Other Computer Sciences Commons^™

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 …

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. …

Dna Analysis Using Grammatical Inference, Cory Cook

Master's Projects

An accurate language definition capable of distinguishing between coding and non-coding DNA has important applications and analytical significance to the field of computational biology. The method proposed here uses positive sample grammatical inference and statistical information to infer languages for coding DNA.

An algorithm is proposed for the searching of an optimal subset of input sequences for the inference of regular grammars by optimizing a relevant accuracy metric. The algorithm does not guarantee the finding of the optimal subset; however, testing shows improvement in accuracy and performance over the basis algorithm.

Testing shows that the accuracy of inferred languages for …

Library Writers Reward Project, Saravana Kumar Gajendran

Master's Projects

Open-source library development exploits the distributed intelligence of participants in Internet communities. Nowadays, contribution to the open-source community is fading [16] (Stackalytics, 2016) as there is not much recognition for library writers. They can start exploring ways to generate revenue as they actively contribute to the open-source community.

This project helps library writers to generate revenue in the form of bitcoins for their contribution. Our solution to generate revenue for library writers is to integrate bitcoin mining with existing JavaScript libraries, such as jQuery. More use of the library leads to more revenue for the library writers. It uses the …

Multiple Sequence Alignment With Pro Le Hidden Markov Models, Shubhangi Rakhonde

Master's Projects

The human genome consists of various patterns and sequences that are of biolog- ical signi cance. Capturing these patterns can help us in resolving various mysteries related to the genome, like how genomes evolve, how diseases occur due to genetic mutation, how viruses mutate to cause new disease and what is the cure for these diseases. All these applications are covered in the study of bioinformatics.

One of the very common tasks in bioinformatics involves simultaneous alignment of a number of biological sequences. In bioinformatics, this is widely known as Mul- tiple Sequence Alignment. Multiple sequence alignments help in grouping …

Interactive Computer Science Exercises In Edx, Hong Le

Master's Projects

This project focuses on improving online learning courses for Computer Science. My approach is to create a platform in which interactive exercises can be implemented for students to work on. Methodology includes creating plugins for interactive exercises using XBlock, a component architecture for building independent online courses on edX. The exercises are based on existing exercises like CodeCheck and Wiley’s InterActivities Exercise System. In order to integrate these exercises, I implemented CodeCheck XBlock and Interactive XBlock. These Xblocks allow students to work on interactive exercises on edX, and instructors to view and download students’ submissions.

Pattern Discovery In Dna Using Stochastic Automata, Shweta Shweta

Master's Projects

We consider the problem of identifying similarities between different species of DNA. To do this we infer a stochastic finite automata from a given training data and compare it with a test data. The training and test data consist of DNA sequence of different species. Our method first identifies sentences in DNA. To identify sentences we read DNA sequence one character at a time, 3 characters form a codon and codons form proteins (also known as amino acid chains).Each amino acid in proteins belongs to a group. In total we have 5 groups’ polar, non-polar, acidic, basic and stop codons. …

An Open Source Advertisement Server, Pushkar Umaranikar

Master's Projects

This report describes a new online advertisement system and its implementation for the Yioop open source search engine. This system was implemented for my CS298 project. It supports both selling advertisements and displaying them within search results. The selling of advertisement is done using a novel auction system, which we describe in this paper. With this auction system, it is possible to create an advertisement, attach keywords to it, and add it to the advertisement inventory. An advertisement is displayed on a search results page if the search keyword matches the keywords attached to the advertisement. Display of advertisements is …

Driver Telematics Analysis, Karthik Vakati

Master's Projects

For automobile insurance firms, telemetric analysis represents a valuable and growing way to identify the risk associated with each driver. The pricing decisions of an insurer are best accounted for if they are made considering the driver’s behavior instead of just the vehicle characteristics and the best way to understand a driver’s behavior is to leverage the telemetric analysis. Decisions made on such factors can eventually lead to increased premium or reduced liability for unsafe or reckless drivers and can also help in transitioning the burden to the policies that lead to increased liability.

The dataset provided for this project …

Maximizing The Speed Of Influence In Social Networks, Yubo Wang

Master's Projects

Influence maximization in social networks is the problem of selecting a limited

size of influential users as seed nodes so that the influence from these seed nodes can propagate to the largest number of other nodes in the network. Previous studies in influence maximization focused on three areas, i.e., designing propagation models, improving algorithms of seed-node selection and exploiting the structure of social networks. However, most of these studies ignored the time constraint in influence propagation. In this paper, I studied how to maximize influence propagation in a given time, i.e., maximizing the speed of influence propagation in social networks. …

Social Network Leverage Search, Payal Gupta

Master's Projects

Social networks are at an all time high, nowadays. They make the world a smaller place to live in. People can stay in touch with friends and can make new friends on these social networks which traditionally were not possible without internet service. The possibilities provided by social networks enable vast and immediate contact. People tend to spend lot of time on the social networks like Facebook, LinkedIn and Twitter peeping into their friend‟s accounts and trying to stay connected with the world.
However, recently people have started closing their accounts on these famous social networks after having been irritated …

Rna Secondary Structure Prediction Tool, Meenakshee Mali

Master's Projects

Ribonucleic Acid (RNA) is one of the major macromolecules essential to all forms of life. Apart from the important role played in protein synthesis, it performs several important functions such as gene regulation, catalyst of biochemical reactions and modification of other RNAs. In some viruses, instead of DNA, RNA serves as the carrier of genetic information. RNA is an interesting subject of research in the scientific community. It has lead to important biological discoveries. One of the major problems researchers are trying to solve is the RNA structure prediction problem. It has been found that the structure of RNA is …

Substitution Cipher With Non­Prefix Codes, Rashmi Bangalore Muralidhar

Master's Projects

Substitution ciphers normally use prefix free codes ­ there is no code word which is the prefix of some other code word. Prefix free codes are used for encryption because it makes the decryption process easier at the receiver's end.
In this project, we study the feasibility of substitution ciphers with non­prefix codes. The advantage of using non­prefix codes is that extracting statistical information is more difficult. However, the ciphertext is nontrivial to decrypt.
We present a dynamic programming technique for decryption and verify that the plaintext can be recovered. This shows that substitution ciphers with non­prefix codes are feasible. …

User Monitor & Feedback Mechanism For Social Scientific Study On Laptop Energy Reduction, Namrata Buddhadev

Master's Projects

The dawn of the laptop era presents new challenges to the computing research community. Performance is no longer the end all be all of computing research because a new, significant requirement has cropped up: reducing the power consumption and improving battery usage. The key restriction to mobility is the constant need to be near a power outlet to recharge the laptop battery. Thus, extending battery life without compromising performance is a pressing concern.
A research named as "iGreen" was proposed to stimulate power consumption awareness and behavioral change among laptop users via interactive energy-usage feedback with college students as the …

Automated Penetration Testing, Neha Samant

Master's Projects

Penetration testing is used to search for vulnerabilities that might exist in a system. The testing usually involves simulating different types of attacks on the target system. This type of testing provides an organized and controlled way to identify security shortcomings. The resources and time required for comprehensive testing can make penetration testing cost intensive. Consequently, such tests are usually only performed during important milestones.
In this project we have automated the penetration testing process for several protocol-based attacks. Our automated penetration testing application covers several attacks based on HTTP, SIP and TCP/IP. The objective of this work is to …

Online And Offline Ebook Management System Using W-Cms, Rohan Vibhandik

Master's Projects

In this internet and smart-phone era paper books are almost obsolete. Many developers have come up with the eBooks which can be read online on computer or on a smart-phone. Users can now access them offline any time without carrying a bulky pBook (Paper Book). The stable eBook application should restrict and control the use of contents to protect the copyrights. Encryption and enforcement of digital policies are generally managed by Digital Rights Management (DRM). The stable system for online as well as offline readers safeguard the intellectual properties for authors, publishers by providing a protection to their digital content, …

Fbchatters: A Facebook Application For Gtalk, Ronak Shah

Master's Projects

The motto of this project is to provide accessibility to Google talk (gtalk) service within a Facebook account by creating Facebook application called FBchatters and also by creating Firefox plug-in called FBchatters. Most of all internet users have account on Facebook and Google. Social network site, Facebook has more than 600 million users and half of them log on to Facebook in any given day [1]. Google also has 170 million users who are using gmail and gtalk services every day. There are lot of users who do chatting simultaneously on Facebook and Gtalk. Also, Google talk provides a facility …

An Executable Packer, Neel Bavishi

Master's Projects

This thesis addresses the topic of development and advancement of the Packer technology. It aims to prove that with the implementation of advanced code encryption and cryptographic techniques in conjunction with standard packing
methods, testing binaries with anti-virus will become increasingly difficult.
Study on this topic reveals that the idea of encoding data has already been established, but it is still not fully incorporated into a technique to pack an executable file. There are some noticeable defects as un-packer tools have also made a great advancement in the field of dynamic analysis. The addition of new capability to recognize emulation …

Similarity Tests For Metamorphic Virus Detection, Mahim Patel

Master's Projects

A metamorphic computer virus generates copies of itself using code morphing techniques. A new virus has the same functionality as the parent but it has a different internal structure. The goal of the metamorphic virus writer is to produce viral copies that have no common signature. If the viral copies are sufficiently different, they can evade signature detection, which is the most widely-used anti-virus technique.
In previous research, hidden Markov models (HMMs) have been used to detect some metamorphic viruses. However, recent research has shown that it is possible for carefully designed metamorphic viruses to evade HMM-based detection.
In this …

Robust Watermarking Using Hidden Markov Models, Mausami Mungale

Master's Projects

Software piracy is the unauthorized copying or distribution of software. It is a growing problem that results in annual losses in the billions of dollars. Prevention is a difficult problem since digital documents are easy to copy and distribute. Watermarking is a possible defense against software piracy. A software watermark consists of information embedded in the software, which allows it to be identified. A watermark can act as a deterrent to unauthorized copying, since it can be used to provide evidence for legal action against those responsible for piracy.
In this project, we present a novel software watermarking scheme that …

Decompiler For Pseudo Code Generation, Ankit Patel

Master's Projects

Decompiling is an area of interest for researchers in the field of software reverse engineering. When the source code from a high-level programming language is compiled, it loses a great deal of information, including code structure, syntax, and punctuation.
The purpose of this research is to develop an algorithm that can efficiently decompile assembly language into pseudo C code. There are tools available that claim to extract high-level code from an executable file, but the results of these tools tend to be inaccurate and unreadable.
Our proposed algorithm can decompile assembly code to recover many basic high-level programming structures, including …

Video Chat Application For Facebook, Shirali Chokshi

Master's Projects

This project is mainly written for the facebook users. In today’s world, there are many social networking sites available. Among those social networking web sites, facebook is widely used web site. Like all other social networking web sites, Facebook also provides many features to attract more and more users. But it lacks in providing the most important feature of social networking, i.e. video chat. I explore the different options and requirements needed to build the video chat application. I have also described the integration of the application with the facebook.

Ab Initio Protein Structure Prediction Algorithms, Maciej Kicinski

Master's Projects

Genes that encode novel proteins are constantly being discovered and added to databases, but the speed with which their structures are being determined is not keeping up with this rate of discovery. Currently, homology and threading methods perform the best for protein structure prediction, but they are not appropriate to use for all proteins. Still, the best way to determine a protein's structure is through biological experimentation. This research looks into possible methods and relations that pertain to ab initio protein structure prediction. The study includes the use of positional and transitional probabilities of amino acids obtained from a non-redundant …

Metamorphic Detection Via Emulation, Sushant Priyadarshi

Master's Projects

In parallel with improvements in anti-virus technologies, computer virus writers have developed innovative viruses that are challenging to detect. Metamorphic viruses change their appearance from one generation to another by using various code obfuscation techniques. Today, signature detection is the most common method used in anti-virus products, but well designed metamorphic viruses cannot be detected using signatures. Hence, there is a need for a more robust anti-virus technology.
To counter metamorphic virus, a very successful tool based on hidden Markov models (HMM) has been previously developed. This tool was able to detect all hacker produced metamorphic viruses on which it …

Dynamic Code Checksum Generator, Ashish Sharma

Master's Projects

A checksum (i.e., a cryptographic hash) of a file can be used as an integrity check, if an attacker tries to change the code in an executable file, a checksum can be used to detect the tampering. While it is easy to compute a checksum for any static file, it is possible for an attacker to tamper with an executable file as it is being loaded into memory, or after it has been loaded. Therefore, it would be more useful to checksum an executable file dynamically only after the file has been loaded into memory. However, checksumming dynamic code is …

Jshield: A Java Anti-Reversing Tool, Deepti Kundu

Master's Projects

Java is a platform independent language.    Java programs can be executed on any machine, irrespective of its hardware or the operating system, as long as a Java virtual machine for that platform is available. A Java compiler converts the source code into „bytecode‟ instead of native binary machine code. This bytecode contains a lot of information from and about the source code, which makes it easy to decompile, and hence, vulnerable to „reverse engineering attacks‟. In addition to the obvious security implications, businesses and the wider software engineering community also risk widespread IP theft - proprietary algorithms, for example, that …

Java Smell Detector, Nitin Mathur

Master's Projects

“Code Smell” or “Bad Smell”, at the very least, is an indicator of badly written code and is often indicative of deeper problems in software design. In layman terms, it signals flaws in the core foundation or architecture of the software that can cause any number of more serious problems – from usability and runtime performance to supportability and enhancement. These problems can mostly be prevented by the systematic refactoring of the code. Refactoring is the process (and according to some, an ‘art’) of making incremental changes to existing source code to improve its nonfunctional attributes, without modifying its external …

Online Application Monitoring Tool, Sathya Anandan

Master's Projects

In some classes, students take online tests and some types of network activity (for example trying to find the answers in www.google.com) will be considered as cheating during the exam. It would be useful if instructor could monitor online activities of each student to detect cheating. The goal of this project is to develop such a tool using client/server architecture. Tool should display the student's hostname and the website visited during unauthorized web activity. Professor should able to see the applications opened by all students and he will have an option to view the log files of all the students …

Computational Mirna Target Prediction In Animals, Leyan Tang

Master's Projects

miRNAs are a class of small RNA molecules about 22 nucleotides long that regulate gene expression at the post-transcriptional level. The discovery of the second miRNA 10 years ago was as much a surprise in its own way as the very structure of DNA discovered a half century earlier[1]. How could these small molecules regulate so many genes? During the past decade the complex cascade of regulation has been investigated and reported in detail[2]. The regions of the genome called untranslated regions, or UTRs, proved true to their name: they were indeed untranslated, but certainly not unimportant: they act as …

Intrusion Detection And Prevention System: Sql-Injection Attacks, Varian Luong

Master's Projects

Personally identifiable information (PII) is information regarding things such as bank accounts, retirement or stock investment accounts, credit card accounts, medical records, or insurance claims. There is a need to protect the PII in databases that are connected to the ubiquitous, global network that is the Internet. If there is any vulnerability in the protection in a system that holds PII, then it presents an opportunity for an unauthorized person to access this PII. One of the techniques available to would- be information thieves is SQL injection (SQL-I). In this project, a system is developed to analyze the values submitted …