either scheme, the limit distribution is the same and conventional standard error formulas remain asymptotically valid, but the rate of convergence is slower the faster the propensity score degenerates. The practical import of these results is twofold. When overlap is limited, standard methods can perform poorly in smaller samples, as asymptotic approximations are inadequate owing to the slower rate of convergence. However, in larger samples, standard methods can work quite well even when the propensity score is small.

International Journal of Fatigue, 2018

The ability to perform accurate remnant life predictions is crucial to ensure the integrity of en... more The ability to perform accurate remnant life predictions is crucial to ensure the integrity of engineering components that experience fatigue loading during operation. This is conventionally done with periodic inspections, where results from non-destructive evaluation and estimation of the operating conditions are obtained to perform remnant life predictions using empirical crack growth laws. However, remnant life predictions made with this approach are very sensitive to their input parameters; uncertainty in each parameter would aggregate and result in great uncertainty in the final prediction. Recent technological advances have made permanently installed monitoring systems increasingly viable, making it possible to obtain and monitor trends in damage growth rate. It is proposed that the rate of damage growth can be used to more accurately and confidently gauge the integrity of an engineering component and perform remnant life predictions using the Failure Forecast Method. A statistical analysis of an example fatigue crack growth test was performed to compare the uncertainties of the remnant life predictions made using the conventional inspection approach, which utilises nominally-known operating conditions and empirical crack growth laws, and the proposed rate-based monitoring approach. Results show that the remnant life predictions made using the Failure Forecast Method produce significantly more accurate and confident predictions compared to the inspection approach. The Failure Forecast Method can also be adapted to accommodate load changes. An example fatigue test with a 20% load reduction after a period of crack growth was performed and the life predictions made with inspection data at the time of the load change and monitoring data up to that point were compared. Again it was shown that the uncertainty in the life prediction with the Failure Forecast Method using the monitoring data was lower than that with the inspection approach, but the improvement was smaller than in the constant load case because data on the load change and the Paris law exponent were required, thus increasing the uncertainty. The study has shown that the frequent data obtained from permanently installed monitoring systems provides new opportunities in remnant life estimates and potentially opens the way to increasing the intervals between outages and reducing design conservatism.

Scientific reports, Jan 5, 2018

Intraoperative image-guided surgical navigation for craniospinal procedures has significantly imp... more Intraoperative image-guided surgical navigation for craniospinal procedures has significantly improved accuracy by providing an avenue for the surgeon to visualize underlying internal structures corresponding to the exposed surface anatomy. Despite the obvious benefits of surgical navigation, surgeon adoption remains relatively low due to long setup and registration times, steep learning curves, and workflow disruptions. We introduce an experimental navigation system utilizing optical topographical imaging (OTI) to acquire the 3D surface anatomy of the surgical cavity, enabling visualization of internal structures relative to exposed surface anatomy from registered preoperative images. Our OTI approach includes near instantaneous and accurate optical measurement of >250,000 surface points, computed at >52,000 points-per-second for considerably faster patient registration than commercially available benchmark systems without compromising spatial accuracy. Our experience of 171 ...

Pediatric surgery international, Jan 26, 2017

Short segment Hirschsprung's disease (HSCR) carries a better prognosis than long segment dise... more Short segment Hirschsprung's disease (HSCR) carries a better prognosis than long segment disease, but the definition of short is controversial. The objective of this study is to determine anatomically the extent of disease involvement that would be associated with a better functional outcome. This is a retrospective multicenter (n = 3) study with patients (≥ 3 years) who had transanal pullthrough operation done for aganglionosis limited to the recto-sigmoid colon were reviewed. The extent of disease involvement and bowel resection was retrieved by reviewing the operative records as well as histopathological reports of the resected specimens. Clinical assessment was performed according to the criteria of a seven-itemed bowel function score (BFS) (maximum score = 20). Manometric assessment was performed with anorectal manometry. The study period started from 2003 to 45 patients were studied with median age at assessment = 52.0 months and operation = 3.0 months. The disease involve...

Processing of transcripts at the 3’-end involves cleavage at a polyadenylation site followed by t... more Processing of transcripts at the 3’-end involves cleavage at a polyadenylation site followed by the addition of a poly(A)-tail. By selecting which polyadenylation site is cleaved, alternative polyadenylation enables genes to produce transcript isoforms with different 3’-ends. To facilitate the identification and treatment of disease-causing mutations that affect polyadenylation and to understand the underlying regulatory processes, a computational model that can accurately predict polyadenylation patterns based on genomic features is desirable. Previous works have focused on identifying candidate polyadenylation sites and classifying sites which may be tissue-specific. What is lacking is a predictive model of the underlying mechanism of site selection, competition, and processing efficiency in a tissue-specific manner. We develop a deep learning model that trains on 3’-end sequencing data and predicts tissue-specific site selection among competing polyadenylation sites in the 3’ unt...

Proceedings of the IEEE, 2016

This paper provides an introduction to machine learning tasks that are relevant to important prob... more This paper provides an introduction to machine learning tasks that are relevant to important problems in genomic medicine.

Heart, Lung and Circulation, 2015

Journal of Biomedical Optics, 2015

Vitrification is an increasingly popular method of embryo cryopreservation that is used in assist... more Vitrification is an increasingly popular method of embryo cryopreservation that is used in assisted reproductive technology. Although vitrification has high post-thaw survival rates compared to other freezing techniques, its long-term effects on embryo development are still poorly understood. We demonstrate an application of full-field optical coherence tomography (FF-OCT) to visualize the effects of vitrification on live single-cell (2 pronuclear) mouse embryos without harmful labels. Using FF-OCT, we observed that vitrification causes a significant increase in the aggregation of structures within the embryo cytoplasm, consistent with reports in literature based on fluorescence techniques. We quantify the degree of aggregation with an objective metric, the cytoplasmic aggregation (CA) score, and observe a high degree of correlation between the CA scores of FF-OCT images of embryos and of fluorescence images of their mitochondria. Our results indicate that FF-OCT shows promise as a label-free assessment of the effects of vitrification on embryo mitochondria distribution. The CA score provides a quantitative metric to describe the degree to which embryos have been affected by vitrification and could aid clinicians in selecting embryos for transfer.

Bioinformatics (Oxford, England), Jan 15, 2014

Alternative splicing (AS) is a regulated process that directs the generation of different transcr... more Alternative splicing (AS) is a regulated process that directs the generation of different transcripts from single genes. A computational model that can accurately predict splicing patterns based on genomic features and cellular context is highly desirable, both in understanding this widespread phenomenon, and in exploring the effects of genetic variations on AS. Using a deep neural network, we developed a model inferred from mouse RNA-Seq data that can predict splicing patterns in individual tissues and differences in splicing patterns across tissues. Our architecture uses hidden variables that jointly represent features in genomic sequences and tissue types when making predictions. A graphics processing unit was used to greatly reduce the training time of our models with millions of parameters. We show that the deep architecture surpasses the performance of the previous Bayesian method for predicting AS patterns. With the proper optimization procedure and selection of hyperparamete...

Canadian family physician Médecin de famille canadien, 2002

PLoS ONE, 2012

This study examined the dissociable neural effects of a ¯na ¯pa ¯nasati (focused-attention medita... more This study examined the dissociable neural effects of a ¯na ¯pa ¯nasati (focused-attention meditation, FAM) and metta ¯(lovingkindness meditation, LKM) on BOLD signals during cognitive (continuous performance test, CPT) and affective (emotionprocessing task, EPT, in which participants viewed affective pictures) processing. Twenty-two male Chinese expert meditators (11 FAM experts, 11 LKM experts) and 22 male Chinese novice meditators (11 FAM novices, 11 LKM novices) had their brain activity monitored by a 3T MRI scanner while performing the cognitive and affective tasks in both meditation and baseline states. We examined the interaction between state (meditation vs. baseline) and expertise (expert vs. novice) separately during LKM and FAM, using a conjunction approach to reveal common regions sensitive to the expert meditative state. Additionally, exclusive masking techniques revealed distinct interactions between state and group during LKM and FAM. Specifically, we demonstrated that the practice of FAM was associated with expertise-related behavioral improvements and neural activation differences in attention task performance. However, the effect of state LKM meditation did not carry over to attention task performance. On the other hand, both FAM and LKM practice appeared to affect the neural responses to affective pictures. For viewing sad faces, the regions activated for FAM practitioners were consistent with attention-related processing; whereas responses of LKM experts to sad pictures were more in line with differentiating emotional contagion from compassion/emotional regulation processes. Our findings provide the first report of distinct neural activity associated with forms of meditation during sustained attention and emotion processing.