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Evolvability: What Is It And How Do We Get It?, Matthew Moreno 2017 University of Puget Sound

Evolvability: What Is It And How Do We Get It?, Matthew Moreno

Honors Program Theses

Biological organisms exhibit spectacular adaptation to their environments. However, another marvel of biology lurks behind the adaptive traits that organisms exhibit over the course of their lifespans: it is hypothesized that biological organisms also exhibit adaptation to the evolutionary process itself. That is, biological organisms are thought to possess traits that facilitate evolution. The term evolvability was coined to describe this type of adaptation. The question of evolvability has special practical relevance to computer science researchers engaged in longstanding efforts to harness evolution as an algorithm for automated design. It is hoped that a more nuanced understanding of biological evolution ...


The Marketing Of Sacrifice, Enda McGovern 2017 Sacred Heart University

The Marketing Of Sacrifice, Enda Mcgovern

Enda McGovern

Slides from a presentation made by Enda McGovern from the Department of Marketing at Sacred Heart University to the University's Board of Trustees. He outlines plans for a class to marketing students whose core text will be Pope Francis' encyclical on June 18, 2015, which lays out and argument for a new partnership between science and religion to combat human-driven climate change.


Switching Between Page Replacement Algorithms Based On Work Load During Runtime In Linux Kernel, Praveen Subramaniyam 2017 San Jose State University

Switching Between Page Replacement Algorithms Based On Work Load During Runtime In Linux Kernel, Praveen Subramaniyam

Master's Projects

Today’s computers are equipped with multiple processor cores to execute multiple programs effectively at a single point of time. This increase in the number of cores needs to be equipped with a huge amount of physical memory to keep multiple applications in memory at a time and to effectively switch between them, without getting affected by the low speed disk memory. The physical memory of today’s world has become so cheap such that all the computer systems are always equipped with sufficient amount of physical memory required effectively to run most of the applications. Along with the memory ...


Cascaded Facial Detection Algorithms To Improve Recognition, Edmund Yee 2017 San Jose State University

Cascaded Facial Detection Algorithms To Improve Recognition, Edmund Yee

Master's Projects

The desire to be able to use computer programs to recognize certain biometric qualities of people have been desired by several different types of organizations. One of these qualities worked on and has achieved moderate success is facial detection and recognition. Being able to use computers to determine where and who a face is has generated several different algorithms to solve this problem with different benefits and drawbacks. At the backbone of each algorithm is the desire for it to be quick and accurate. By cascading face detection algorithms, accuracy can be improved but runtime will subsequently be increased. Neural ...


Shopbot: An Image Based Search Application For E-Commerce Domain, Nishant Goel 2017 San Jose State University

Shopbot: An Image Based Search Application For E-Commerce Domain, Nishant Goel

Master's Projects

For the past few years, e-commerce has changed the way people buy and sell products. People use this business model to do business over the Internet. In this domain, Human-Computer Interaction has been gaining momentum. Lately, there has been an upsurge in agent based applications in the form of intelligent personal assistants (also known as Chatbots) which make it easier for users to interact with digital services via a conversation, in the same way we talk to humans. In e- commerce, these assistants offer mainly text-based or speech based search capabilities. They can handle search for most products, but cannot ...


Implementing Dynamic Coarse & Fine Grained Taint Analysis For Rhino Javascript, Tejas Saoji 2017 San Jose State University

Implementing Dynamic Coarse & Fine Grained Taint Analysis For Rhino Javascript, Tejas Saoji

Master's Projects

Web application systems today are at great risk from attackers. They use methods like cross-site scripting, SQL injection, and format string attacks to exploit vulnerabilities in an application. Standard techniques like static analysis, code audits seem to be inadequate in successfully combating attacks like these. Both the techniques point out the vulnerabilities before an application is run. However, static analysis may result in a higher rate of false positives, and code audits are time-consuming and costly. Hence, there is a need for reliable detection mechanisms.

Dynamic taint analysis offers an alternate solution — it marks the incoming data from the untrusted ...


Dynamic Information Flow Analysis In Ruby, Vigneshwari Chandrasekaran 2017 San Jose State University

Dynamic Information Flow Analysis In Ruby, Vigneshwari Chandrasekaran

Master's Projects

With the rapid increase in usage of the internet and online applications, there is a huge demand for applications to handle data privacy and integrity. Applications are already complex with business logic; adding the data safety logic would make them more complicated. The more complex the code becomes, the more possibilities it opens for security-critical bugs. To solve this conundrum, we can push this data safety handling feature to the language level rather than the application level. With a secure language, developers can write their application without having to worry about data security.

This project introduces dynamic information flow analysis ...


Comparing Authentic And Cryptic 5’ Splice Sites Using Hidden Markov Models And Decision Trees, Pratikshya Mishra 2017 San Jose State University

Comparing Authentic And Cryptic 5’ Splice Sites Using Hidden Markov Models And Decision Trees, Pratikshya Mishra

Master's Projects

Splicing is the editing of the precursor mRNA produced during transcription. The mRNA contains a large number of nucleotides in the introns and exons which are spliced to remove the introns and bind the exons to produce the mature mRNA which is translated to generate proteins. Hence accurate splicing at 5’ and 3’ splice sites (authentic splice sites (AuthSS)) is of foremost importance. The 5’ and 3’ splice sites are characterized by consensus sequences. Eukaryotic genome also contains splice sites known as Cryptic Splice Sites (CSS) that match the consensus. But the CSS are activated only when there is a ...


Transcriptase–Light: A Polymorphic Virus Construction Kit, Saurabh Borwankar 2017 San Jose State University

Transcriptase–Light: A Polymorphic Virus Construction Kit, Saurabh Borwankar

Master's Projects

Many websites use JavaScript to display dynamic and interactive content. Hence, attackers are developing JavaScript–based malware. In this paper, we focus on Transcriptase JavaScript malware.

The high–level and dynamic nature of the JavaScript language helps malware writers to create polymorphic and metamorphic malware using obfuscation techniques. These types of malware change their internal structure on each infection, making them difficult to detect with traditional methods. These types of malware can be detected using machine learning methods.

This project creates Transcriptase–Light, a new polymorphic construction kit. We perform an experiment with the Transcriptase–Light against a hidden Markov ...


Policy-Agnostic Programming On The Client-Side, Kushal Palesha 2017 San Jose State University

Policy-Agnostic Programming On The Client-Side, Kushal Palesha

Master's Projects

Browser security has become a major concern especially due to web pages becoming more complex. These web applications handle a lot of information, including sensitive data that may be vulnerable to attacks like data exfiltration, cross-site scripting (XSS), etc. Most modern browsers have security mechanisms in place to prevent such attacks but they still fall short in preventing more advanced attacks like evolved variants of data exfiltration. Moreover, there is no standard that is followed to implement security into the browser.

A lot of research has been done in the field of information flow security that could prove to be ...


Computational Analysis Of Cryptic Splice Sites, Remya Mohanan 2017 San Jose State University

Computational Analysis Of Cryptic Splice Sites, Remya Mohanan

Master's Projects

DNA in the nucleus of all eukaryotes is transcribed into mRNA where it is then translated into proteins. The DNA which is transcribed into mRNA is composed of coding and non-coding regions called exons and introns, respectively. It undergoes a post-trancriptional process called splicing where the introns or the non-coding regions are removed from the pre-mRNA to give the mature mRNA. Splicing of pre-mRNAs at 5 ́ and 3ˊ ends is a crucial step in the gene expression pathway. The mis-splicing by the spliceosome at different sites known as cryptic splice sites is caused by mutations which will affect the primary ...


Reducing Query Latency For Information Retrieval, Swapnil Satish Kamble 2017 San Jose State University

Reducing Query Latency For Information Retrieval, Swapnil Satish Kamble

Master's Projects

As the world is moving towards Big Data, NoSQL (Not only SQL) databases are gaining much more popularity. Among the other advantages of NoSQL databases, one of their key advantage is that they facilitate faster retrieval for huge volumes of data, as compared to traditional relational databases. This project deals with one such popular NoSQL database, Apache HBase. It performs quite efficiently in cases of retrieving information using the rowkey (similar to a primary key in a SQL database). But, in cases where one needs to get information based on non-rowkey columns, the response latency is higher than what we ...


Library For Writing Contracts For Java Programs Using Prolog, Yogesh Dixit 2017 San Jose State University

Library For Writing Contracts For Java Programs Using Prolog, Yogesh Dixit

Master's Projects

Today many large and complex software systems are being developed in Java. Although, software always has bugs, it is very important that these developed systems are more reliable despite these bugs.

One way that we can help achieve this is the Design by Contract (DbC) paradigm, which was first introduced by Bertrand Meyer, the creator of Eiffel. The concept of DbC was introduced for software developers so that they can produce more reliable software systems with a little extra cost. Using programming contracts allows developer to specify details such as input conditions and expected output conditions. Doing this makes it ...


Application Of Computational Methods To Study The Selection Of Authentic And Cryptic Splice Sites, Tapomay Dey 2017 San Jose State University

Application Of Computational Methods To Study The Selection Of Authentic And Cryptic Splice Sites, Tapomay Dey

Master's Projects

Proteins are building blocks of the bodies of eukaryotes, and the process of synthesizing proteins from DNA is crucial for the good health of an organism [13]. However, some mutations in the DNA may disrupt the selection of 5’ or 3’ splice sites by a spliceosome. An important research question is whether the disruptions have a stochastic relation to the position of nucleotides in the vicinity of the known authentic and cryptic splice sites. This can be achieved by proving that the authentic and cryptic splice sites are intrinsically different. However, the behavior of the spliceosome is not accurately known ...


Influence Detection And Spread Estimation In Social Networks, Madhura Kaple 2017 San Jose State University

Influence Detection And Spread Estimation In Social Networks, Madhura Kaple

Master's Projects

A social network is an online platform, where people communicate and share information with each other. Popular social network features, which make them di erent from traditional communication platforms, are: following a user, re-tweeting a post, liking and commenting on a post etc. Many companies use various social networking platforms extensively as a medium for marketing their products. A xed amount of budget is alloted by the companies to maximize the positive in uence of their product. Every social network consists of a set of users (people) with connections between them. Each user has the potential to extend its in ...


A Chatbot Framework For Yioop, Harika Nukala 2017 San Jose State University

A Chatbot Framework For Yioop, Harika Nukala

Master's Projects

Over the past few years, messaging applications have become more popular than Social networking sites. Instead of using a specific application or website to access some service, chatbots are created on messaging platforms to allow users to interact with companies’ products and also give assistance as needed. In this project, we designed and implemented a chatbot Framework for Yioop. The goal of the Chatbot Framework for Yioop project is to provide a platform for developers in Yioop to build and deploy chatbot applications. A chatbot is a web service that can converse with users using artificial intelligence in messaging platforms ...


Headline Generation Using Deep Neural Networks, Dhruven Vora 2017 San Jose State University

Headline Generation Using Deep Neural Networks, Dhruven Vora

Master's Projects

News headline generation is one of the important text summarization tasks. Human generated news headlines are generally intended to catch the eye rather than provide useful information. There have been many approaches to generate meaningful headlines by either using neural networks or using linguistic features. In this report, we are proposing a novel approach based on integrating Hedge Trimmer, which is a grammar based extractive summarization system with a deep neural network abstractive summarization system to generate meaningful headlines. We analyze the results against current recurrent neural network based headline generation system.


A Ltihub For Composite Assignments, Sunita Rajain 2017 San Jose State University

A Ltihub For Composite Assignments, Sunita Rajain

Master's Projects

Learning management systems (LMS) such as Canvas and Blackboard use Learning Tool Interoperability (LTI) as their main integration point for external learning tools. Each external tool provider has to implement LTI specifications or follow LTI standards that is a time consuming and complex process as there is no easy to follow specification available. Through this project, I have developed a system that follows the LTI specifications and integrates the CodeCheck autograder and interactive exercises with any LMS. I developed a Java based web app named LTIHub that acts as a mediator between LMS and any Learning Tool Provider. The LTIHub ...


Uncovering Functional Relationships In Leukemia, Reginald McGee 2017 Mathematical Biosciences Institute

Uncovering Functional Relationships In Leukemia, Reginald Mcgee

Biology and Medicine Through Mathematics Conference

No abstract provided.


Exploring An Autoimmune Hair Loss Condition Through Mathematical Modeling And Sensitivity Analysis, Atanaska Dobreva, Ralf Paus, Nick Cogan 2017 Florida State University

Exploring An Autoimmune Hair Loss Condition Through Mathematical Modeling And Sensitivity Analysis, Atanaska Dobreva, Ralf Paus, Nick Cogan

Biology and Medicine Through Mathematics Conference

No abstract provided.


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