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Victoria University Research Repository (VURR, formerly known as VUIR) is an open access repository that showcases the research and scholarly outputs of VU staff and higher degree research students. Full-text versions of the research may be available with the permission of the authors, and when copyright allows.

About VURR The VU Research Repository (previously known as VUIR) is an open access repository that contains the research papers and theses of VU staff and higher degree research students.

Submit a paper The VU Research Repository is indexed by Google, Trove & OAIster. Submit your research outputs and make them available to the world.

All of VSpace@VU

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The Virtual University, Pakistan’s first University based completely on modern Information and Communication Technologies, was established by the Government as a public sector, not-for-profit institution with a clear mission: to provide extremely affordable world class education to aspiring students all over the country.

Using free-to-air satellite television broadcasts and the Internet, the Virtual University allows students to follow its rigorous programs regardless of their physical locations. It thus aims at alleviating the lack of capacity in the existing universities while simultaneously tackling the acute shortage of qualified professors in the country. By identifying the top Professors of the country, regardless of their institutional affiliations, and requesting them to develop and deliver hand-crafted courses, the Virtual University aims at providing the very best courses to not only its own students but also to students of all other universities in the country.

VSpace is a growing collection of Virtual University’s research that includes peer-reviewed articles, technical reports, working papers, theses and more. This electronic repository contains selected theses and dissertations of Masters and PhD students from all VU departments. The end users can search, navigate and download these publications using this website.

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Dspace preserves and enables easy and open access to all types of digital content including text, images, moving images, mpegs and data sets.

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Welcome to the Institutional Repository of Vidyasagar University

Dspace@vu is the open access institutional repository of vidyasagar university. research outputs of vu - journal papers, conference papers, reports, theses, patents etc. - are uploaded/self-archived by vu faculty members / resarchers who do research on different specialized areas . interested users can freely download and use documents as most of them are directly accessible and full-text downloadable. 'request copy' forms can be used for documents to which direct full-text download is restricted due to publisher embargo. "this repository is administrated by central library , vidyasagar university". digitized administrative documents ,articles of the journals published by the university and old question papers of vidyasagar university as and when made available have been uploaded in this repository repository is indexed by google, google scholar, oaister, roar, opendoar, base "academic departments are requested to submit to the university library the list of on-going phd theses and other research projects taken up by the respective departments with relevant details for uploading in this repository. this information will highlight the research activities in the university as a whole.", recent submissions, communities in dspace.

Choose a community to browse its collections.

Academic Documents 286

Publication , Ph.D Theses etc

Administrative Documents 3378

Annual Reports, Executive Council Resolution, Court Meeting Resolution, IQAC

Convocation Addresses 20

Hon'ble Vice Chancellor , Chief Guest Address

Distance Education ( e-SLM) 60

Events @ vu 61.

Seminar , Conference , Syposia etc hosted at Vidyasagar University (VU)

Miscellaneous Documents 27

Old question paper archive 1136, vidyasagar university periodicals repository 1257.

• 4492 Vidyasagar University
• 21 Vidyasagar, University
• 18 Bhakat, Ram Kumar
• 17 Sau, Sachinandan
• 13 Banerjee, Neepa
• 13 Das, Bhupendra Chandra
• 13 Mukherjee, Shankarashis
• 12 Das, Pinaki
• 12 Jana, R N
• 12 Jana, Sebak Kumar
• 186 Question Papers
• 47 Seventh Executive Council Meeting
• 47 UG[Gen] Question Papers
• 47 UG[H] Question Papers
• 26 Eighth Executive Council Meeting
• 26 Mathematics
• 1212 2020 - 2024
• 4696 2010 - 2019
• 257 2000 - 2009
• 38 1990 - 1999
• 1 1987 - 1989

Doctoral school

Submitting the final version of the thesis - Amsterdam UMC/VU

PhD candidates whose manuscript has been approved by the Doctoral Committee AND after the title page has been approved in Hora Finita

Submit and print the final version of the dissertation and prepare for the defence ceremony

No later than 6 weeks prior to the confirmed date of the defence ceremony

Depends on printing timelines

• According to the Doctorate Regulations (art. 20), the PhD candidate decides whether the dissertation is printed or reproduced in a similar way. A condition here is that the result must meet requirements of reasonable legibility. The dissertation will be published in a conveniently-sized format and in glue-bound or spiral-bound form, or with a stitched binding. Printing of at least 5 copies of the dissertation is obligitory
• Not sure about the possibilities, deadlines, the process of printing your thesis? Check the ASAP website regularly: ASAP organizes once a year a 'printers fair' on both location AMC and VUmc, and several times in a year workshops 'innovative thesis printing'
• Make an appointment with the printer of your dissertation. Never print your dissertation before you have received the final decision with the definitive date of your defence from the VU Amsterdam Beadle’s Office (s ee ' Defence Date' )
• You need to send 5 copies of your dissertation to the Beadle by three weeks before the PhD ceremony. Address: Vrije Universiteit Amsterdam, Bureau Pedel, HG 2D-05, De Boelelaan 1105, 1081 HV  Amsterdam. If, for any reason, this is not possible, the Beadle reserves the right to postpone the ceremony to another date**
• The Beadle will make sure that two copies of the dissertation will be received by the University Library and two copies by the Amsterdam UMC Office of Doctorate Affairs ( Bureau Promotiezaken) (one for the Dean and one for the Chair of the public defence)*
• The PhD candidate will provide the members of the Thesis Committee with a copy
• Submit the final PhD dissertation in Hora Finita (tab ‘Ceremony’ ( Plechtigheid ')) and fill in the license agreement. With the license agreement permission is given for online publishing through the digital academic repository of VU University, and where needed, which articles should be placed under embargo for publication

*In case you want to compete for the  PhD Thesis Design Award , please send an email to the Doctoral School , including the email address at which we can reach you in future time

** Note : One of the two printed theses will be sent to the chairman of the defence ceremony. The second printed thesis we will keep in store for ( no longer than ) exactly one month after the date of your defence . Please feel free to collect it, or have it collected, at our office of Doctorate Affairs. Unfortunately we shall not return it to you by mail

Necessary documents:

Final version of the dissertation

Requirements & instructions for submission of an electronic version of the dissertation

• Convert the dissertation to a PDF or a PDF/A format, as a single or multiple file, without file protection
• Make sure the dissertation is complete (i.e., includes cover page, sections covered by an embargo (even if a permanent embargo) any material appended separately such as supplementary annexes, a propositions sheet, a list of changes made to the dissertation)
• The dissertations’ contents uploaded in Hora Finita must be absolutely identical to the printed version (including the cover, title page, publishing details, layout, orthography, pagination)
• The VU University Library will check the upload and publishes the digital dissertation online in the VU Research Portal (Pure) after approval
• As an alternative the PhD candidate can also click on the link in the Hora Finita Checklist to upload the dissertation

Printing your thesis

• Not sure about the possibilities, deadlines, the process of printing your thesis? Check the  ASAP website  regularly: ASAP organizes once a year a 'printers fair' on both location AMC and VUmc, and several times in a year workshops 'innovative thesis printing'
• You can request all your notifications for design, printing and illustration via the Amsterdam UMC 'Service Portaal' , being the application-desk both Amsterdam UMC locations. No access to the Service Portaal? Then send an email to the 'Huisdrukkerij'

Statements of commercial nature

If a PhD candidate intends to acknowledge support for their doctoral research from outside the university in writing, this may only be done following consultation with the supervisor and with the permission of the Doctorate Board. Statements of a commercial nature are not allowed in the thesis itself (source: procedural regulation no. 16 of the VU Amsterdam  Doctorate Regulations ). PhD candidates who violate this rule may be required to reprint their thesis

VU University Library

Check the website of the VU University Library regularly, to find useful information (also link below: Publish in Open Access)

Reimbursement for PhD costs

For all Amsterdam UMC PhD candidates: click here for the summarizing schedule of the following regulations for compensation:

• For information about a refund for printing costs  click here
• For information about the Graduation Bonus (CAO Regulation)   click here

Invitation:

• Amsterdam UMC Workshop 'Finishing my PhD trajectory'

VU Meet the Beadle

For more information on both events: Check  step 8

Do you include, or are you planning to include propositions ( stellingen) in your thesis?

If you think (some of) your propositions are a game changer in the medical field, you can submit your best 2 propositions to the "Nederlands Tijdschrift voor Geneeskunde (NTvG)" magazine and perhaps they will be featured in the next issue

Note : A propositions sheet should not be included as part of the dissertation, but as a separate page

Note: Please be aware to update your email address in Hora Finita, at the moment this changes. For example when you are no longer a VUmc (or Amsterdam UMC) employee. If we don't have a current email address, we won't be able to reach you

• Thesis (information on VU-website)
• Publish in Open Access

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Theses and Dissertations

Find a dissertation or thesis.

• Research Repository @ WVU - This collection contains theses, dissertations, problem reports, and project reports (ETDs) from West Virginia University graduate students. The Libraries are currently in the process of adding more documents to this collection.
• Proquest Dissertations and Theses Fulltext - This database is the world’s most comprehensive collection of dissertations and theses, spanning from 1861 to the present day and offering full text for most of the dissertations added since 1997. Many WVU theses and dissertations are available in this database. If you can't find what you are looking for, please contact Emily Fidelman at [email protected] . 
• Networked Digital Library of Theses and Dissertations A comprehensive search of all Electronic Thesis and Dissertation (ETD) sites worldwide.

Submit a Dissertation or Thesis

WVU Electronic Theses and Dissertations

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Repository meant for procedures related to my Master's Thesis at the VU

jaccobroere/vu-msc-thesis

Folders and files, repository files navigation, msc thesis: achieving smoothness in sparse spatio-temporal autoregressive modelling via the graph-guided fused lasso.

Author: Jacco Broere

Date: 2023-07-01

This repository contains all the necessary code for replicating the results in my MSc thesis.

1. Structure of the repository

The src/ folder contains all source code that is used for computation and plotting. It consists of four subfolders:

• src/compute contains all the source code related to estimation of the models and the computation of necessary preprocessing, hyperparameter optimzation etc.
• src/plotting contains all the source code related to plotting the results and generating the visuals used in the thesis
• src/simulation contains all the source code related to simulating the data for the simulation study in the thesis (Note that Design 1, 2, and 3 in the thesis text correspond to B, C, and D in this repository, respectively)
• src/playgrounds this contains no essential code, and was mostly used to quickly explore certain ideas and test things

src/compute/R/model_fitting.R is the main file that contains the code to run the models for the simulation experiment. This file uses the model and cross-validation fucntions from model_cv_wrappers.R , utils.R , Rcpp/cpp_utils.R , and vhat_sigmahat.R .

For the simulation study, there are some parts that are precomputed, such as the penalty matrices and their inverses. These are computed in Julia ( https://julialang.org/ ), and can be found in src/compute/jl/ .

Note that in many of the scripts, the code makes use of an environment variable PROJ_DIR that is set to the root of the project. This is done to make the code portable. You should set this environment variable to run the code as is. Or you should replace the lines that make use of this with an explicit path to the root of the project. Note that you can also use the Docker image that I provide later on in this README, which already has this environment variable set.

Moreover, Note that many of the scripts import some sort of utils function at the top of the file. These utils functions are often located in some child folder or in the same folder directly.

This folder is used to store the output of the estimated models, tables, figures, plots etc. Essentially, it covers all output of models.

The data/ folder is meant to store the data related to simulation, and it will also contain the precalculated matrices, such as the the penalty matrix, its inverse and the graphs pertaining to the different simulation designs.

1.4 scripts/

The scripts/ folder contains all the bash scripts, and Kubernetes (k8s) configuration files that can be used to run the models and pipelines in succession for multiple designs in succession. The k8s files can be used to parallellize the computation of the simulation study over multiple cores or machines. This especially beneficial on strong machines or in the cloud (AWS, GCP, Azure etc.).

The scripts in this folder contain comments at the top of the files with instructions on how to get it working. The bash scripts contain most of the logic needed to be able to run the Kubernetes jobs on your computer or in the cloud. It uses kubectl (which is shipped by Docker Desktop, https://docs.docker.com/desktop/kubernetes/ ) to manage the jobs and pods.

To reproduce the table in the thesis, you can run either of the following to scripts:

• scripts/run_local_full_design.sh in the Docker environment described in the next section or on your local machine, if all the dependencies are setup correctly. I recommend using the Docker environment, to avoid any dependency issues.
• scripts/run_k8s_full_per_design.sh using Kubernetes, this requires a bit more setup, but can be more efficient machine capable of strong parallelization. Note that you should first setup the Persistent Volumes using scripts/k8s/pv/setup_pv.yml replacing the host locations with the directories on your own host machine, and the Docker image jaccusaurelius/vu-msc-thesis:workspace should be available on your machine. The instructions on how to pull it are in the next section. The amount of parallelism can be controlled in scripts/k8s/mc_simuulation_TEMPLATE.yml

1.5 docker/

If you are unfamiliar with Docker, I recommend this article and website for some reference on how to get Docker working on your machine ( https://www.stacksimplify.com/aws-eks/docker-basics/get-docker-image-from-docker-hub-and-run-/ )

This folder contains the Dockerfile that is used to build the Docker image that is used to run the models and pipelines, such that it can be run consistently and in the same way on every machine. This is especially handy to manage package and software dependencies across machines. Note that the main Docker image to run the models is available on Dockerhub ( https://hub.docker.com/repository/docker/jaccusaurelius/vu-msc-thesis/general ). The jaccusaurelius/vu-msc-thesis:workspace is the image that was used for most of the computations in the thesis. The Dockerfile in this folder can be used to reconstruct a newer version of this image.

To make use of the Docker environment on your computer, after you have installed Docker, you can run the following command while in the root of the project:

MacOS/Linux:

Windows (Powershell):

1.6 admm_src_zhu/

This is a copy of the source code that was written by Zhu et al. (2017), we use their Augmented ADMM algorithm to solve the generalized LASSO problems as part of the novel GF-SPLASH estimators we developed.

1.7 archive/

This folder is used to store old and unused code that was written during development and testing of the code for this thesis. It is mostly very messy, however, there it can be nice to keep as there is some valuable code in there that might be useful when reviving certain interesting ideas in the future, which I wasn't able to completely or succesfully implement in time for the thesis.

• Python 7.2%