Computer Sciences Commons^™

Randomized Parameterized Algorithms For The Kidney Exchange Problem, Mugang Lin, Jianxin Wang, Qilong Feng, Bin Fu

Computer Science Faculty Publications

In order to increase the potential kidney transplants between patients and their incompatible donors, kidney exchange programs have been created in many countries. In the programs, designing algorithms for the kidney exchange problem plays a critical role. The graph theory model of the kidney exchange problem is to find a maximum weight packing of vertex-disjoint cycles and chains for a given weighted digraph. In general, the length of cycles is not more than a given constant L (typically 2 L 5), and the objective function corresponds to maximizing the number of possible kidney transplants. In this paper, we study the …

Overview Of The Biocreative Vi Precision Medicine Track: Mining Protein Interactions And Mutations For Precision Medicine, Rezarta Islamaj Doğan, Sun Kim, Andrew Chatr-Aryamontri, Chih-Hsuan Wei, Donald C. Comeau, Rui Antunes, Sérgio Matos, Qingyu Chen, Aparna Elangovan, Nagesh C. Panyam, Karin Verspoor, Hongfang Liu, Yanshan Wang, Zhuang Liu, Berna Altınel, Zehra Melce Hüsünbeyi, Arzucan Özgür, Aris Fergadis, Chen-Kai Wang, Hong-Jie Dai, Tung Tran, Ramakanth Kavuluru, Ling Luo, Albert Steppi, Jinfeng Zhang, Jinchan Qu, Zhiyong Lu

Computer Science Faculty Publications

The Precision Medicine Initiative is a multicenter effort aiming at formulating personalized treatments leveraging on individual patient data (clinical, genome sequence and functional genomic data) together with the information in large knowledge bases (KBs) that integrate genome annotation, disease association studies, electronic health records and other data types. The biomedical literature provides a rich foundation for populating these KBs, reporting genetic and molecular interactions that provide the scaffold for the cellular regulatory systems and detailing the influence of genetic variants in these interactions. The goal of BioCreative VI Precision Medicine Track was to extract this particular type of information and …

Getting Things Done For The Glory Of God, Todd W. Neller

Computer Science Faculty Publications

The seminar covered a fusion of David Allen’s Getting Things Done; Covey, Merrill and Merrill’s First Things First; and Matt Perman’s What’s Best Next books on time management, with a view to being a good steward of time and effort for the glory of God. More information is available at http://cs.gettysburg.edu/~tneller/resources/gtd/index.html

Elf3 Is An Antagonist Of Oncogenic-Signalling-Induced Expression Of Emt-Tf Zeb1, D Liu, Y Skomorovska, J Song, E Bowler, R Harris, R Ravasz, S Bai, Marzieh Ayati, K Tamai, Mehmet Koyuturk

Computer Science Faculty Publications

Background: Epithelial-to-mesenchymal transition (EMT) is a key step in the transformation of epithelial cells into migratory and invasive tumour cells. Intricate positive and negative regulatory processes regulate EMT. Many oncogenic signalling pathways can induce EMT, but the specific mechanisms of how this occurs, and how this process is controlled are not fully understood.

Methods: RNA-Seq analysis, computational analysis of protein networks and large-scale cancer genomics datasets were used to identify ELF3 as a negative regulator of the expression of EMT markers. Western blotting coupled to siRNA as well as analysis of tumour/normal colorectal cancer panels was used to …

Predicting Public Opinion On Drug Legalization: Social Media Analysis And Consumption Trends, Farahnaz Golrooy Motlagh, Saeedeh Shekarpour, Amit Sheth, Krishnaprasad Thirunarayan, Michael L. Raymer

Computer Science Faculty Publications

In this paper, we focus on the collection and analysis of relevant Twitter data on a state-by-state basis for (i) measuring public opinion on marijuana legalization by mining sentiment in Twitter data and (ii) determining the usage trends for six distinct types of marijuana. We overcome the challenges posed by the informal and ungrammatical nature of tweets to analyze a corpus of 306,835 relevant tweets collected over the four-month period, preceding the November 2015 Ohio Marijuana Legalization ballot and the four months after the election for all states in the US. Our analysis revealed two key insights: (i) the people …

Reachability Analysis For Neural Feedback Systems Using Regressive Polynomial Rule Inference, Souradeep Dutta, Xin Chen, Sriram Sankaranarayanan

Computer Science Faculty Publications

We present an approach to construct reachable set overapproxi- mations for continuous-time dynamical systems controlled using neural network feedback systems. Feedforward deep neural net- works are now widely used as a means for learning control laws through techniques such as reinforcement learning and data-driven predictive control. However, the learning algorithms for these net- works do not guarantee correctness properties on the resulting closed-loop systems. Our approach seeks to construct overapproxi- mate reachable sets by integrating a Taylor model-based flowpipe construction scheme for continuous differential equations with an approach that replaces the neural network feedback law for a small subset of …

Computational Thinking Bins: Outreach And More, Briana B. Morrison, Brian Dorn, Michelle Friend

Computer Science Faculty Publications

Computational Thinking Bins are stand alone, individual boxes, each containing an activity for groups of students that teaches a computing concept. We have a devised a system that has allowed us to create an initial set, test the set, continually improve and add to our set. We currently use these bins in outreach events for middle and high school students. As we have shared this resource with K-12 teachers, many have expressed an interest in acquiring their own set. In this paper we will share our experience throughout the process, introduce the bins, and explain how you can create your …

Full Tilt: Universal Constructors For General Shapes With Uniform External Forces, Jose Balanza-Martinez, Austin Luchsinger, David Caballero, Rene Reyes, Angel A. Cantu, Robert Schweller, Luis Angel Garcia, Tim Wylie

Computer Science Faculty Publications

We investigate the problem of assembling general shapes and patterns in a model in which particles move based on uniform external forces until they encounter an obstacle. In this model, corresponding particles may bond when adjacent with one another. Succinctly, this model considers a 2D grid of “open” and “blocked” spaces, along with a set of slidable polyominoes placed at open locations on the board. The board may be tilted in any of the 4 cardinal directions, causing all slidable polyominoes to move maximally in the specified direction until blocked. By successively applying a sequence of such tilts, along with …

Crazy Sequential Representations Of Numbers For Small Bases, Tim Wylie

Computer Science Faculty Publications

Throughout history, recreational mathematics has always played a prominent role in advancing research. Following in this tradition, in this paper we extend some recent work with crazy sequential representations of numbers− equations made of sequences of one through nine (or nine through one) that evaluate to a number. All previous work on this type of puzzle has focused only on base ten numbers and whether a solution existed. We generalize this concept and examine how this extends to arbitrary bases, the ranges of possible numbers, the combinatorial challenge of finding the numbers, efficient algorithms, and some interesting patterns across any …

Drug Repositioning Based On Bounded Nuclear Norm Regularization, Mengyun Yang, Huimin Lao, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Motivation: Computational drug repositioning is a cost-effective strategy to identify novel indications for existing drugs. Drug repositioning is often modeled as a recommendation system problem. Taking advantage of the known drug–disease associations, the objective of the recommendation system is to identify new treatments by filling out the unknown entries in the drug–disease association matrix, which is known as matrix completion. Underpinned by the fact that common molecular pathways contribute to many different diseases, the recommendation system assumes that the underlying latent factors determining drug–disease associations are highly correlated. In other words, the drug–disease matrix to be completed is low-rank. Accordingly, …

Ieee Access Special Section Editorial: Wirelessly Powered Networks, And Technologies, Theofanis P. Raptis, Nuno B. Carvalho, Diego Masotti, Lei Shu, Cong Wang, Yuanyuan Yang

Computer Science Faculty Publications

Wireless Power Transfer (WPT) is, by definition, a process that occurs in any system where electrical energy is transmitted from a power source to a load without the connection of electrical conductors. WPT is the driving technology that will enable the next stage in the current consumer electronics revolution, including battery-less sensors, passive RF identification (RFID), passive wireless sensors, the Internet of Things and 5G, and machine-to-machine solutions. WPT-enabled devices can be powered by harvesting energy from the surroundings, including electromagnetic (EM) energy, leading to a new communication networks paradigm, the Wirelessly Powered Networks.

A Survey Of Attention Deficit Hyperactivity Disorder Identification Using Psychophysiological Data, S. De Silva, S. Dayarathna, G. Ariyarathne, D. Meedeniya, Sampath Jayarathna

Computer Science Faculty Publications

Attention Deficit Hyperactivity Disorder (ADHD) is one of the most common neurological disorders among children, that affects different areas in the brain that allows executing certain functionalities. This may lead to a variety of impairments such as difficulties in paying attention or focusing, controlling impulsive behaviours and overreacting. The continuous symptoms may have a severe impact in the long-term. This paper explores the ADHD identification studies using eye movement data and functional Magnetic Resonance Imaging (fMRI). This study discusses different machine learning techniques, existing models and analyses the existing literature. We have identified the current challenges and possible future directions …

Sec-Lib: Protecting Scholarly Digital Libraries From Infected Papers Using Active Machine Learning Framework, Nir Nissim, Aviad Cohen, Jian Wu, Andrea Lanzi, Lior Rokach, Yuval Elovici, Lee Giles

Computer Science Faculty Publications

Researchers from academia and the corporate-sector rely on scholarly digital libraries to access articles. Attackers take advantage of innocent users who consider the articles' files safe and thus open PDF-files with little concern. In addition, researchers consider scholarly libraries a reliable, trusted, and untainted corpus of papers. For these reasons, scholarly digital libraries are an attractive-target and inadvertently support the proliferation of cyber-attacks launched via malicious PDF-files. In this study, we present related vulnerabilities and malware distribution approaches that exploit the vulnerabilities of scholarly digital libraries. We evaluated over two-million scholarly papers in the CiteSeerX library and found the library …

Eeg-Based Processing And Classification Methodologies For Autism Spectrum Disorder: A Review, Gunavaran Brihadiswaran, Dilantha Haputhanthri, Sahan Gunathilaka, Dulani Meedeniya, Sampath Jayarathna

Computer Science Faculty Publications

Autism Spectrum Disorder is a lifelong neurodevelopmental condition which affects social interaction, communication and behaviour of an individual. The symptoms are diverse with different levels of severity. Recent studies have revealed that early intervention is highly effective for improving the condition. However, current ASD diagnostic criteria are subjective which makes early diagnosis challenging, due to the unavailability of well-defined medical tests to diagnose ASD. Over the years, several objective measures utilizing abnormalities found in EEG signals and statistical analysis have been proposed. Machine learning based approaches provide more flexibility and have produced better results in ASD classification. This paper presents …

Electroencephalogram (Eeg) For Delineating Objective Measure Of Autism Spectrum Disorder, Sampath Jayarathna, Yasith Jayawardana, Mark Jaime, Sashi Thapaliya

Computer Science Faculty Publications

Autism spectrum disorder (ASD) is a developmental disorder that often impairs a child's normal development of the brain. According to CDC, it is estimated that 1 in 6 children in the US suffer from development disorders, and 1 in 68 children in the US suffer from ASD. This condition has a negative impact on a person's ability to hear, socialize, and communicate. Subjective measures often take more time, resources, and have false positives or false negatives. There is a need for efficient objective measures that can help in diagnosing this disease early as possible with less effort. EEG measures the …

Clinical Big Data And Deep Learning: Applications, Challenges, And Future Outlooks, Ying Yu, Liangliang Liu, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

The explosion of digital healthcare data has led to a surge of data-driven medical research based on machine learning. In recent years, as a powerful technique for big data, deep learning has gained a central position in machine learning circles for its great advantages in feature representation and pattern recognition. This article presents a comprehensive overview of studies that employ deep learning methods to deal with clinical data. Firstly, based on the analysis of the characteristics of clinical data, various types of clinical data (e.g., medical images, clinical notes, lab results, vital signs and demographic informatics) are discussed and details …

Multi-View Cluster Analysis With Incomplete Data To Understand Treatment Effects, Guoqing Chao, Jiangwen Sun, Jin Lu, An-Li Wang, Daniel D. Langleben, Chiang-Shan Li, Jinbo Bi

Computer Science Faculty Publications

Multi-view cluster analysis, as a popular granular computing method, aims to partition sample subjects into consistent clusters across different views in which the subjects are characterized. Frequently, data entries can be missing from some of the views. The latest multi-view co-clustering methods cannot effectively deal with incomplete data, especially when there are mixed patterns of missing values. We propose an enhanced formulation for a family of multi-view co-clustering methods to cope with the missing data problem by introducing an indicator matrix whose elements indicate which data entries are observed and assessing cluster validity only on observed entries. In comparison with …

Web Archives At The Nexus Of Good Fakes And Flawed Originals, Michael L. Nelson

Computer Science Faculty Publications

[Summary] The authenticity, integrity, and provenance of resources we encounter on the web are increasingly in question. While many people are inured to the possibility of altered images, the easy accessibility of powerful software tools that synthesize audio and video will unleash a torrent of convincing “deepfakes” into our social discourse. Archives will no longer be monopolized by a countable number of institutions such as governments and publishers, but will become a competitive space filled with social engineers, propagandists, conspiracy theorists, and aspiring Hollywood directors. While the historical record has never been singular nor unmalleable, current technologies empower an unprecedented …

Automatic Slide Generation For Scientific Papers, Athar Sefid, Jian Wu, Prasenjit Mitra, C. Lee Giles

Computer Science Faculty Publications

We describe our approach for automatically generating presentation slides for scientific papers using deep neural networks. Such slides can help authors have a starting point for their slide generation process. Extractive summarization techniques are applied to rank and select important sentences from the original document. Previous work identified important sentences based only on a limited number of features that were extracted from the position and structure of sentences in the paper. Our method extends previous work by (1) extracting a more comprehensive list of surface features, (2) considering semantic or meaning of the sentence, and (3) using context around the …

Discerning Novel Splice Junctions Derived From Rna-Seq Alignment: A Deep Learning Approach, Yi Zhang, Xinan Liu, James N. Macleod, Jinze Liu

Computer Science Faculty Publications

Background: Exon splicing is a regulated cellular process in the transcription of protein-coding genes. Technological advancements and cost reductions in RNA sequencing have made quantitative and qualitative assessments of the transcriptome both possible and widely available. RNA-seq provides unprecedented resolution to identify gene structures and resolve the diversity of splicing variants. However, currently available ab initio aligners are vulnerable to spurious alignments due to random sequence matches and sample-reference genome discordance. As a consequence, a significant set of false positive exon junction predictions would be introduced, which will further confuse downstream analyses of splice variant discovery and abundance estimation.

Results: …

Facepet: Enhancing Bystanders’ Facial Privacy With Smart Wearables/Internet Of Things, Alfredo J. Perez, Sherali Zeadally, Luis Y. Matos Garcia, Jason A. Mouloud, Scott Griffith

Computer Science Faculty Publications

Given the availability of cameras in mobile phones, drones and Internet-connected devices, facial privacy has become an area of major interest in the last few years, especially when photos are captured and can be used to identify bystanders’ faces who may have not given consent for these photos to be taken and be identified. Some solutions to protect facial privacy in photos currently exist. However, many of these solutions do not give a choice to bystanders because they rely on algorithms that de-identify photos or protocols to deactivate devices and systems not controlled by bystanders, thereby being dependent on the …

X-Search: An Open Access Interface For Cross-Cohort Exploration Of The National Sleep Research Resource, Licong Cui, Ningzhou Zeng, Matthew Kim, Remo Mueller, Emily Ruth Hankosky, Susan Redline, Guo-Qiang Zhang

Computer Science Faculty Publications

Background: The National Sleep Research Resource (NSRR) is a large-scale, openly shared, data repository of de-identified, highly curated clinical sleep data from multiple NIH-funded epidemiological studies. Although many data repositories allow users to browse their content, few support fine-grained, cross-cohort query and exploration at study-subject level. We introduce a cross-cohort query and exploration system, called X-search, to enable researchers to query patient cohort counts across a growing number of completed, NIH-funded studies in NSRR and explore the feasibility or likelihood of reusing the data for research studies.

Methods: X-search has been designed as a general framework with two loosely-coupled components: …

Seqothello: Querying Rna-Seq Experiments At Scale, Ye Yu, Jinpeng Liu, Xinan Liu, Yi Zhang, Eamonn Magner, Erik Lehnert, Chen Qian, Jinze Liu

Computer Science Faculty Publications

We present SeqOthello, an ultra-fast and memory-efficient indexing structure to support arbitrary sequence query against large collections of RNA-seq experiments. It takes SeqOthello only 5 min and 19.1 GB memory to conduct a global survey of 11,658 fusion events against 10,113 TCGA Pan-Cancer RNA-seq datasets. The query recovers 92.7% of tier-1 fusions curated by TCGA Fusion Gene Database and reveals 270 novel occurrences, all of which are present as tumor-specific. By providing a reference-free, alignment-free, and parameter-free sequence search system, SeqOthello will enable large-scale integrative studies using sequence-level data, an undertaking not previously practicable for many individual labs.

The Design Of An Emerging/Multi-Paradigm Programming Languages Course, Saverio Perugini

Computer Science Faculty Publications

We present the design of a new special topics course, Emerging/Multi-paradigm Languages, on the recent trend toward more dynamic, multi-paradigm languages. To foster course adoption, we discuss the design of the course, which includes language presentations/papers and culminating, ��inal projects/papers. The goal of this article is to inspire and facilitate course adoption.

Developing A Contemporary Operating Systems Course, Saverio Perugini, David J. Wright

Computer Science Faculty Publications

The objective of this tutorial presentation is to foster innovation in the teaching of operating systems (os) at the undergraduate level as part of a three-year NSF-funded IUSE (Improving Undergraduate STEM Education) project titled “Engaged Student Learning: Reconceptualizing and Evaluating a Core Computer Science Course for Active Learning and STEM Student Success” (2017–2020).

An Application Of The Actor Model Of Concurrency In Python: A Euclidean Rhythm Music Sequencer, Daniel P. Prince, Saverio Perugini

Computer Science Faculty Publications

We present a real-time sequencer, implementing the Euclidean rhythm algorithm, for creative generation of drum sequences by musicians or producers. We use the Actor model of concurrency to simplify the communication required for interactivity and musical timing, and generator comprehensions and higher-order functions to simplify the implementation of the Euclidean rhythm algorithm. The resulting application sends Musical Instrument Digital Interface (MIDI) data interactively to another application for sound generation.

Chameleon: A Customizable Language For Teaching Programming Languages, Saverio Perugini, Jack L. Watkin

Computer Science Faculty Publications

ChAmElEoN is a programming language for teaching students the concepts and implementation of computer languages. We describe its syntax and semantics, the educational aspects involved in the implementation of a variety of interpreters for it, its malleability, and student feedback to inspire its use for teaching languages.

An Outlier Detection Algorithm Based On Cross-Correlation Analysis For Time Series Dataset, Hui Lu, Yaxian Liu, Zongming Fei, Chongchong Guan

Computer Science Faculty Publications

Outlier detection is a very essential problem in a variety of application areas. Many detection methods are deficient for high-dimensional time series data sets containing both isolated and assembled outliers. In this paper, we propose an Outlier Detection method based on Cross-correlation Analysis (ODCA). ODCA consists of three key parts. They are data preprocessing, outlier analysis, and outlier rank. First, we investigate a linear interpolation method to convert assembled outliers into isolated ones. Second, a detection mechanism based on the cross-correlation analysis is proposed for translating the high-dimensional data sets into 1-D cross-correlation function, according to which the isolated outlier …

Imapsplice: Alleviating Reference Bias Through Personalized Rna-Seq Alignment, Xinan Liu, James N. Macleod, Jinze Liu

Computer Science Faculty Publications

Genomic variants in both coding and non-coding sequences can have functionally important and sometimes deleterious effects on exon splicing of gene transcripts. For transcriptome profiling using RNA-seq, the accurate alignment of reads across exon junctions is a critical step. Existing algorithms that utilize a standard reference genome as a template sometimes have difficulty in mapping reads that carry genomic variants. These problems can lead to allelic ratio biases and the failure to detect splice variants created by splice site polymorphisms. To improve RNA-seq read alignment, we have developed a novel approach called iMapSplice that enables personalized mRNA transcriptome profiling. The …

Query-Constraint-Based Mining Of Association Rules For Exploratory Analysis Of Clinical Datasets In The National Sleep Research Resource, Rashmie Abeysinghe, Licong Cui

Computer Science Faculty Publications

Background: Association Rule Mining (ARM) has been widely used by biomedical researchers to perform exploratory data analysis and uncover potential relationships among variables in biomedical datasets. However, when biomedical datasets are high-dimensional, performing ARM on such datasets will yield a large number of rules, many of which may be uninteresting. Especially for imbalanced datasets, performing ARM directly would result in uninteresting rules that are dominated by certain variables that capture general characteristics.

Methods: We introduce a query-constraint-based ARM (QARM) approach for exploratory analysis of multiple, diverse clinical datasets in the National Sleep Research Resource (NSRR). QARM enables rule mining on …