subject:(prediction)

University of Alberta

1. Ghazimirsaied, Seyedahmad. Extending HCCI Low Load Operation Using Chaos Prediction and Feedback Control.

Degree: PhD, Department of Mechanical Engineering, 2012, University of Alberta

URL: https://era.library.ualberta.ca/files/4m90dv928

► Homogenous Charge Compression Ignition (HCCI) is a promising technology that offers high fuel economy and low oxides of nitrogen and particulate emission for automotive and… (more)

Subjects/Keywords: prediction; hcci

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APA (6^th Edition):

Ghazimirsaied, S. (2012). Extending HCCI Low Load Operation Using Chaos Prediction and Feedback Control. (Doctoral Dissertation). University of Alberta. Retrieved from https://era.library.ualberta.ca/files/4m90dv928

Chicago Manual of Style (16^th Edition):

Ghazimirsaied, Seyedahmad. “Extending HCCI Low Load Operation Using Chaos Prediction and Feedback Control.” 2012. Doctoral Dissertation, University of Alberta. Accessed February 26, 2021. https://era.library.ualberta.ca/files/4m90dv928.

MLA Handbook (7^th Edition):

Ghazimirsaied, Seyedahmad. “Extending HCCI Low Load Operation Using Chaos Prediction and Feedback Control.” 2012. Web. 26 Feb 2021.

Vancouver:

Ghazimirsaied S. Extending HCCI Low Load Operation Using Chaos Prediction and Feedback Control. [Internet] [Doctoral dissertation]. University of Alberta; 2012. [cited 2021 Feb 26]. Available from: https://era.library.ualberta.ca/files/4m90dv928.

Council of Science Editors:

Ghazimirsaied S. Extending HCCI Low Load Operation Using Chaos Prediction and Feedback Control. [Doctoral Dissertation]. University of Alberta; 2012. Available from: https://era.library.ualberta.ca/files/4m90dv928

Vanderbilt University

2. Boyles, Robert William. Mechanical Design of an Instrumented Cane for Gait Prediction by Physical Therapists.

Degree: MS, Mechanical Engineering, 2015, Vanderbilt University

URL: http://hdl.handle.net/1803/14485

► Many individuals at some point in their lives will utilize an assisted walking device to help them move around. Physical therapists use their experience to… (more)

Subjects/Keywords: gait prediction

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APA (6^th Edition):

Boyles, R. W. (2015). Mechanical Design of an Instrumented Cane for Gait Prediction by Physical Therapists. (Thesis). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/14485

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Boyles, Robert William. “Mechanical Design of an Instrumented Cane for Gait Prediction by Physical Therapists.” 2015. Thesis, Vanderbilt University. Accessed February 26, 2021. http://hdl.handle.net/1803/14485.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Boyles, Robert William. “Mechanical Design of an Instrumented Cane for Gait Prediction by Physical Therapists.” 2015. Web. 26 Feb 2021.

Vancouver:

Boyles RW. Mechanical Design of an Instrumented Cane for Gait Prediction by Physical Therapists. [Internet] [Thesis]. Vanderbilt University; 2015. [cited 2021 Feb 26]. Available from: http://hdl.handle.net/1803/14485.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Boyles RW. Mechanical Design of an Instrumented Cane for Gait Prediction by Physical Therapists. [Thesis]. Vanderbilt University; 2015. Available from: http://hdl.handle.net/1803/14485

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Johannesburg

3. Erasmus, Adrian Dean. A tracking theory of prediction.

Degree: 2015, University of Johannesburg

URL: http://hdl.handle.net/10210/14056

►

M.A. (Philosophy)

The purpose of my project is to provide necessary and sufficient conditions for a prediction to be considered good. Alex Broadbent (2013) claims… (more)

Subjects/Keywords: Prediction (Logic)

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APA (6^th Edition):

Erasmus, A. D. (2015). A tracking theory of prediction. (Thesis). University of Johannesburg. Retrieved from http://hdl.handle.net/10210/14056

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Erasmus, Adrian Dean. “A tracking theory of prediction.” 2015. Thesis, University of Johannesburg. Accessed February 26, 2021. http://hdl.handle.net/10210/14056.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Erasmus, Adrian Dean. “A tracking theory of prediction.” 2015. Web. 26 Feb 2021.

Vancouver:

Erasmus AD. A tracking theory of prediction. [Internet] [Thesis]. University of Johannesburg; 2015. [cited 2021 Feb 26]. Available from: http://hdl.handle.net/10210/14056.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Erasmus AD. A tracking theory of prediction. [Thesis]. University of Johannesburg; 2015. Available from: http://hdl.handle.net/10210/14056

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

4. park, ju-hwa. The Psychological Reality of the Markov Property of Causal Bayes Nets.

Degree: PhD, Cognitive Sciences, 2012, Brown University

URL: https://repository.library.brown.edu/studio/item/bdr:297597/

► Previous research has questioned the causal Bayes net formalism reporting the violation of the Markov principle which lies at the heart of the causal Bayes… (more)

▼ Previous research has questioned the causal Bayes net formalism reporting the violation of the Markov principle which lies at the heart of the causal Bayes net formalism. Two sets of studies attempted to test the current hypotheses about the violation of the Markov principle. Of particular interest was whether causal representation of causal learning is consistent with that of causal prediction. In contrast to the causal Bayes nets view which assumes the consistency, I proposed an alternative hypothesis called the different abstraction level hypothesis, claiming that a mental representation of causal structure learning is different from that of causal prediction and the difference is the source of the violation. To be specific, the mechanistic knowledge is not a part of a mental causal model when we define an event in question as a cause or an effect (structure learning) in general, but it is a part of the mental model when we make causal predictions. The first set (Experiments 1-4) examines the role of mechanisms in causal predictions providing a pair of causal statements which describe a common cause structure. The second set of experiments (Experiments 5-7) gave participants causally sufficient dependency information among three abstract sliders and asked them to learn the causal relation, a common cause, a chain, and a common effect structure. Overall, all seven experiments showed that causal predictions were not just a matter of causal structure. Rather, the results demonstrated that causal predictions were mediated by mechanisms between a cause and effect. Critically, when mechanisms were construed as the same, participants violated the screening-off rule while they respected the screening off rule when mechanisms were different. Despite the differences in probability judgments, causal graphs that participants drew in both conditions were not different (Experiment 5 and 7). Together, the thesis effectively isolated under what condition adults violate or respect the Markov principle enhancing the current understanding of how mechanisms constraint causal predictions given a specific causal structure. Advisors/Committee Members: Sloman, Steven (Director), Sobel, David (Reader), Serre, Thomas (Reader).

Subjects/Keywords: causal prediction

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APA (6^th Edition):

park, j. (2012). The Psychological Reality of the Markov Property of Causal Bayes Nets. (Doctoral Dissertation). Brown University. Retrieved from https://repository.library.brown.edu/studio/item/bdr:297597/

Chicago Manual of Style (16^th Edition):

park, ju-hwa. “The Psychological Reality of the Markov Property of Causal Bayes Nets.” 2012. Doctoral Dissertation, Brown University. Accessed February 26, 2021. https://repository.library.brown.edu/studio/item/bdr:297597/.

MLA Handbook (7^th Edition):

park, ju-hwa. “The Psychological Reality of the Markov Property of Causal Bayes Nets.” 2012. Web. 26 Feb 2021.

Vancouver:

park j. The Psychological Reality of the Markov Property of Causal Bayes Nets. [Internet] [Doctoral dissertation]. Brown University; 2012. [cited 2021 Feb 26]. Available from: https://repository.library.brown.edu/studio/item/bdr:297597/.

Council of Science Editors:

park j. The Psychological Reality of the Markov Property of Causal Bayes Nets. [Doctoral Dissertation]. Brown University; 2012. Available from: https://repository.library.brown.edu/studio/item/bdr:297597/

Università della Svizzera italiana

5. D'Ambros, Marco. On the evolution of source code and software defects.

Degree: 2010, Università della Svizzera italiana

URL: http://doc.rero.ch/record/21151

► Software systems are subject to continuous changes to adapt to new and changing requirements.This phenomenon, known as software evolution, leads in the long term to… (more)

▼ Software systems are subject to continuous changes to adapt to new and changing requirements.This phenomenon, known as software evolution, leads in the long term to software aging: The size and the complexity of systems increase, while their quality decreases. In this context, it is no wonder that software maintenance claims the most part of a software system's cost.The analysis of software evolution helps practitioners deal with the negative effects of software aging. With the advent of the Internet and the consequent widespread adoption of distributed development tools, such as software configuration management and issue tracking systems, a vast amount of valuable information concerning software evolution has become available. In the last two decades, researchers have focused on mining and analyzing this data, residing in various software repositories, to understand software evolution and support maintenance activities. However, most approaches target a specific maintenance task, and consider only one of the several facets of software evolution. Such approaches, and the infrastructures that implement them, cannot be extended to address different maintenance problems. In this dissertation, we propose an integrated view of software evolution that combines different evolutionary aspects. Our thesis is that an integrated and flexible approach supports an extensible set of software maintenance activities. To this aim, we present a meta-model that integrates two aspects of software evolution: source code and software defects. We implemented our approach in a framework that, by retrieving information from source code and defect repositories, serves as a basis to create analysis techniques and tools. To show the flexibility of our approach, we extended our meta-model and framework with e-mail information extracted from development mailing lists. To validate our thesis, we devised and evaluated, on top of our approach, a number of novel analysis techniques that achieve two goals: 1. Inferring the causes of problems in a software system. We propose three retrospective analysis techniques, based on interactive visualizations, to analyze the evolution of source code, software defects, and their co-evolution. These techniques support various maintenance tasks, such as system restructuring, re- documentation, and identification of critical software components. 2. Predicting the future of a software system. We present four analysis techniques aimed at anticipating the locations of future defects, and investigating the impact of certain source code properties on the presence of defects. They support two maintenance tasks: defect prediction and software quality analysis. By creating our framework and the mentioned techniques on top of it, we provide evidence that an integrated view of software evolution, combining source code and software defects information, supports an extensible set of software maintenance tasks. Advisors/Committee Members: Michele (Dir.).

Subjects/Keywords: Defect prediction

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APA (6^th Edition):

D'Ambros, M. (2010). On the evolution of source code and software defects. (Thesis). Università della Svizzera italiana. Retrieved from http://doc.rero.ch/record/21151

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

D'Ambros, Marco. “On the evolution of source code and software defects.” 2010. Thesis, Università della Svizzera italiana. Accessed February 26, 2021. http://doc.rero.ch/record/21151.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

D'Ambros, Marco. “On the evolution of source code and software defects.” 2010. Web. 26 Feb 2021.

Vancouver:

D'Ambros M. On the evolution of source code and software defects. [Internet] [Thesis]. Università della Svizzera italiana; 2010. [cited 2021 Feb 26]. Available from: http://doc.rero.ch/record/21151.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

D'Ambros M. On the evolution of source code and software defects. [Thesis]. Università della Svizzera italiana; 2010. Available from: http://doc.rero.ch/record/21151

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Università della Svizzera italiana

6. Verbosio, Fabio. High performance selected inversion methods for sparse matrices: direct and stochastic approaches to selected inversion.

Degree: 2019, Università della Svizzera italiana

URL: http://doc.rero.ch/record/324252

► The explicit evaluation of selected entries of the inverse of a given sparse matrix is an important process in various application fields and is gaining… (more)

▼ The explicit evaluation of selected entries of the inverse of a given sparse matrix is an important process in various application fields and is gaining visibility in recent years. While a standard inversion process would require the computation of the whole inverse who is, in general, a dense matrix, state-of-the-art solvers perform a selected inversion process instead. Such approach allows to extract specific entries of the inverse, e.g., the diagonal, avoiding the standard inversion steps, reducing therefore time and memory requirements. Despite the complexity reduction already achieved, the natural direction for the development of the selected inversion software is the parallelization and distribution of the computation, exploiting multinode implementations of the algorithms. In this work we introduce parallel, high performance selected inversion algorithms suitable for both the computation and estimation of the diagonal of the inverse of large, sparse matrices. The first approach is built on top of a sparse factorization method and a distributed computation of the Schur-complement, and is specifically designed for the parallel treatment of large, dense matrices including a sparse block. The second is based on the stochastic estimation of the matrix diagonal using a stencil-based, matrix-free Krylov subspace iteration. We implement the two solvers and prove their excellent performance on Cray supercomputers, focusing on both the multinode scalability and the numerical accuracy. Finally, we include the solvers into two distinct frameworks designed for the solution of selected inversion problems in real-life applications. First, we present a parallel, scalable framework for the log-likelihood maximization in genomic prediction problems including marker by environment effects. Then, we apply the matrix-free estimator to the treatment of large-scale three-dimensional nanoelectronic device simulations with open boundary conditions. Advisors/Committee Members: Olaf (Dir.).

Subjects/Keywords: Genomic prediction

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APA (6^th Edition):

Verbosio, F. (2019). High performance selected inversion methods for sparse matrices: direct and stochastic approaches to selected inversion. (Thesis). Università della Svizzera italiana. Retrieved from http://doc.rero.ch/record/324252

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Verbosio, Fabio. “High performance selected inversion methods for sparse matrices: direct and stochastic approaches to selected inversion.” 2019. Thesis, Università della Svizzera italiana. Accessed February 26, 2021. http://doc.rero.ch/record/324252.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Verbosio, Fabio. “High performance selected inversion methods for sparse matrices: direct and stochastic approaches to selected inversion.” 2019. Web. 26 Feb 2021.

Vancouver:

Verbosio F. High performance selected inversion methods for sparse matrices: direct and stochastic approaches to selected inversion. [Internet] [Thesis]. Università della Svizzera italiana; 2019. [cited 2021 Feb 26]. Available from: http://doc.rero.ch/record/324252.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Verbosio F. High performance selected inversion methods for sparse matrices: direct and stochastic approaches to selected inversion. [Thesis]. Università della Svizzera italiana; 2019. Available from: http://doc.rero.ch/record/324252

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Illinois – Urbana-Champaign

7. Li, Weiwei. Toward better subseasonal-to-seasonal prediction: physics-oriented model evaluation and predictability of tropical cyclones.

Degree: PhD, Atmospheric Sciences, 2017, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/98184

► Skillful subseasonal-to-seasonal (hereafter S2S; 10 days - 12 weeks) prediction can greatly benefit decision-making on resource management and agricultural planning that falls into the weekly… (more)

▼ Skillful subseasonal-to-seasonal (hereafter S2S; 10 days - 12 weeks) prediction can greatly benefit decision-making on resource management and agricultural planning that falls into the weekly to seasonal time ranges. The S2S prediction, bridging the traditional weather forecasting and climate prediction, remains a challenge for global numerical models. This is mostly because the sources of predictability on S2S timescales are not fully understood and/or not well represented in global models. My Ph.D. thesis research seeks to improve the model performance and the S2S prediction by 1) developing a suite of "physics-oriented" model evaluation metrics that can not only assess how model performs but also help to reveal possible error sources, and 2) investigating sources of predictability of high-impact weather phenomena with a special focus on tropical cyclones (TCs). The analysis is expected to provide useful guidance on model development and improvement. My thesis first evaluated the Madden-Julian oscillation (MJO) - the dominant mode of tropical subseasonal variability and an important source of predictability on S2S timescales. Both the Navy Operational Global Atmospheric Prediction System (NOGAPS) and Global Forecasting System (GFS) exhibit relatively low predictive skill when the MJO initiates over the Indian Ocean and when the active convection of the MJO is over the Maritime Continent. Further analyses indicated a dry bias within the marine boundary layer and a misrepresented shallow heating mode in the NOGAPS, suggesting a model deficiency in cumulus parameterization. The diabatic heating biases are associated with weaker trade winds, weaker Hadley and Walker circulations over the Pacific, and weaker cross-equatorial flow over the Indian Ocean. The TC prediction was evaluated in the National Centers for Environmental Prediction (NCEP) Global Ensemble Forecasting System (GEFS) with forecast lead time up to 2 weeks. It shows that the GEFS has large errors of TCs on the regional scale. The negative genesis biases over the western North Pacific are associated with a weaker-than-observed monsoon trough, the erroneous genesis pattern over the eastern North Pacific is related to a southward displacement of the ITCZ, and the positive genesis biases near the Cape Verde islands and negative biases farther downstream over the Atlantic can be attributed to the hyperactive African easterly waves and stronger deep convective heating. The biases are associated with the deficiencies in the cumulus schemes of the GEFS. The precipitation initiates too early with respect to the column water vapor. And there is a dry bias in the column water vapor, which increases with the forecast lead times. The GEFS also underpredicts moderate-to-heavy precipitation. The analyses suggest that improvement in the cumulus parameterization may reduce the model mean state errors and enhance the TC prediction on the regional scale. The predictability of TCs was investigated on interannual, subseasonal, and synoptic timescales using the GEFS… Advisors/Committee Members: Wang, Zhuo (advisor), Wang, Zhuo (Committee Chair), Peng, Melinda S (committee member), Rauber, Bob (committee member), Wuebbles, Donald J (committee member).

Subjects/Keywords: Prediction; Predictability

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APA (6^th Edition):

Li, W. (2017). Toward better subseasonal-to-seasonal prediction: physics-oriented model evaluation and predictability of tropical cyclones. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/98184

Chicago Manual of Style (16^th Edition):

Li, Weiwei. “Toward better subseasonal-to-seasonal prediction: physics-oriented model evaluation and predictability of tropical cyclones.” 2017. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed February 26, 2021. http://hdl.handle.net/2142/98184.

MLA Handbook (7^th Edition):

Li, Weiwei. “Toward better subseasonal-to-seasonal prediction: physics-oriented model evaluation and predictability of tropical cyclones.” 2017. Web. 26 Feb 2021.

Vancouver:

Li W. Toward better subseasonal-to-seasonal prediction: physics-oriented model evaluation and predictability of tropical cyclones. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2017. [cited 2021 Feb 26]. Available from: http://hdl.handle.net/2142/98184.

Council of Science Editors:

Li W. Toward better subseasonal-to-seasonal prediction: physics-oriented model evaluation and predictability of tropical cyclones. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2017. Available from: http://hdl.handle.net/2142/98184

NSYSU

8. Tong, Ting-Chi. Bandwidth Optimized Integrated Predictive Pixel Compensator of H.264 Decoder.

Degree: Master, Computer Science and Engineering, 2008, NSYSU

URL: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0807108-200335

► In this thesis, a high-efficient integrated pixel compensator architecture for the H.264/AVC standard has been proposed which can provide both inter and intra prediction functions… (more)

▼ In this thesis, a high-efficient integrated pixel compensator architecture for the H.264/AVC standard has been proposed which can provide both inter and intra prediction functions for luma and chroma components of pixels. By decomposing the algorithms used for both prediction methods into small micro-operation steps, the fundamental arithmetic processing unit architecture capable for performing these operations can be first determined. Next, by considering the possible reference sample transfer issue, the overall compensator architecture will be built by using parallel processing units with some input and intermediate buffers which can be dynamically configured to perform proper computation schedules of different modes suitable for the nature input order of reference samples. The proposed design not only can avoid the additional data transposition buffer, but most importantly the data transfer time spent to fetch the reference samples can be overlapped with the data computation time. Since both arithmetic units and the intermediate data buffer for both inter and intra prediction processes have been shared, our integrated design can achieve more than 30% reduction of gate count compared with the sum of the separate designs. Our design can also lead to more than 38% saving of gate count compared with the previous designs. In addition to the data-path design, this thesis also addresses the memory bandwidth optimization issue which is especially important for the luma interpolation process. A new data-reuse buffer design based on a two-dimensional cache architecture to explore the possible data reuse among the inter and intra partitions will be proposed. The proposed design can be easily integrated with the H.264 interpolator to reduce the enormous demand of memory access. Our experimental results shows that our saving of memory bandwidth can be 20% more than what the best design can achieve by exploring the intra-partition data reuse only. Besides, our compensator can decode the videos up to HDTV resolution, and be applied for the dedicated H.264 hardware codec for various consumer devices. Advisors/Committee Members: Chuen-Yau Chen (chair), Yun-Nan Chang (committee member), Shen-Fu Hsiao (chair).

Subjects/Keywords: Predictive Pixel Compensator; Inter Prediction; Intra Prediction

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APA (6^th Edition):

Tong, T. (2008). Bandwidth Optimized Integrated Predictive Pixel Compensator of H.264 Decoder. (Thesis). NSYSU. Retrieved from http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0807108-200335

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Tong, Ting-Chi. “Bandwidth Optimized Integrated Predictive Pixel Compensator of H.264 Decoder.” 2008. Thesis, NSYSU. Accessed February 26, 2021. http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0807108-200335.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Tong, Ting-Chi. “Bandwidth Optimized Integrated Predictive Pixel Compensator of H.264 Decoder.” 2008. Web. 26 Feb 2021.

Vancouver:

Tong T. Bandwidth Optimized Integrated Predictive Pixel Compensator of H.264 Decoder. [Internet] [Thesis]. NSYSU; 2008. [cited 2021 Feb 26]. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0807108-200335.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Tong T. Bandwidth Optimized Integrated Predictive Pixel Compensator of H.264 Decoder. [Thesis]. NSYSU; 2008. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0807108-200335

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Vanderbilt University

9. Karakaş, Mert. BCL::Fold - de novo protein structure prediction by assembly of secondary structure elements.

Degree: PhD, Chemical and Physical Biology, 2011, Vanderbilt University

URL: http://hdl.handle.net/1803/14981

► Structural information facilitates understanding of protein function and activity. The limitations of experimental methods for protein structure elucidation in applicability to certain types and families… (more)

▼ Structural information facilitates understanding of protein function and activity. The limitations of experimental methods for protein structure elucidation in applicability to certain types and families of proteins, necessitates use of computational methods for protein structure prediction. Template-based methods utilize structural information from template proteins with available structures and high sequence similarity to the protein of interest. However, in the absence of such template proteins, de novo methods can be used to generate structural models. State of the art de novo methods are limited to smaller size proteins due to the size of the conformational search space that needs to be sampled. In this study, we introduce BCL::Fold, a novel de novo protein structure method and accompanying energy potentials. BCL::Fold discontinues the chain and works by assembling secondary structure elements (SSEs); namely α-helices and β-strands. This approach leverages the fact that SSEs more readily define the topology of a protein compared to flexible loop regions. This allows the decoupling of determination of a topology from building of flexible loop regions, which in turn divides the structure prediction problem into two more manageable portions. BCL::Fold employs a Monte-Carlo Metropolis minimization where SSE-based moves allow rapid sampling of conformational search space, while knowledge based-potentials are used to evaluate how native-like the generated structural models are. BCL::Fold was benchmarked on a set of proteins with diverse sequence lengths, secondary structure contents and topologies. A native-like structural model was obtained at comparable levels to Rosetta, one of the top-performing de novo methods. Energy potentials were also evaluated and shown to successfully discriminate native-like structural models. Accurate prediction of residue pairs, apart in the sequence but in close proximity in the structure, provides insight into the topology of a protein and therefore limits the conformational search space to be sampled in protein structure prediction. BCL::Contact is a novel method which utilizes artificial neural networks and provides rapid prediction of residue pair contacts. BCL::Contact improved the accuracy of protein structure prediction by Rosetta. Advisors/Committee Members: Brandt Eichman (committee member), Charles Sanders (committee member), Phoebe Stewart (committee member), Jens Meiler (committee member), Albert Beth (Committee Chair).

Subjects/Keywords: protein structure prediction; contact prediction; de novo

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Karakaş, M. (2011). BCL::Fold - de novo protein structure prediction by assembly of secondary structure elements. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/14981

Chicago Manual of Style (16^th Edition):

Karakaş, Mert. “BCL::Fold - de novo protein structure prediction by assembly of secondary structure elements.” 2011. Doctoral Dissertation, Vanderbilt University. Accessed February 26, 2021. http://hdl.handle.net/1803/14981.

MLA Handbook (7^th Edition):

Karakaş, Mert. “BCL::Fold - de novo protein structure prediction by assembly of secondary structure elements.” 2011. Web. 26 Feb 2021.

Vancouver:

Karakaş M. BCL::Fold - de novo protein structure prediction by assembly of secondary structure elements. [Internet] [Doctoral dissertation]. Vanderbilt University; 2011. [cited 2021 Feb 26]. Available from: http://hdl.handle.net/1803/14981.

Council of Science Editors:

Karakaş M. BCL::Fold - de novo protein structure prediction by assembly of secondary structure elements. [Doctoral Dissertation]. Vanderbilt University; 2011. Available from: http://hdl.handle.net/1803/14981

University of Windsor

10. Sanghvi, Shikhar. A Feature Based Model for Negative Sign Prediction in Signed Social Networks.

Degree: MS, Computer Science, 2020, University of Windsor

URL: https://scholar.uwindsor.ca/etd/8480

► People hold all kinds of positive and negative feelings for one another. Social networking online serves as a platform for showcasing such relationships, whether friendly… (more)

Subjects/Keywords: Link prediction; Sign prediction; Signed social networks

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APA (6^th Edition):

Sanghvi, S. (2020). A Feature Based Model for Negative Sign Prediction in Signed Social Networks. (Masters Thesis). University of Windsor. Retrieved from https://scholar.uwindsor.ca/etd/8480

Chicago Manual of Style (16^th Edition):

Sanghvi, Shikhar. “A Feature Based Model for Negative Sign Prediction in Signed Social Networks.” 2020. Masters Thesis, University of Windsor. Accessed February 26, 2021. https://scholar.uwindsor.ca/etd/8480.

MLA Handbook (7^th Edition):

Sanghvi, Shikhar. “A Feature Based Model for Negative Sign Prediction in Signed Social Networks.” 2020. Web. 26 Feb 2021.

Vancouver:

Sanghvi S. A Feature Based Model for Negative Sign Prediction in Signed Social Networks. [Internet] [Masters thesis]. University of Windsor; 2020. [cited 2021 Feb 26]. Available from: https://scholar.uwindsor.ca/etd/8480.

Council of Science Editors:

Sanghvi S. A Feature Based Model for Negative Sign Prediction in Signed Social Networks. [Masters Thesis]. University of Windsor; 2020. Available from: https://scholar.uwindsor.ca/etd/8480

Princeton University

11. Zhang, Yue. A systematic investigation of prediction error and learning in infancy .

Degree: PhD, 2020, Princeton University

URL: http://arks.princeton.edu/ark:/88435/dsp014j03d2576

► Prediction, or the ability to use past experiences to generate expectations about future sensory input, is increasingly believed to be crucial for adult cognition and… (more)

Subjects/Keywords: Development; Eyetracking; Learning; Prediction; Prediction Error; Pupillometry

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APA (6^th Edition):

Zhang, Y. (2020). A systematic investigation of prediction error and learning in infancy . (Doctoral Dissertation). Princeton University. Retrieved from http://arks.princeton.edu/ark:/88435/dsp014j03d2576

Chicago Manual of Style (16^th Edition):

Zhang, Yue. “A systematic investigation of prediction error and learning in infancy .” 2020. Doctoral Dissertation, Princeton University. Accessed February 26, 2021. http://arks.princeton.edu/ark:/88435/dsp014j03d2576.

MLA Handbook (7^th Edition):

Zhang, Yue. “A systematic investigation of prediction error and learning in infancy .” 2020. Web. 26 Feb 2021.

Vancouver:

Zhang Y. A systematic investigation of prediction error and learning in infancy . [Internet] [Doctoral dissertation]. Princeton University; 2020. [cited 2021 Feb 26]. Available from: http://arks.princeton.edu/ark:/88435/dsp014j03d2576.

Council of Science Editors:

Zhang Y. A systematic investigation of prediction error and learning in infancy . [Doctoral Dissertation]. Princeton University; 2020. Available from: http://arks.princeton.edu/ark:/88435/dsp014j03d2576

NSYSU

12. Chang, Hsiao-Yen. Refinement of All-atom Backbone Prediction of Proteins.

Degree: Master, Computer Science and Engineering, 2008, NSYSU

URL: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0820108-215243

► The all-atom protein backbone reconstruction problem (PBRP) is to rebuild the 3D coordinates of all atoms on the backbone which includes N, C, and O… (more)

Subjects/Keywords: backbone; prediction; protein

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APA (6^th Edition):

Chang, H. (2008). Refinement of All-atom Backbone Prediction of Proteins. (Thesis). NSYSU. Retrieved from http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0820108-215243

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Chang, Hsiao-Yen. “Refinement of All-atom Backbone Prediction of Proteins.” 2008. Thesis, NSYSU. Accessed February 26, 2021. http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0820108-215243.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Chang, Hsiao-Yen. “Refinement of All-atom Backbone Prediction of Proteins.” 2008. Web. 26 Feb 2021.

Vancouver:

Chang H. Refinement of All-atom Backbone Prediction of Proteins. [Internet] [Thesis]. NSYSU; 2008. [cited 2021 Feb 26]. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0820108-215243.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Chang H. Refinement of All-atom Backbone Prediction of Proteins. [Thesis]. NSYSU; 2008. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0820108-215243

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Tulane University

13. Hui Shao. Updating Risk Engine for Diabetes Progression and Mortality in the United States: the Building, Relating, Acting, Validating for Outcomes (BRAVO) of Diabetes Risk Engine.

Degree: 2017, Tulane University

URL: https://digitallibrary.tulane.edu/islandora/object/tulane:75487

► Background The prediction of diabetes-related comorbidities and mortality over lifetime has significant clinical and policy implications. A prediction model can be used for economic evaluation… (more)

▼ Background The prediction of diabetes-related comorbidities and mortality over lifetime has significant clinical and policy implications. A prediction model can be used for economic evaluation on diabetes medications, comparative effectiveness review (CER) over different therapeutic plans, and estimation of the expected long-tern outcomes for different treatment goals (e.g., HbA1c). Most of the current diabetes prediction models heavily relied on the UKPDS risk engine and Framingham equation, which used data from 1970s on European populations. These populations were significantly different from current US population in various ways including race, different health related concept, treatment algorithm, screening method of comorbidities and even definition of diabetes. In addition, UKPDS risk engine does not include impact of hypoglycemia, which emerged as an important issue in the management of diabetes due to its impact on quality of life, cardiovascular events and mortality. Furthermore, with the advancement of the medical technology and innovation in redefining treatment guideline during the last decades, the rates of cardiovascular events, all-cause mortality and event related mortality have fundamentally changed, especially the survival rates from CVD events has substantially increased. There is an urgent needs to develop a new risk engine that more adaptable to the current US population. Objective The objective of this study was to update risk engine using a cohort of patients with type 2 diabetes in the United States. Methods A total of 21 equations for forecasting diabetes-related microvascular and macrovascular events, hypoglycemia, mortality, and progression of diabetes risk factors were estimated using data on 10,251 patients from the Action to Control Cardiovascular Risk in Diabetes (ACCORD) trial. Left truncated proportional hazard model was applied to fit each event equation using diabetes duration as time index, and a variety of distributions including Weibull and Gompertz distribution were tested. 10-folds cross-validation or bootstrapped validation was applied to account for overfitting issue. Predicted cumulative incidence rates was plotted against the observed cumulative incidence to serve as internal validation to evaluate the prediction accuracy of the BRAVO risk engine on ACCORD data. External validation was performed through applying the BRAVO risk engine onto population from other clinical trials. Results The BRAVO risk engine’s forecast felled within the 95% confidence interval for the occurrence of observed events at each time point through 40 years after diabetes onset. The model prediction provides accurate prediction according to the internal validation and external validation process, and good face validity on risk factors were established by endocrinologists. Severe hypoglycemia was found to be an important risk factor for congestive heart failure (CHF), myocardial infarction (MI), angina, blindness, and associated with increased mortality. Racial factor was included in more… Advisors/Committee Members: Lizheng Shi (Thesis advisor), School of Public Health & Tropical Medicine Global Health Management and Policy (Degree granting institution).

Subjects/Keywords: Diabetes; Simulation; Prediction

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APA (6^th Edition):

Shao, H. (2017). Updating Risk Engine for Diabetes Progression and Mortality in the United States: the Building, Relating, Acting, Validating for Outcomes (BRAVO) of Diabetes Risk Engine. (Thesis). Tulane University. Retrieved from https://digitallibrary.tulane.edu/islandora/object/tulane:75487

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Shao, Hui. “Updating Risk Engine for Diabetes Progression and Mortality in the United States: the Building, Relating, Acting, Validating for Outcomes (BRAVO) of Diabetes Risk Engine.” 2017. Thesis, Tulane University. Accessed February 26, 2021. https://digitallibrary.tulane.edu/islandora/object/tulane:75487.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Shao, Hui. “Updating Risk Engine for Diabetes Progression and Mortality in the United States: the Building, Relating, Acting, Validating for Outcomes (BRAVO) of Diabetes Risk Engine.” 2017. Web. 26 Feb 2021.

Vancouver:

Shao H. Updating Risk Engine for Diabetes Progression and Mortality in the United States: the Building, Relating, Acting, Validating for Outcomes (BRAVO) of Diabetes Risk Engine. [Internet] [Thesis]. Tulane University; 2017. [cited 2021 Feb 26]. Available from: https://digitallibrary.tulane.edu/islandora/object/tulane:75487.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Shao H. Updating Risk Engine for Diabetes Progression and Mortality in the United States: the Building, Relating, Acting, Validating for Outcomes (BRAVO) of Diabetes Risk Engine. [Thesis]. Tulane University; 2017. Available from: https://digitallibrary.tulane.edu/islandora/object/tulane:75487

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Alberta

14. Morrison, Kimberly H. Factors that Influence Daily Human-Caused Forest Fires in Alberta.

Degree: MS, Department of Renewable Resources, 2016, University of Alberta

URL: https://era.library.ualberta.ca/files/cxd07gs955

► Humans are the major cause of forest fires in the spring in Alberta, and have resulted in major property damage in both the Flat Top… (more)

Subjects/Keywords: prediction; wildfire; Alberta

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APA (6^th Edition):

Morrison, K. H. (2016). Factors that Influence Daily Human-Caused Forest Fires in Alberta. (Masters Thesis). University of Alberta. Retrieved from https://era.library.ualberta.ca/files/cxd07gs955

Chicago Manual of Style (16^th Edition):

Morrison, Kimberly H. “Factors that Influence Daily Human-Caused Forest Fires in Alberta.” 2016. Masters Thesis, University of Alberta. Accessed February 26, 2021. https://era.library.ualberta.ca/files/cxd07gs955.

MLA Handbook (7^th Edition):

Morrison, Kimberly H. “Factors that Influence Daily Human-Caused Forest Fires in Alberta.” 2016. Web. 26 Feb 2021.

Vancouver:

Morrison KH. Factors that Influence Daily Human-Caused Forest Fires in Alberta. [Internet] [Masters thesis]. University of Alberta; 2016. [cited 2021 Feb 26]. Available from: https://era.library.ualberta.ca/files/cxd07gs955.

Council of Science Editors:

Morrison KH. Factors that Influence Daily Human-Caused Forest Fires in Alberta. [Masters Thesis]. University of Alberta; 2016. Available from: https://era.library.ualberta.ca/files/cxd07gs955

15. Erar Hood, Bahar. Whole Genome Regression for Modeling Gene by Treatment Interactions in Structured Populations.

Degree: Biostatistics, 2017, Brown University

URL: https://repository.library.brown.edu/studio/item/bdr:730659/

► A critical aspect of personalized medicine is the development of methods that evaluate genetic predisposition to respond to a treatment. Whole genome prediction (WGP) methods… (more)

▼ A critical aspect of personalized medicine is the development of methods that evaluate genetic predisposition to respond to a treatment. Whole genome prediction (WGP) methods have been shown to improve predictive accuracy in genetically complex traits. However, the methodology is not tailored for outcome prediction in human randomized clinical trials (RCTs). In this thesis, a novel statistical tool for predicting responsiveness to treatment in RCTs is developed using whole genome regression modeling of univariate continuous outcomes, categorical outcomes, and multiple correlated outcomes. The proposed adaptive Bayesian WGP method accounts for the underlying genetic heterogeneity present in populations, which are often targeted in RCTs, using a mixed model approach. Under this model, small effects regulated by the treatment that would normally go undetected and disregarded are captured by the unconstrained covariance structure of genetic random effects. This flexible method improves existing methodology by capturing the genetic correlation across treatment groups so that the model can readily adapt to different levels and forms of genetic structure present in the whole target population. This method is extended to allow the modeling of categorical and multivariate or longitudinal outcomes. Computational challenges that arise in the implementation of this multi-group model are addressed by employing an efficient estimation approach that allows application to large datasets at a reasonable computational cost. Predictive accuracy of adaptive BWGP is compared to other methods using simulated phenotypes generated from real genotypes under various scenarios. Results demonstrate that adaptive BWGP performs better or at least as well as stratified methods, such as BayesC, Bayesian Ridge Regression and Bayesian LASSO. The gain in prediction accuracy is highest for moderately and highly heritable traits under realistic effect regulation scenarios. Applications on real RCT outcomes from the Look AHEAD trial are also used to demonstrate how benefit from treatment can be predicted in practice using adaptive BWGP. Advisors/Committee Members: Papandonatos, George (Director), Istrail, Sorin (Reader), Wu, Zhijin (Reader), Bauer, Cici (Reader), McCaffery, Jeanne (Reader).

Subjects/Keywords: Whole genome prediction

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APA (6^th Edition):

Erar Hood, B. (2017). Whole Genome Regression for Modeling Gene by Treatment Interactions in Structured Populations. (Thesis). Brown University. Retrieved from https://repository.library.brown.edu/studio/item/bdr:730659/

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Erar Hood, Bahar. “Whole Genome Regression for Modeling Gene by Treatment Interactions in Structured Populations.” 2017. Thesis, Brown University. Accessed February 26, 2021. https://repository.library.brown.edu/studio/item/bdr:730659/.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Erar Hood, Bahar. “Whole Genome Regression for Modeling Gene by Treatment Interactions in Structured Populations.” 2017. Web. 26 Feb 2021.

Vancouver:

Erar Hood B. Whole Genome Regression for Modeling Gene by Treatment Interactions in Structured Populations. [Internet] [Thesis]. Brown University; 2017. [cited 2021 Feb 26]. Available from: https://repository.library.brown.edu/studio/item/bdr:730659/.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Erar Hood B. Whole Genome Regression for Modeling Gene by Treatment Interactions in Structured Populations. [Thesis]. Brown University; 2017. Available from: https://repository.library.brown.edu/studio/item/bdr:730659/

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Harvard University

16. Davis, Joshua Seth. Circulating microRNAs and Both Association With Methacholine PC20 and Prediction of Asthma Exacerbation in the Childhood Asthma Management Program (CAMP) Cohort.

Degree: Master of Medical Sciences, 2017, Harvard University

URL: http://nrs.harvard.edu/urn-3:HUL.InstRepos:41940985

► Background: Circulating microRNAs have shown promise both as a non-invasive biomarker and a predictor of disease activity. Prior asthma studies with clinical, biochemical, or genomic… (more)

▼ Background: Circulating microRNAs have shown promise both as a non-invasive biomarker and a predictor of disease activity. Prior asthma studies with clinical, biochemical, or genomic tests have failed to demonstrate excellent prediction of asthma exacerbation. This thesis hypothesizes that circulating miRNA would reveal: 1) candidate biomarkers related to airway hyperresponsiveness (AHR) and provide biologic insights into asthma epigenetic influences, 2) a panel of circulating miRNA in a pediatric asthma cohort or a combined microRNA-clinical asthma exacerbation score that may have superior predictive capability compared to the clinical asthma exacerbation score alone, and 3) the power of machine learning techniques such as backpropagation neural networks and XGBoost that may provide both improved prediction of exacerbations or perhaps yield insight into complex non-linear behavior. Methods: Serum samples were obtained at randomization for 160 children in the Childhood Asthma Management Program and were profiled using the TaqMan miRNA array set containing 754 miRNAs. For Aims 2 and 3, only 153 subjects had complete information on steroid bursts in the first year after randomization. Aim 1: The association of the isolated miRNA with methacholine PC20 was assessed. Network and pathway analyses were performed. Functional validation of two significant miRNAs was performed in human airway smooth muscle cells (HASMs). Aim 2: Dichotomized data for asthma exacerbation from the first year after randomization to the inhaled corticosteroid arm were used for binary logistic regression with microRNA cycle threshold and clinical exacerbation score. Ontology and pathway analyses were performed for significant miRNAs Aim 3: Dichotomized data for asthma exacerbation as in Aim 2 was used for both backpropagation and resilient backpropagation neural networks and XGBoost with miRNA features selected by the Kruskal Test for binary and multiclass classification. Randomized hyperparameter optimization was used for all 3 algorithms. The neural network metric for classification was mean misclassification error. The XGBoost metric for classification was AUROC. Results: Aim 1: Of 155 well-detected circulating miRNAs, eight were significantly associated with PC20 with the strongest association with miR-296-5p. Pathway analysis revealed miR-16-5p as a network hub, and involvement of multiple miRNAs interacting with genes in the FoxO and Hippo signaling pathways by KEGG analysis. Functional validation of two miRNA in HASM showed effects on cell growth and diameter. Aim 2: Of the 125 well-detected circulating miRNA, 12 had significant odd ratios for exacerbation with the most significant being miR-206. Each doubling of expression of the 12 miRNA resulted in between a 25-67% increase in risk of exacerbation. Stepwise logistic regression resulted in a three miRNA model that, when combined with the clinical score, demonstrated an AUROC of 0.81, which was superior to either the clinical model alone (AUROC 0.67) or miRNA model (AUROC 0.71). The… Advisors/Committee Members: Tantisira, Kelan G. (committee member), Lu, Quan (committee member), Weiss, Scott T. (committee member).

Subjects/Keywords: asthma; microrna; prediction

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APA (6^th Edition):

Davis, J. S. (2017). Circulating microRNAs and Both Association With Methacholine PC20 and Prediction of Asthma Exacerbation in the Childhood Asthma Management Program (CAMP) Cohort. (Masters Thesis). Harvard University. Retrieved from http://nrs.harvard.edu/urn-3:HUL.InstRepos:41940985

Chicago Manual of Style (16^th Edition):

Davis, Joshua Seth. “Circulating microRNAs and Both Association With Methacholine PC20 and Prediction of Asthma Exacerbation in the Childhood Asthma Management Program (CAMP) Cohort.” 2017. Masters Thesis, Harvard University. Accessed February 26, 2021. http://nrs.harvard.edu/urn-3:HUL.InstRepos:41940985.

MLA Handbook (7^th Edition):

Davis, Joshua Seth. “Circulating microRNAs and Both Association With Methacholine PC20 and Prediction of Asthma Exacerbation in the Childhood Asthma Management Program (CAMP) Cohort.” 2017. Web. 26 Feb 2021.

Vancouver:

Davis JS. Circulating microRNAs and Both Association With Methacholine PC20 and Prediction of Asthma Exacerbation in the Childhood Asthma Management Program (CAMP) Cohort. [Internet] [Masters thesis]. Harvard University; 2017. [cited 2021 Feb 26]. Available from: http://nrs.harvard.edu/urn-3:HUL.InstRepos:41940985.

Council of Science Editors:

Davis JS. Circulating microRNAs and Both Association With Methacholine PC20 and Prediction of Asthma Exacerbation in the Childhood Asthma Management Program (CAMP) Cohort. [Masters Thesis]. Harvard University; 2017. Available from: http://nrs.harvard.edu/urn-3:HUL.InstRepos:41940985

University of Illinois – Chicago

17. Ahmed, Madiha. Tornado Path Prediction Using Data Driven Techniques.

Degree: 2018, University of Illinois – Chicago

URL: http://hdl.handle.net/10027/22977

► Each year around 800-1400 tornadoes occur in the United States. Although a very small number of these tornadoes result in injuries and fatalities, the destruction… (more)

▼ Each year around 800-1400 tornadoes occur in the United States. Although a very small number of these tornadoes result in injuries and fatalities, the destruction caused by these events can be catastrophic. Despite having advance warning mechanisms and alert systems, the entire prevention of tornado casualties is still quite challenging (1). Studies have indicated that the rate of tornado-related fatalities and injuries are higher when effective warnings are not issued and people do not have access to suitable storm shelters (2). Tornado warnings are issued based upon the atmospheric disturbances being detected on Doppler radars. This system, however, provides the national average lead time of 13 minutes which is insufficient when families are expected to evacuate the areas under danger (3). The National Oceanic and Atmospheric Administration (NOAA) is currently working on developing a warn-on-forecast system to potentially improve the lead time for warnings before the formation of tornadoes (4). Upon studying numerous tornadoes, however, it became evident that the issues pertaining to tornado casualties could not simply be improved by extending warning times. The lack of communication between individuals and officials creates confusion about appropriate actions that individuals must take. Officials believe that by generating the warnings they have performed their job and the responsibility to take appropriate actions were then on the individuals. Individuals, on the other hand, seek to obtain more information regarding the arrival of a tornado, rather than simply relying on current warning mechanisms such as sirens and warnings broadcasted on television and radio. This communication dilemma results in preventable casualties (5). For the present model, the tornado path was predicted for El-Reno, Oklahoma tornado that had occurred on May 31, 2013. For Model 1, the exact locations were determined by calculating the latitude and longitude points based upon the previously predicted locations. The data was divided into one and two-minute intervals. For Model 2, the same locations were predicted based on the previous original locations that would be provided by the radar in the actual scenario. Results showed that the distance between the predicted and the original locations were reduced significantly when the locations were predicted from the prior original locations in Model 2. Furthermore, the predicted path of the tornado was divided into different circles of diameter equal to the width of tornadoes which are usually around 0.17 miles to 0.28 miles (6). Results indicated that 90% of the locations were predicted successfully when the diameter/width of the tornado was around 0.3 miles. To improve the communication gap between officials and individuals when providing warnings to people in a tornado’s path, the usage of UAVs (unmanned aerial vehicles) is proposed. UAVs equipped with cameras and Global Positioning Systems (GPS) can continuously map the land features of the area stricken by the disaster and provide updates… Advisors/Committee Members: Houshang, Darabi (advisor), Williams, Quintin (committee member), Sharabiani, Ashkan (committee member), Houshang, Darabi (chair).

Subjects/Keywords: Tornado; Path Prediction

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APA (6^th Edition):

Ahmed, M. (2018). Tornado Path Prediction Using Data Driven Techniques. (Thesis). University of Illinois – Chicago. Retrieved from http://hdl.handle.net/10027/22977

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Ahmed, Madiha. “Tornado Path Prediction Using Data Driven Techniques.” 2018. Thesis, University of Illinois – Chicago. Accessed February 26, 2021. http://hdl.handle.net/10027/22977.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Ahmed, Madiha. “Tornado Path Prediction Using Data Driven Techniques.” 2018. Web. 26 Feb 2021.

Vancouver:

Ahmed M. Tornado Path Prediction Using Data Driven Techniques. [Internet] [Thesis]. University of Illinois – Chicago; 2018. [cited 2021 Feb 26]. Available from: http://hdl.handle.net/10027/22977.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Ahmed M. Tornado Path Prediction Using Data Driven Techniques. [Thesis]. University of Illinois – Chicago; 2018. Available from: http://hdl.handle.net/10027/22977

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Rice University

18. Cheng, Yushao. Template-based Protein Structure Prediction and its Applications.

Degree: PhD, Engineering, 2013, Rice University

URL: http://hdl.handle.net/1911/76475

► Protein structure prediction, also called protein folding, is one of the most significant and challenging research areas in computational biophysics and structural bioinformatics. With the… (more)

▼ Protein structure prediction, also called protein folding, is one of the most significant and challenging research areas in computational biophysics and structural bioinformatics. With the rapid growth of PDB database, template-based modeling such as homology modeling and threading has become a popular method in protein structure prediction. However, it is still hard to detect good templates when the sequence identity is below 30%. In chapter 1, a profile-profile alignment method is proposed. It uses evolutionary and structural profiles to detect homologs, and a z-score-based method to rank templates. The performance of this method in the critical assessment of protein structure prediction experiments (CASP) was reported. In chapter 2, p53 mutations are studied as an application of protein structure prediction. The TP53 gene encodes a tumor suppressor protein called p53, and p53 mutations occur in about half of human cancers. Experimental studies showed that p53 cancer mutants can be reactivated by mutations on other sites. Machine learning technologies were used in this research. Multiple classifiers were built to predict whether a p53 mutant (single-point or multiple-point) would be transcriptionally active or not, based on features extracted from amino acid sequences and structures. The mutant structures were modeled using template-based protein structure prediction. Theses features were selected and analyzed using different feature selection methods, and classifiers were built under different learning settings, such as supervised learning and semi-supervised learning. The performances of these classifiers were analyzed and compared. Besides the study of single proteins, protein complexes in yeast are studied in chapter 3. Multiple classifiers were built to predict whether several given proteins can form a protein complex, based on features generated from amino acid sequences and protein-protein interaction network. Theses features were selected and analyzed using different feature selection methods. Also, these classifiers were built under different learning settings, such as supervised learning and active learning. The performances of these classifiers were analyzed and compared. Advisors/Committee Members: Ma, Jianpeng (advisor), Diehl, Michael R. (committee member), Tao, Yizhi Jane (committee member).

Subjects/Keywords: Protein structure prediction

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APA (6^th Edition):

Cheng, Y. (2013). Template-based Protein Structure Prediction and its Applications. (Doctoral Dissertation). Rice University. Retrieved from http://hdl.handle.net/1911/76475

Chicago Manual of Style (16^th Edition):

Cheng, Yushao. “Template-based Protein Structure Prediction and its Applications.” 2013. Doctoral Dissertation, Rice University. Accessed February 26, 2021. http://hdl.handle.net/1911/76475.

MLA Handbook (7^th Edition):

Cheng, Yushao. “Template-based Protein Structure Prediction and its Applications.” 2013. Web. 26 Feb 2021.

Vancouver:

Cheng Y. Template-based Protein Structure Prediction and its Applications. [Internet] [Doctoral dissertation]. Rice University; 2013. [cited 2021 Feb 26]. Available from: http://hdl.handle.net/1911/76475.

Council of Science Editors:

Cheng Y. Template-based Protein Structure Prediction and its Applications. [Doctoral Dissertation]. Rice University; 2013. Available from: http://hdl.handle.net/1911/76475

Rice University

19. Zong, David Mao. Methods for Predicting Synthetic Gene Circuits.

Degree: PhD, Natural Sciences, 2020, Rice University

URL: http://hdl.handle.net/1911/108076

► Mature engineering disciplines use computational tools to test designs before they are built, which allows rapid engineering design-build-test cycles. Synthetic biology is an immature engineering… (more)

Subjects/Keywords: Synthetic Biology; Prediction

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APA (6^th Edition):

Zong, D. M. (2020). Methods for Predicting Synthetic Gene Circuits. (Doctoral Dissertation). Rice University. Retrieved from http://hdl.handle.net/1911/108076

Chicago Manual of Style (16^th Edition):

Zong, David Mao. “Methods for Predicting Synthetic Gene Circuits.” 2020. Doctoral Dissertation, Rice University. Accessed February 26, 2021. http://hdl.handle.net/1911/108076.

MLA Handbook (7^th Edition):

Zong, David Mao. “Methods for Predicting Synthetic Gene Circuits.” 2020. Web. 26 Feb 2021.

Vancouver:

Zong DM. Methods for Predicting Synthetic Gene Circuits. [Internet] [Doctoral dissertation]. Rice University; 2020. [cited 2021 Feb 26]. Available from: http://hdl.handle.net/1911/108076.

Council of Science Editors:

Zong DM. Methods for Predicting Synthetic Gene Circuits. [Doctoral Dissertation]. Rice University; 2020. Available from: http://hdl.handle.net/1911/108076

Tampere University

20. Hakola, Ville. Predicting Marine Traffic in the Ice-Covered Baltic Sea .

Degree: 2020, Tampere University

URL: https://trepo.tuni.fi/handle/10024/120219

► Icebreaking activity and seasonal ice propose challenges for marine traffic prediction in the Baltic Sea. Traffic prediction is a vital part in the planning of… (more)

Subjects/Keywords: Marine Traffic ; AIS ; Route Prediction ; Trajectory Prediction ; ETA Prediction ; Traffic Prediction ; Winter Navigation

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APA (6^th Edition):

Hakola, V. (2020). Predicting Marine Traffic in the Ice-Covered Baltic Sea . (Masters Thesis). Tampere University. Retrieved from https://trepo.tuni.fi/handle/10024/120219

Chicago Manual of Style (16^th Edition):

Hakola, Ville. “Predicting Marine Traffic in the Ice-Covered Baltic Sea .” 2020. Masters Thesis, Tampere University. Accessed February 26, 2021. https://trepo.tuni.fi/handle/10024/120219.

MLA Handbook (7^th Edition):

Hakola, Ville. “Predicting Marine Traffic in the Ice-Covered Baltic Sea .” 2020. Web. 26 Feb 2021.

Vancouver:

Hakola V. Predicting Marine Traffic in the Ice-Covered Baltic Sea . [Internet] [Masters thesis]. Tampere University; 2020. [cited 2021 Feb 26]. Available from: https://trepo.tuni.fi/handle/10024/120219.

Council of Science Editors:

Hakola V. Predicting Marine Traffic in the Ice-Covered Baltic Sea . [Masters Thesis]. Tampere University; 2020. Available from: https://trepo.tuni.fi/handle/10024/120219

University of Edinburgh

21. Thompson, Douglas David. Predicted risk of harm versus treatment benefit in large randomised controlled trials.

Degree: PhD, 2015, University of Edinburgh

URL: http://hdl.handle.net/1842/15843

► Most drugs come with unwanted, and perhaps harmful, side-effects. Depending on the size of the treatment benefit such harms may be tolerable. In acute stroke,… (more)

▼ Most drugs come with unwanted, and perhaps harmful, side-effects. Depending on the size of the treatment benefit such harms may be tolerable. In acute stroke, treatment with aspirin and treatment with alteplase have both proven to be effective in reducing the odds of death or dependency in follow-up. However, in both cases, treated patients are subject to a greater risk of haemorrhage – a serious side-effect which could result in early death or greater dependency. Current treatment licenses are restricted so as to avoid treating those with certain traits or risk factors associated with bleeding. It is plausible however that a weighted combination of all these factors would achieve better discrimination than an informal assessment of each individual risk factor. This has the potential to help target treatment to those most likely to benefit and avoid treating those at greater risk from harm. This thesis will therefore: (i) explore how predictions of harm and benefit are currently made; (ii) seek to make improvements by adopting more rigorous methodological approaches in model development; and (iii) investigate how the predicted risk of harm and treatment benefit could be used to strike an optimal balance. Statistical prediction is not an exact science. Before clinical utility can be established it is essential that the performance of any prediction method be assessed at the point of application. A prediction method must attain certain desirable properties to be of any use, namely: good discrimination – which quantifies how well the prediction method can separate events from non-events; and good calibration – which measures how close the obtained predicted risks match the observed. A comparison of informal predictions made by clinicians and formal predictions made by clinical prediction models is presented using a prospective observational study of stroke patients seen at a single centre hospital in Edinburgh. These results suggest that both prediction methods achieve similar discrimination. A stratified framework based on predicted risks obtained from clinical prediction models is considered using data from large randomised trials. First, with three of the largest aspirin trials it is shown that there is no evidence to suggest that the benefit of aspirin on reducing six month death or dependency varies with the predicted risk of benefit or with the predicted risk of harm. Second, using data from the third International Stroke Trial (IST3) a similar question is posed of the effect of alteplase and the predicted risk of symptomatic intracranial haemorrhage. It was found that this relationship corresponded strongly with the relationship associated with stratifying patients according to their predicted risk of death or dependency in the absence of treatment: those at the highest predicted risk from either event stand to experience the largest absolute benefit from alteplase with no indication of harm amongst those at lower predicted risk. It is concluded that prediction models for harmful side-effects based on simple…

Subjects/Keywords: 616.8; prediction; stroke

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APA (6^th Edition):

Thompson, D. D. (2015). Predicted risk of harm versus treatment benefit in large randomised controlled trials. (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/15843

Chicago Manual of Style (16^th Edition):

Thompson, Douglas David. “Predicted risk of harm versus treatment benefit in large randomised controlled trials.” 2015. Doctoral Dissertation, University of Edinburgh. Accessed February 26, 2021. http://hdl.handle.net/1842/15843.

MLA Handbook (7^th Edition):

Thompson, Douglas David. “Predicted risk of harm versus treatment benefit in large randomised controlled trials.” 2015. Web. 26 Feb 2021.

Vancouver:

Thompson DD. Predicted risk of harm versus treatment benefit in large randomised controlled trials. [Internet] [Doctoral dissertation]. University of Edinburgh; 2015. [cited 2021 Feb 26]. Available from: http://hdl.handle.net/1842/15843.

Council of Science Editors:

Thompson DD. Predicted risk of harm versus treatment benefit in large randomised controlled trials. [Doctoral Dissertation]. University of Edinburgh; 2015. Available from: http://hdl.handle.net/1842/15843

University of Waterloo

22. Baron, Kilby. Evaluating the Effectiveness of Code2Vec for Bug Prediction When Considering That Not All Bugs Are the Same.

Degree: 2020, University of Waterloo

URL: http://hdl.handle.net/10012/16343

► Bug prediction is an area of research focused on predicting where in a software project future bugs will occur. The purpose of bug prediction models… (more)

Subjects/Keywords: bug prediction; code2vec

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APA (6^th Edition):

Baron, K. (2020). Evaluating the Effectiveness of Code2Vec for Bug Prediction When Considering That Not All Bugs Are the Same. (Thesis). University of Waterloo. Retrieved from http://hdl.handle.net/10012/16343

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Baron, Kilby. “Evaluating the Effectiveness of Code2Vec for Bug Prediction When Considering That Not All Bugs Are the Same.” 2020. Thesis, University of Waterloo. Accessed February 26, 2021. http://hdl.handle.net/10012/16343.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Baron, Kilby. “Evaluating the Effectiveness of Code2Vec for Bug Prediction When Considering That Not All Bugs Are the Same.” 2020. Web. 26 Feb 2021.

Vancouver:

Baron K. Evaluating the Effectiveness of Code2Vec for Bug Prediction When Considering That Not All Bugs Are the Same. [Internet] [Thesis]. University of Waterloo; 2020. [cited 2021 Feb 26]. Available from: http://hdl.handle.net/10012/16343.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Baron K. Evaluating the Effectiveness of Code2Vec for Bug Prediction When Considering That Not All Bugs Are the Same. [Thesis]. University of Waterloo; 2020. Available from: http://hdl.handle.net/10012/16343

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Waterloo

23. Chong, Michael. Commit-Level vs. File-Level Vulnerability Prediction.

Degree: 2016, University of Waterloo

URL: http://hdl.handle.net/10012/10867

► Helping software development teams find and repair vulnerabilities before they are released and exploited can prevent costs due to loss of data, availability, and reputation.… (more)

Subjects/Keywords: Vulnerability Prediction; Commit-level Prediction; File-level Prediction

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APA (6^th Edition):

Chong, M. (2016). Commit-Level vs. File-Level Vulnerability Prediction. (Thesis). University of Waterloo. Retrieved from http://hdl.handle.net/10012/10867

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Chong, Michael. “Commit-Level vs. File-Level Vulnerability Prediction.” 2016. Thesis, University of Waterloo. Accessed February 26, 2021. http://hdl.handle.net/10012/10867.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Chong, Michael. “Commit-Level vs. File-Level Vulnerability Prediction.” 2016. Web. 26 Feb 2021.

Vancouver:

Chong M. Commit-Level vs. File-Level Vulnerability Prediction. [Internet] [Thesis]. University of Waterloo; 2016. [cited 2021 Feb 26]. Available from: http://hdl.handle.net/10012/10867.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Chong M. Commit-Level vs. File-Level Vulnerability Prediction. [Thesis]. University of Waterloo; 2016. Available from: http://hdl.handle.net/10012/10867

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Texas – Austin

24. Farooq, Muhammad Umar, active 2013. Improving prediction accuracy of hard-to-predict branches using data value correlation.

Degree: PhD, Electrical and Computer Engineering, 2013, University of Texas – Austin

URL: http://hdl.handle.net/2152/23191

► Performance of modern pipelined processor depends on steady flow of useful instructions for processing. Branch instruction disrupts sequential flow of instructions by presenting multiple paths… (more)

▼ Performance of modern pipelined processor depends on steady flow of useful instructions for processing. Branch instruction disrupts sequential flow of instructions by presenting multiple paths through which a program can proceed. By predicting branch outcome early, branch predictors allow processor to continue fetching instructions from the predicted path. History-based dynamic branch predictors have shown to reach high prediction accuracy, yet certain branch types continue to mispredict. These are multitarget indirect branches and data-dependent direct and indirect branches. These are hard-to-predict branches since their outcome do not always exhibit repeatable patterns. This thesis describes branch prediction schemes for improving prediction accuracy of hard-to-predict branches using data value correlation. In these schemes, instead of relying on branch history information, compiler identifies program instructions whose output value strongly correlates with branch outcome. These correlated instructions are tracked at run-time, and their output is used for making branch predictions. Specifically, this thesis proposes following two branch prediction schemes: (i) Value-based BTB indexing (VBBI) is a low cost, compiler-guided scheme for predicting multi-target indirect branches. For every indirect branch, compiler identifies an instruction whose output strongly correlates with targets taken by the indirect branch. At run-time, multiple branch targets are stored and subsequently accessed from BTB using index formed by hashing indirect branch PC with output of the correlated instruction. (ii) Store-Load-Branch (SLB) predictor is a compiler-assisted branch prediction scheme for data-dependent branches. Typically, data-dependent branches are associated with program data structures such as arrays, linked list etc., and follow store-load-branch execution sequence. A set of memory locations is written at an earlier point in a program. Later, these locations are read, and used for evaluating branch condition. Branch outcome depends on values stored in data structure, which, normally do not have repeatable patterns. In SLB scheme, compiler identifies all program points where data structure associated with a data-dependent branch is modified. These marked store instructions are tracked at run-time, and stored values are used for computing branch flags ahead of time. Later, when branch instruction is fetched, pre-computed flags are read, and used for making predictions. This thesis introduces new branch prediction schemes, describes hardware structures and compiler analysis for implementing these schemes, evaluates their performance impact, and estimates their area, power and timing overhead. Advisors/Committee Members: John, Lizy Kurian (advisor).

Subjects/Keywords: Branch prediction; Compiler guided; Indirect branch prediction; Value based branch prediction

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APA (6^th Edition):

Farooq, Muhammad Umar, a. 2. (2013). Improving prediction accuracy of hard-to-predict branches using data value correlation. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/23191

Chicago Manual of Style (16^th Edition):

Farooq, Muhammad Umar, active 2013. “Improving prediction accuracy of hard-to-predict branches using data value correlation.” 2013. Doctoral Dissertation, University of Texas – Austin. Accessed February 26, 2021. http://hdl.handle.net/2152/23191.

MLA Handbook (7^th Edition):

Farooq, Muhammad Umar, active 2013. “Improving prediction accuracy of hard-to-predict branches using data value correlation.” 2013. Web. 26 Feb 2021.

Vancouver:

Farooq, Muhammad Umar a2. Improving prediction accuracy of hard-to-predict branches using data value correlation. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2013. [cited 2021 Feb 26]. Available from: http://hdl.handle.net/2152/23191.

Council of Science Editors:

Farooq, Muhammad Umar a2. Improving prediction accuracy of hard-to-predict branches using data value correlation. [Doctoral Dissertation]. University of Texas – Austin; 2013. Available from: http://hdl.handle.net/2152/23191

Vanderbilt University

25. Fischer, Axel Walter. In silico prediction of protein structures and ensembles.

Degree: PhD, Chemistry, 2018, Vanderbilt University

URL: http://hdl.handle.net/1803/10422

► Determination of a protein’s structural equilibrium constitution remains a challenge. Experimental techniques like X-ray crystallography or nuclear magnetic resonance spectroscopy either are only able to… (more)

▼ Determination of a protein’s structural equilibrium constitution remains a challenge. Experimental techniques like X-ray crystallography or nuclear magnetic resonance spectroscopy either are only able to determine single snapshots of the protein or are not applicable due to the protein's size or dynamics. Orthogonal techniques like electron paramagnetic resonance (EPR) spectroscopy are able to capture all significant populations of the protein but the obtainable data are typically too sparse to unambiguously determine a structural ensemble. Computational methods on the other hand, suffer from necessary simplifications of the structure sampling and free energy evaluation. In order to solve these existing problems, I developed a computational prediction pipeline for protein structures and ensembles that supports incorporation of limited experimental data from EPR spectroscopy and chemical cross-linking. The pipeline encompasses coarse-grained Monte Carlo Metropolis sampling using BCL::Fold, high-resolution refinement using Rosetta, and stability evaluations using molecular dynamics simulations. Novel methods were developed to incorporate the experimental data into the pipeline. Both types of experimental data significantly improved the average accuracy of the sampled models as well as the discrimination between accurate and inaccurate models. In addition, a novel loop sampling algorithm consisting of conformation hashing and cyclic coordinate descent was developed. The algorithm is substantially faster than other available algorithms and samples the conformation of the protein’s major population in 94 % of all cases. The developed methods were applied to determine the structure and dynamics of the Bcl-2-associated X protein (BAX), exotoxin U (ExoU), and the efflux-multidrug resistance protein (EmrE) in conjunction with structural data obtained through EPR spectroscopy. Advisors/Committee Members: Carlos F. Lopez (committee member), Terry P. Lybrand (committee member), Hassane S. Mchaourab (committee member), Michael P. Stone (committee member), Jens Meiler (Committee Chair).

Subjects/Keywords: de novo prediction; emre; protein modeling; epr; loop modeling; protein ensemble prediction; protein structure prediction

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APA (6^th Edition):

Fischer, A. W. (2018). In silico prediction of protein structures and ensembles. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/10422

Chicago Manual of Style (16^th Edition):

Fischer, Axel Walter. “In silico prediction of protein structures and ensembles.” 2018. Doctoral Dissertation, Vanderbilt University. Accessed February 26, 2021. http://hdl.handle.net/1803/10422.

MLA Handbook (7^th Edition):

Fischer, Axel Walter. “In silico prediction of protein structures and ensembles.” 2018. Web. 26 Feb 2021.

Vancouver:

Fischer AW. In silico prediction of protein structures and ensembles. [Internet] [Doctoral dissertation]. Vanderbilt University; 2018. [cited 2021 Feb 26]. Available from: http://hdl.handle.net/1803/10422.

Council of Science Editors:

Fischer AW. In silico prediction of protein structures and ensembles. [Doctoral Dissertation]. Vanderbilt University; 2018. Available from: http://hdl.handle.net/1803/10422

Royal Holloway, University of London

26. Petej, Ivan. Small and large scale probabilistic classifiers with guarantees of validity.

Degree: PhD, 2018, Royal Holloway, University of London

URL: https://pure.royalholloway.ac.uk/portal/en/publications/small-and-large-scale-probabilistic-classifiers-with-guarantees-of-validity(0b4f2ee3-8a2c-4ace-815f-440de3af6858).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.792821

► This thesis addresses and expands research in probabilistic prediction with a particular emphasis on generating forecasts which are well calibrated. Chapter 1 describes standard techniques… (more)

▼ This thesis addresses and expands research in probabilistic prediction with a particular emphasis on generating forecasts which are well calibrated. Chapter 1 describes standard techniques in machine learning and outlines two methods - conformal prediction and Venn prediction - both which serve as important building blocks for the remainder of the results in this thesis. Chapter 2 introduces the field of probabilistic machine learning and highlights some of the advantages and challenges of the methods developed to date. Chapter 3 proposes a new method of probabilistic prediction which is based on conformal prediction - a machine learning method for generating prediction sets that are guaranteed to have a specified coverage probability. The method is applied to the standard USPS data set with encouraging results. Chapter 4 focuses on the study of Venn prediction, concentrating on binary prediction problems. Venn predictors produce probability-type predictions for the labels of test objects which are guaranteed to be well calibrated under the standard assumption that the observations are generated independently from the same distribution. A new class of Venn predictors is introduced, called Venn-Abers predictors, which are based on the idea of isotonic regression. Promising empirical results are demonstrated both for Venn-Abers predictors and for their more computationally efficient simplified version. Chapter 5 studies theoretically and empirically a method of turning machine learning algorithms into probabilistic predictors that, as the Venn-Abers predictors described in the preceding chapter, automatically enjoy a property of validity (perfect calibration) but are computationally more efficient. The price to pay for perfect calibration is that these probabilistic predictors produce imprecise probabilities. When these imprecise probabilities are merged into precise probabilities, the resulting predictors, while losing the theoretical property of perfect calibration, are shown to be consistently more accurate than the existing methods in empirical studies.

Subjects/Keywords: Venn machine; reliable probabilistic prediction; additional information; transfer; Conformal Prediction; Probabilistic prediction; Class membership probability

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APA (6^th Edition):

Petej, I. (2018). Small and large scale probabilistic classifiers with guarantees of validity. (Doctoral Dissertation). Royal Holloway, University of London. Retrieved from https://pure.royalholloway.ac.uk/portal/en/publications/small-and-large-scale-probabilistic-classifiers-with-guarantees-of-validity(0b4f2ee3-8a2c-4ace-815f-440de3af6858).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.792821

Chicago Manual of Style (16^th Edition):

Petej, Ivan. “Small and large scale probabilistic classifiers with guarantees of validity.” 2018. Doctoral Dissertation, Royal Holloway, University of London. Accessed February 26, 2021. https://pure.royalholloway.ac.uk/portal/en/publications/small-and-large-scale-probabilistic-classifiers-with-guarantees-of-validity(0b4f2ee3-8a2c-4ace-815f-440de3af6858).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.792821.

MLA Handbook (7^th Edition):

Petej, Ivan. “Small and large scale probabilistic classifiers with guarantees of validity.” 2018. Web. 26 Feb 2021.

Vancouver:

Petej I. Small and large scale probabilistic classifiers with guarantees of validity. [Internet] [Doctoral dissertation]. Royal Holloway, University of London; 2018. [cited 2021 Feb 26]. Available from: https://pure.royalholloway.ac.uk/portal/en/publications/small-and-large-scale-probabilistic-classifiers-with-guarantees-of-validity(0b4f2ee3-8a2c-4ace-815f-440de3af6858).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.792821.

Council of Science Editors:

Petej I. Small and large scale probabilistic classifiers with guarantees of validity. [Doctoral Dissertation]. Royal Holloway, University of London; 2018. Available from: https://pure.royalholloway.ac.uk/portal/en/publications/small-and-large-scale-probabilistic-classifiers-with-guarantees-of-validity(0b4f2ee3-8a2c-4ace-815f-440de3af6858).html ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.792821

27. Sehlberg, Jimmy. Steam Prediction at an Integrated Pulp and Paper Mill : Mondi Dynäs in Kramfors Municipality.

Degree: Energy Science, 2020, Luleå University of Technology

URL: http://urn.kb.se/resolve?urn=urn:nbn:se:ltu:diva-79636

► The most important energy carrier at an integrated pulp and paper mill is steam, it is essential to power components and machinery. The components… (more)

▼ The most important energy carrier at an integrated pulp and paper mill is steam, it is essential to power components and machinery. The components create variations in the steam grid network, variations that exceed the capacity of the steam accumulator. To avoid steam shortages, production leans towards having the accumulator nearly filled, eventually leading to periods with over production. Abundantly produced steam must be released from the steam grid network, and this is done without energy recovery. The purpose has therefore been to create a computer model with the ability to predict steam consumption for the entire mill. The prediction shall eventually be used in the control systems for steam producers and the accumulator. By knowing future steam demand, production can be planned more efficiently and so can the accumulation level of steam. This will allow a greater range of operation since the predictor can provide information on when significant steam demand changes will occur. The most important energy carrier at an integrated pulp and paper mill is steam, it is essential to power components and machinery. The components create variations in the steam grid network, variations that exceed the capacity of the steam accumulator. To avoid steam shortages, production leans towards having the accumulator nearly ﬁlled, eventually leading to periods with over production. Abundantly produced steam must be released from the steam grid network, and this is done without energy recovery. The purpose has therefore been to create a computer model with the ability to predict steam consumption for the entire mill. The prediction shall eventually be used in the control systems for steam producers and the accumulator. By knowing future steam demand, production can be planned more eﬃciently and so can the accumulation level of steam. This will allow a greater range of operation since the predictor can provide information on when signiﬁcant steam demand changes will occur.By creating separate predictor models for the largest steam consumers, the ﬁnal predictor consists of four minor predictor models. The ﬁrst is related to ﬁve batch digesters, the second to one of the two paper machines (PM5), the third to the other paper machine (PM6), ﬁnally the forth to all other consumers. The separate predictors have been created by gathering historical process data connected to their operation. Analyses and correlations have been made to show what has signiﬁcant eﬀects on their steam consumption. The ﬁnal predictor has shown the possibility of having an R² above 0.7 for up to one hour ahead. Even though, it is possible to have 60 minutes of accurate prediction. Reliable prediction ranges are determined for the four separate predictors. The reliable prediction range for the two paper machines has a potential of 15 minutes and the R² is still above 0.8 for that time ahead. The predictions for digesters have an R² above 0.6 for up to 25 minutes ahead. The steam demand from other components can be…

Subjects/Keywords: Steam prediction; Prediction; Industrial prediction; ångprediktion; Engineering and Technology; Teknik och teknologier; Energy Systems; Energisystem

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APA (6^th Edition):

Sehlberg, J. (2020). Steam Prediction at an Integrated Pulp and Paper Mill : Mondi Dynäs in Kramfors Municipality. (Thesis). Luleå University of Technology. Retrieved from http://urn.kb.se/resolve?urn=urn:nbn:se:ltu:diva-79636

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Sehlberg, Jimmy. “Steam Prediction at an Integrated Pulp and Paper Mill : Mondi Dynäs in Kramfors Municipality.” 2020. Thesis, Luleå University of Technology. Accessed February 26, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:ltu:diva-79636.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Sehlberg, Jimmy. “Steam Prediction at an Integrated Pulp and Paper Mill : Mondi Dynäs in Kramfors Municipality.” 2020. Web. 26 Feb 2021.

Vancouver:

Sehlberg J. Steam Prediction at an Integrated Pulp and Paper Mill : Mondi Dynäs in Kramfors Municipality. [Internet] [Thesis]. Luleå University of Technology; 2020. [cited 2021 Feb 26]. Available from: http://urn.kb.se/resolve?urn=urn:nbn:se:ltu:diva-79636.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Sehlberg J. Steam Prediction at an Integrated Pulp and Paper Mill : Mondi Dynäs in Kramfors Municipality. [Thesis]. Luleå University of Technology; 2020. Available from: http://urn.kb.se/resolve?urn=urn:nbn:se:ltu:diva-79636

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Georgia Tech

28. Mejri, Mohamed. Prediction of inner wood defects from outer bark shape.

Degree: MS, Electrical and Computer Engineering, 2020, Georgia Tech

URL: http://hdl.handle.net/1853/62864

► The analysis of the internal structure of trees is highly important for both forest experts, biological scientists, and the wood industry. Traditionally, CT-scanners are considered… (more)

Subjects/Keywords: Outer shape to inner density prediction; Voxel-wise prediction; Sequence-to-sequence prediction

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APA (6^th Edition):

Mejri, M. (2020). Prediction of inner wood defects from outer bark shape. (Masters Thesis). Georgia Tech. Retrieved from http://hdl.handle.net/1853/62864

Chicago Manual of Style (16^th Edition):

Mejri, Mohamed. “Prediction of inner wood defects from outer bark shape.” 2020. Masters Thesis, Georgia Tech. Accessed February 26, 2021. http://hdl.handle.net/1853/62864.

MLA Handbook (7^th Edition):

Mejri, Mohamed. “Prediction of inner wood defects from outer bark shape.” 2020. Web. 26 Feb 2021.

Vancouver:

Mejri M. Prediction of inner wood defects from outer bark shape. [Internet] [Masters thesis]. Georgia Tech; 2020. [cited 2021 Feb 26]. Available from: http://hdl.handle.net/1853/62864.

Council of Science Editors:

Mejri M. Prediction of inner wood defects from outer bark shape. [Masters Thesis]. Georgia Tech; 2020. Available from: http://hdl.handle.net/1853/62864

Virginia Tech

29. Burbey, Ingrid. Predicting Future Locations and Arrival Times of Individuals.

Degree: PhD, Electrical and Computer Engineering, 2011, Virginia Tech

URL: http://hdl.handle.net/10919/27551

► This work has two objectives: a) to predict people's future locations, and b) to predict when they will be at given locations. Current location-based applications… (more)

▼ This work has two objectives: a) to predict people's future locations, and b) to predict when they will be at given locations. Current location-based applications react to the user's current location. The progression from location-awareness to location-prediction can enable the next generation of proactive, context-predicting applications. Existing location-prediction algorithms predict someone's next location. In contrast, this dissertation predicts someone's future locations. Existing algorithms use a sequence of locations and predict the next location in the sequence. This dissertation incorporates temporal information as timestamps in order to predict someone's location at any time in the future. Sequence predictors based on Markov models have been shown to be effective predictors of someone's next location. This dissertation applies a Markov model to two-dimensional, timestamped location information to predict future locations. This dissertation also predicts when someone will be at a given location. These predictions can support presence or understanding co-workers’ routines. Predicting the times that someone is going to be at a given location is a very different and more difficult problem than predicting where someone will be at a given time. A location-prediction application may predict one or two key locations for a given time, while there could be hundreds of correct predictions for times of the day that someone will be in a given location. The approach used in this dissertation, a heuristic model loosely based on Market Basket Analysis, is the first to predict when someone will arrive at any given location. The models are applied to sparse, WiFi mobility data collected on PDAs given to 275 college freshmen. The location-prediction model predicts future locations with 78-91% accuracy. The temporal-prediction model achieves 33-39% accuracy. If a tolerance of plus/minus twenty minutes is allowed, the prediction rates rise to 77%-91%. This dissertation shows the characteristics of the timestamped, location data which lead to the highest number of correct predictions. The best data cover large portions of the day, with less than three locations for any given timestamp. Advisors/Committee Members: Martin, Thomas L. (committeechair), Tront, Joseph G. (committee member), Pérez-Quiñones, Manuel A. (committee member), Jones, Mark T. (committee member), Midkiff, Scott F. (committee member).

Subjects/Keywords: Location Awareness; Context Prediction; Location Prediction; Time-of-Arrival Prediction; Context Awareness

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APA (6^th Edition):

Burbey, I. (2011). Predicting Future Locations and Arrival Times of Individuals. (Doctoral Dissertation). Virginia Tech. Retrieved from http://hdl.handle.net/10919/27551

Chicago Manual of Style (16^th Edition):

Burbey, Ingrid. “Predicting Future Locations and Arrival Times of Individuals.” 2011. Doctoral Dissertation, Virginia Tech. Accessed February 26, 2021. http://hdl.handle.net/10919/27551.

MLA Handbook (7^th Edition):

Burbey, Ingrid. “Predicting Future Locations and Arrival Times of Individuals.” 2011. Web. 26 Feb 2021.

Vancouver:

Burbey I. Predicting Future Locations and Arrival Times of Individuals. [Internet] [Doctoral dissertation]. Virginia Tech; 2011. [cited 2021 Feb 26]. Available from: http://hdl.handle.net/10919/27551.

Council of Science Editors:

Burbey I. Predicting Future Locations and Arrival Times of Individuals. [Doctoral Dissertation]. Virginia Tech; 2011. Available from: http://hdl.handle.net/10919/27551

NSYSU

30. Lin, Chih-Ying. Disulfide Bonding State Prediction with SVM Based on Protein Types.

Degree: Master, Computer Science and Engineering, 2010, NSYSU

URL: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0818110-174218

► Disulfide bonds play crucial roles to predict the three-dimensional structure and the function of a protein. This thesis develops two algorithms to predict the disulfide… (more)

Subjects/Keywords: prediction; disulfide bond; protein

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Lin, C. (2010). Disulfide Bonding State Prediction with SVM Based on Protein Types. (Thesis). NSYSU. Retrieved from http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0818110-174218

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Lin, Chih-Ying. “Disulfide Bonding State Prediction with SVM Based on Protein Types.” 2010. Thesis, NSYSU. Accessed February 26, 2021. http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0818110-174218.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Lin, Chih-Ying. “Disulfide Bonding State Prediction with SVM Based on Protein Types.” 2010. Web. 26 Feb 2021.

Vancouver:

Lin C. Disulfide Bonding State Prediction with SVM Based on Protein Types. [Internet] [Thesis]. NSYSU; 2010. [cited 2021 Feb 26]. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0818110-174218.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Lin C. Disulfide Bonding State Prediction with SVM Based on Protein Types. [Thesis]. NSYSU; 2010. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0818110-174218

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

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