Data Science Commons^™

Precise Method To Identify Kinase Drug Targets In Complex Diseases: The First Step Towards Sustainable And Effective Treatment, Hasbanny Irisson, Marzieh Ayati

Research Symposium

Background: Kinases are enzymes that have proven to be important drug targets due to their role in critical biological mechanisms such as phosphorylation. Phosphorylation happens when a kinase catalyzes the transfer of a phosphate group to a protein in a phosphorylated site, which then becomes known as the substrate of the kinase. Any dysregulation of protein phosphorylation causes a wide range of complex diseases including cancer. Thus, discovering the links between kinases and their substrates (i.e. predicting kinase-substrate associations (KSAs)) is crucial in developing effective and sustainable treatments. Presently, less than 5% of phosphorylated sites have an associated kinase, and …

A Case Report: A Patient Rescued By Va-Ecmo After Cardiac Arrest Triggered By Trigeminocardiac Reflex After Nasal Surgery, Xu Zhang, Bin Sun, Chen Pac-Soo, Daqing Ma, Liwei Wang

Faculty, Staff and Student Publications

Rationale:

Cardiac arrest (CA) caused by trigeminocardiac reflex (TCR) after endoscopic nasal surgery is rare. Hence, when a patient suffers from TCR induced CA in the recovery room, most doctors may not be able to find the cause in a short time, and standard cardiopulmonary resuscitation and resuscitation measures may not be effective. Providing circulatory assistance through venous-arterial extracorporeal membrane oxygenation (VA-ECMO) can help healthcare providers gain time to identify the etiology and initiate symptom-specific treatment.

Patient concerns:

We report a rare case of CA after endoscopic nasal surgery treated with VA-ECMO.

Diagnoses:

We excluded myocardial infarction, pulmonary embolism, allergies, …

Privacy-Preserving Federated Learning, Dumindu Samaraweera

Math Department Colloquium Series

AI's applicability across diverse fields is hindered by data sensitivity, privacy concerns, and limited training data availability. Federated Learning (FL) addresses this challenge by enabling collaborative machine learning while preserving data privacy. FL allows clients to engage in model training with their local data, avoiding centralized storage. However, even with FL, security threats persist, jeopardizing model integrity and client data privacy. In this presentation, we will explore our latest findings in this area of research, safeguarding sensitive data from attacks through techniques like secure multiparty computation, homomorphic encryption, and differential privacy within the FL framework, enhancing data protection, and expanding …

Using Artificial Intelligence To Learn Optimal Regimen Plan For Alzheimer’S Disease, Kritib Bhattarai, Sivaraman Rajaganapathy, Trisha Das, Yejin Kim, Yongbin Chen, Alzheimer’S Disease Neuroimaging Initiative, Australian Imaging Biomarkers And Lifestyle Flagship Study Of Ageing, Qiying Dai, Xiaoyang Li, Xiaoqian Jiang, Nansu Zong

Faculty, Staff and Student Publications

BACKGROUND: Alzheimer's disease (AD) is a progressive neurological disorder with no specific curative medications. Sophisticated clinical skills are crucial to optimize treatment regimens given the multiple coexisting comorbidities in the patient population.

OBJECTIVE: Here, we propose a study to leverage reinforcement learning (RL) to learn the clinicians' decisions for AD patients based on the longitude data from electronic health records.

METHODS: In this study, we selected 1736 patients from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. We focused on the two most frequent concomitant diseases-depression, and hypertension, thus creating 5 data cohorts (ie, Whole Data, AD, AD-Hypertension, AD-Depression, and AD-Depression-Hypertension). …

Mapping The Delineation Of Practice To The Amia Foundational Domains For Applied Health Informatics, Todd R Johnson, Eta S Berner, Sue S Feldman, Josette Jones, Annette L Valenta, Damian Borbolla, Gloria Deckard, Laverne Manos

Faculty, Staff and Student Publications

OBJECTIVE: This article reports on the alignment between the foundational domains and the delineation of practice (DoP) for health informatics, both developed by the American Medical Informatics Association (AMIA). Whereas the foundational domains guide graduate-level curriculum development and accreditation assessment, providing an educational pathway to the minimum competencies needed as a health informatician, the DoP defines the domains, tasks, knowledge, and skills that a professional needs to competently perform in the discipline of health informatics. The purpose of this article is to determine whether the foundational domains need modification to better reflect applied practice.

MATERIALS AND METHODS: Using an iterative …

Organizing Pmode Dopplergrams Of Jupiter With Matlab, Brady T. Smith, Deborah Gulledge, Cody Shaw, Gerard Williger

The Cardinal Edge

The interiors of the giant planets are poorly known. At the time of writing, such investigations have been limited to measuring gravitational effects from a handful of orbital probes. The most recent attempt to map the interior is via PMODE (the Planetary Multilevel Oscillations and Dynamics Experiment), designed to explore Jupiter’s core by collecting Dopplergrams. Small radial velocity shifts in Jupiter’s upper cloud decks enable us to map its atmospheric dynamics and consequently its interior via Dioseismology (techniques similar to Helioseismology, applied to Jupiter). This campaign produced a vast dataset with more than 50,000 exposures, every 30 seconds, over 24 …

Effects Of Weight Initialization Methods On Ffn's, Ida K. Karem

The Cardinal Edge

Weight initialization is the method of determining starting values of weights in a neural network. The way this method is done can have massive effects on the network[2, 3, 6, 9] and can halt training if not handled properly. On the other hand, if initialization is chosen tactfully it can improve training and accuracy greatly. The initialization method usually called Normalized Xavier will be referred to as Nox in this paper to avoid confusion with the Xavier initialization method. This study analyzes five methods of weight initialization(Nox, He, Xavier, Plutonian, and Self-Root), two of them …

Sentiment Analysis Of Public Perception Towards Elon Musk On Reddit (2008-2022), Daniel Maya Bonilla, Samuel Iradukunda, Pamela Thomas

The Cardinal Edge

As Elon Musk’s influence in technology and business continues to expand, it becomes crucial to comprehend public sentiment surrounding him in order to gauge the impact of his actions and statements. In this study, we conducted a comprehensive analysis of comments from various subreddits discussing Elon Musk over a 14-year period, from 2008 to 2022. Utilizing advanced sentiment analysis models and natural language processing techniques, we examined patterns and shifts in public sentiment towards Musk, identifying correlations with key events in his life and career. Our findings reveal that public sentiment is shaped by a multitude of factors, including his …

Systematic Investigation Of The Homology Sequences Around The Human Fusion Gene Breakpoints In Pan-Cancer - Bioinformatics Study For A Potential Link To Mmej, Pora Kim, Himansu Kumar, Chengyuan Yang, Ruihan Luo, Jiajia Liu, Xiaobo Zhou

Faculty, Staff and Student Publications

Microhomology-mediated end joining (MMEJ), an error-prone DNA damage repair mechanism, frequently leads to chromosomal rearrangements due to its ability to engage in promiscuous end joining of genomic instability and also leads to increasing mutational load at the sequences flanking the breakpoints (BPs). In this study, we systematically investigated the homology sequences around the genomic breakpoint area of human fusion genes, which were formed by the chromosomal rearrangements initiated by DNA double-strand breakage. Since the RNA-seq data is the typical data set to check the fusion genes, for the known exon junction fusion breakpoints identified from RNA-seq data, we have to …

Machine Learning And Causality For Interpretable And Automated Decision Making, Maria Lentini

Theses and Dissertations

This abstract explores two key areas in decision science: automated and interpretable decision making. In the first part, we address challenges related to sparse user interaction data and high item turnover rates in recommender systems. We introduce a novel algorithm called Multi-View Interactive Collaborative Filtering (MV-ICTR) that integrates user-item ratings and contextual information, improving performance, particularly for cold-start scenarios. In the second part, we focus on Student Prescription Trees (SPTs), which are interpretable decision trees. These trees use a black box "teacher" model to predict counterfactuals based on observed covariates. We experiment with a Bayesian hierarchical binomial regression model as …

Reu-Deim Classification Of Hispanic Voters In Hispanic Groups Using Name And Zip Code Data In Palm Beach, Florida, Kamila Soto-Ortiz

Beyond: Undergraduate Research Journal

When it comes to registering to vote, Hispanic voters can only register as “Hispanic” in the “Race/Ethnicity” category, causing difficulties when analyzing voting trends amongst the Hispanic community. Upon the recent idea that not all Hispanic Groups vote the same, the goal is to create a model that can possibly identify a voter’s Hispanic Group with the information provided on the public Florida voter file. This is accomplished using name and zip code data for all voters in Palm Beach, Florida. This paper will explore the model implemented, its findings and limitations. Palm Beach, Florida, is met with low confidence …

Codesigning A Big Data Analytic Tool For Girl Child Learner Drop Out From Eastern Cape Province -South Africa, Nobert Rangarirai Jere, Nosipho Carol Mavuso, Nelly Sharpley

African Conference on Information Systems and Technology

Developing sustainable solutions is critical for adoption of digital solutions. As the high number of learners dropping out of school continues to increase, it is critical to find innovative ways of predicting and preventing high drop out. Current literature has documented a number of factors that influence learner drop out. Innovative ideas, techniques and activities have been undertaken to motivate learners to stay at school. It is unfortunate that most of the initiatives have not helped to avoid drop out of learners. The study is based on a mixed approached that was used targeting female learns from Oliver Tambo District …

Mettl14 Is A Chromatin Regulator Independent Of Its Rna N6-Methyladenosine Methyltransferase Activity, Xiaoyang Dou, Lulu Huang, Yu Xiao, Chang Liu, Yini Li, Xinning Zhang, Lishan Yu, Ran Zhao, Lei Yang, Chuan Chen, Xianbin Yu, Boyang Gao, Meijie Qi, Yawei Gao, Bin Shen, Shuying Sun, Chuan He, Jun Liu

Faculty, Staff and Student Publications

METTL3 and METTL14 are two components that form the core heterodimer of the main RNA m6A methyltransferase complex (MTC) that installs m6A. Surprisingly, depletion of METTL3 or METTL14 displayed distinct effects on stemness maintenance of mouse embryonic stem cell (mESC). While comparable global hypo-methylation in RNA m6A was observed in Mettl3 or Mettl14 knockout mESCs, respectively. Mettl14 knockout led to a globally decreased nascent RNA synthesis, whereas Mettl3 depletion resulted in transcription upregulation, suggesting that METTL14 might possess an m6A-independent role in gene regulation. We found that METTL14 colocalizes with the repressive H3K27me3 modification. Mechanistically, METTL14, but not METTL3, binds …

A Low-Complexity Algorithm To Determine Spacecraft Trajectories, Sirani Perera

Math Department Colloquium Series

The growing traffic within the Cislunar region has created a need for computationally effective methods to obtain the trajectories of spacecraft in the Cislunar region. By developing algorithms with low time and arithmetic complexities, we can effectively address these needs.

In this talk, we will present a mathematical model that uses interpolation and boundary conditions to obtain trajectories for satellites based on the principles of three-body dynamics. Following the model, we propose a low- complexity algorithm to generate satellite trajectories. Once the algorithm is proposed, we will apply it to the relevant periodic orbits in the Cislunar region. Finally, we …

Pathogen-Driven Crispr Screens Identify Trex1as A Regulator Of Dna Self-Sensing During Influenza Virus Infection, Cason R King, Yiping Liu, Katherine A Amato, Grace A Schaack, Clayton Mickelson, Autumn E Sanders, Tony Hu, Srishti Gupta, Ryan A Langlois, Judith A Smith, Andrew Mehle

Faculty, Staff and Student Publications

Host:pathogen interactions dictate the outcome of infection, yet the limitations of current approaches leave large regions of this interface unexplored. Here, we develop a novel fitness-based screen that queries factors important during the middle to late stages of infection. This is achieved by engineering influenza virus to direct the screen by programming dCas9 to modulate host gene expression. Our genome-wide screen for pro-viral factors identifies the cytoplasmic DNA exonuclease TREX1. TREX1 degrades cytoplasmic DNA to prevent inappropriate innate immune activation by self-DNA. We reveal that this same process aids influenza virus replication. Infection triggers release of mitochondrial DNA into the …

Collagene Enables Privacy-Aware Federated And Collaborative Genomic Data Analysis, Wentao Li, Miran Kim, Kai Zhang, Han Chen, Xiaoqian Jiang, Arif Harmanci

Faculty, Staff and Student Publications

Growing regulatory requirements set barriers around genetic data sharing and collaborations. Moreover, existing privacy-aware paradigms are challenging to deploy in collaborative settings. We present COLLAGENE, a tool base for building secure collaborative genomic data analysis methods. COLLAGENE protects data using shared-key homomorphic encryption and combines encryption with multiparty strategies for efficient privacy-aware collaborative method development. COLLAGENE provides ready-to-run tools for encryption/decryption, matrix processing, and network transfers, which can be immediately integrated into existing pipelines. We demonstrate the usage of COLLAGENE by building a practical federated GWAS protocol for binary phenotypes and a secure meta-analysis protocol. COLLAGENE is available at https://zenodo.org/record/8125935 …

An Electronic Origin Of Charge Order In Infinite-Layer Nickelates, Hanghui Chen, Yi-Feng Yang, Guang-Ming Zhang, Hongquan Liu

Faculty, Staff and Student Publications

A charge order (CO) with a wavevector [Formula: see text] is observed in infinite-layer nickelates. Here we use first-principles calculations to demonstrate a charge-transfer-driven CO mechanism in infinite-layer nickelates, which leads to a characteristic Ni1+-Ni2+-Ni1+ stripe state. For every three Ni atoms, due to the presence of near-Fermi-level conduction bands, Hubbard interaction on Ni-d orbitals transfers electrons on one Ni atom to conduction bands and leaves electrons on the other two Ni atoms to become more localized. We further derive a low-energy effective model to elucidate that the CO state arises from a delicate competition between Hubbard interaction on Ni-d …

Gamerfit-Asd Beta Test: Adapting An Evidence-Based Exergaming And Telehealth Coaching Intervention For Autistic Youth, Daniel P. Hatfield, Aviva Must, Winston Kennedy, Amanda E. Staiano, James Slavet, Rachael A. Sabelli, Carol Curtin, Linda G. Bandini, Phillip Nauta, Christopher Stuetzle, April Bowling

Computer and Data Science Faculty Publications

Background: Health disparities faced by autistic youth are exacerbated by inadequate physical activity (PA) and sleep, whereas healthy PA and sleep may improve mood and function. Adaptive Game Squad (AGS) is an evidence-based telehealth coaching and exergaming intervention to improve PA and sleep for adolescents with diverse neurodevelopmental and psychiatric conditions. This study aimed to adapt AGS for autistic youth ages 10–15 years; beta-test the modified intervention for feasibility, accessibility, and engagement; and further refine the intervention for a larger planned demonstration pilot.

Methods: Interdisciplinary experts adapted AGS to create GamerFit-ASD, a 12-week intervention that included a progressive exergame schedule, …

Uncertainties In Retrieval Of Remote Sensing Reflectance From Ocean Color Satellite Observations, Eder I. Herrera Estrella

Dissertations, Theses, and Capstone Projects

Ocean Color radiometry uses remote sensing to interpret ocean dynamics by retrieving remote sensing reflectance (������) from satellite imagery at different scales and over different time periods. ������ spectrum characterizes the ocean color that we observe, and from which we can discern concentrations of chlorophyll, organic and inorganic particles, and carbon fluxes in the ocean and atmosphere. ������ is derived from the total radiance at the top of the atmosphere (TOA). However, it only represents up to ten percent of the total signal. Hence, the retrieval of ������ from the total radiance at TOA involves the application of atmospheric correction …

Human-Ai Complex Task Planning, Sepideh Nikookar

Dissertations

The process of complex task planning is ubiquitous and arises in a variety of compelling applications. A few leading examples include designing a personalized course plan or trip plan, designing music playlists/work sessions in web applications, or even planning routes of naval assets to collaboratively discover an unknown destination. For all of these aforementioned applications, creating a plan requires satisfying a basic construct, i.e., composing a sequence of sub-tasks (or items) that optimizes several criteria and satisfies constraints. For instance, in course planning, sub-tasks or items are core and elective courses, and degree requirements capture their complex dependencies as constraints. …

Data-Driven 2d Materials Discovery For Next-Generation Electronics, Zeyu Zhang

Dissertations

The development of material discovery and design has lasted centuries in human history. After the concept of modern chemistry and material science was established, the strategy of material discovery relies on the experiments. Such a strategy becomes expensive and time-consuming with the increasing number of materials nowadays. Therefore, a novel strategy that is faster and more comprehensive is urgently needed. In this dissertation, an experiment-guided material discovery strategy is developed and explained using metal-organic frameworks (MOFs) as instances. The advent of 7r-stacked layered MOFs, which offer electrical conductivity on top of permanent porosity and high surface area, opened up new …

On Explainability Of Neural Networks, Cem Benar

Dissertations

It is widely reported that deep neural networks outperform most competitors for a range of applications. The state-of-the-art neural networks have built-in inductive bias of architectural choices, regularizations, optimizer types, and initialization methods. Using inductive bias is intuitive to enhance the model approximation. Deep neural networks are mostly dense and heavily overparameterized. They tend to be biased towards low-rank solutions to reduce complexity and improve generalization performance, known as implicit regularization. The implicit regularization as observed in specific architectures and various real-world data sets suggests to overparameterize neural networks judiciously and learn compressed representations (lower rank approximation) with improved performance. …

Crabr-Net: A Contextual Relational Attention-Based Recognition Network For Remote Sensing Scene Objective, Ningbo Guo, Mingyong Jiang, Lijing Gao, Yizhuo Tang, Jinwei Han, Xiangning Chen

Faculty, Staff and Student Publications

Remote sensing scene objective recognition (RSSOR) plays a serious application value in both military and civilian fields. Convolutional neural networks (CNNs) have greatly enhanced the improvement of intelligent objective recognition technology for remote sensing scenes, but most of the methods using CNN for high-resolution RSSOR either use only the feature map of the last layer or directly fuse the feature maps from various layers in the "summation" way, which not only ignores the favorable relationship information between adjacent layers but also leads to redundancy and loss of feature map, which hinders the improvement of recognition accuracy. In this study, a …

Syllabus For Computational Physics (Phys 39907), Mark D. Shattuck

Open Educational Resources

Syllabus for City College of New York Computational Physics course.

On Digital Productivity Base Of Policies For Cross-Border Data Flows Between Rcep Parties And Its Influences—Taking Digital Integration Index As A Reference, Gui Huang, Ru Tao

Bulletin of Chinese Academy of Sciences (Chinese Version)

This study reviews the newest legislation and policies of Regional Comprehensive Economic Partnership (RCEP) participating countries on cross-border data flow, and then categorized them according to the ban on data transfer, local storage of data, permission-based regulation, and standards-based regulation. By referring to the indexes in the ASEAN Digital Integration Index, the subject and object factors of digital productivity in RCEP parities are sorted out, as well as the status quo of digital economy. Through the introduction of data value chain theory, the decisive impact of digital productivity factors on the policy formulation of cross-border data flow is expounded; by …

Paradigm Review Of Data Localization In India And Its Implications For China, Ying Fan

Bulletin of Chinese Academy of Sciences (Chinese Version)

Data localization is a focal point of global data governance and its impact on global data governance is no longer confined to a single country. Over the years, India has followed a unique policy framework in terms of cross-border data flows and data localization, and its insistence on data sovereignty reflects its position in the international arena. This study uses the Indian data localization paradigm as a research base to discuss the common phenomenon of disconnect between policy motivations and practical effects of data localization, and as an entry point to introduce the latest Indian research findings in this area. …

Research On Multi-Source Heterogeneous Big Data Fusion Based On Wsr, Aihua Li, Weijia Xu, Yong Shi

Bulletin of Chinese Academy of Sciences (Chinese Version)

In the era of multi-source heterogeneous big data, big data presents new features such as cross, diversity and variability. The applications of big data in a wider range of fields have new requirements for data fusion. Under this background, the connotation of data fusion is enriched and expanded. The generalized data fusion includes the fusion of data resources, the fusion of model methods, and the fusion of decision-makers' knowledge and experience. This study analyzes the characteristics of multi-source heterogeneous data fusion at three different fusion levels: data level, information level and decision level, and discusses challenges for data fusion in …

Verifying Empirical Predictive Modeling Of Societal Vulnerability To Hazardous Events: A Monte Carlo Experimental Approach, Yi Victor Wang, Seung Hee Kim, Menas C. Kafatos

Institute for ECHO Articles and Research

With the emergence of large amounts of historical records on adverse impacts of hazardous events, empirical predictive modeling has been revived as a foundational paradigm for quantifying disaster vulnerability of societal systems. This paradigm models societal vulnerability to hazardous events as a vulnerability curve indicating an expected loss rate of a societal system with respect to a possible spectrum of intensity measure (IM) of an event. Although the empirical predictive models (EPMs) of societal vulnerability are calibrated on historical data, they should not be experimentally tested with data derived from field experiments on any societal system. Alternatively, in this paper, …

Developing Electronic Clinical Quality Measures To Assess The Cancer Diagnostic Process, Daniel R Murphy, Andrew J Zimolzak, Divvy K Upadhyay, Li Wei, Preeti Jolly, Alexis Offner, Dean F Sittig, Saritha Korukonda, Riyaa Murugaesh Rekha, Hardeep Singh

Faculty, Staff and Student Publications

OBJECTIVE: Measures of diagnostic performance in cancer are underdeveloped. Electronic clinical quality measures (eCQMs) to assess quality of cancer diagnosis could help quantify and improve diagnostic performance.

MATERIALS AND METHODS: We developed 2 eCQMs to assess diagnostic evaluation of red-flag clinical findings for colorectal (CRC; based on abnormal stool-based cancer screening tests or labs suggestive of iron deficiency anemia) and lung (abnormal chest imaging) cancer. The 2 eCQMs quantified rates of red-flag follow-up in CRC and lung cancer using electronic health record data repositories at 2 large healthcare systems. Each measure used clinical data to identify abnormal results, evidence of …

Federated Generalized Linear Mixed Models For Collaborative Genome-Wide Association Studies, Wentao Li, Han Chen, Xiaoqian Jiang, Arif Harmanci

Faculty, Staff and Student Publications

Federated association testing is a powerful approach to conduct large-scale association studies where sites share intermediate statistics through a central server. There are, however, several standing challenges. Confounding factors like population stratification should be carefully modeled across sites. In addition, it is crucial to consider disease etiology using flexible models to prevent biases. Privacy protections for participants pose another significant challenge. Here, we propose distributed Mixed Effects Genome-wide Association study (