Bioinformatics Commons^™

Current Scenario Of Covid-19 With Epidemiological And Phylogenetic Analysis Of Pakistani Coronavirus: A Review, Asma Altaf, Wafa Iqbal, Sidra Younis, Farah Deeba

Journal of Bioresource Management

A novel corona virus named as 2019 n-CoV was identified to be the actual cause of an outbreak of respiratory illness in Wuhan, China beginning in late December 2019. This respiratory disease was named as COVID-19 by WHO. There are many countries affected by COVID-19 including Pakistan. In this review we have provided a brief introduction of COVID-19 and discussed epidemiological and phylogenetic analysis of Pakistani novel corona virus strain. Our epidemiological analysis of data till 16^th May 2020 showed rapidly increasing number of new cases, while at the same time a higher recovery rate than number of deaths …

Identification And Phylogenetic Analysis Of Channa Species From Riverine System Of Pakistan Using Coi Gene As A Dna Barcoding Marker, Muhammad Kamran, Atif Yaqub, Naila Malkani, Khalid Mahmood Anjum, Muhammad Nabeel Awan, Hamed Paknejad

Journal of Bioresource Management

Channa are the freshwater and important food fish species in Pakistan belonging to family Channidae. However, identification and phylogenetic analysis based on molecular tools of these species in Pakistan was not well known. Herein, the current investigation was conceptualized, which dealt with mitochondrial DNA sequences from three geographically distinct populations of this species from Pakistan’s water system. DNA from fin tissues was extracted. COI region of mtDNA was amplified using universal primers for fish. PCR products were sequenced. Phylogenetic analysis conducted in the present study, i.e. neighbor-joining (NJ) cladogram, maximum likelihood, K2P genetic divergence and histogram suggests that the studied …

Multi-Label Model For Toxicity Prediction, Xiu Huan Yap, Michael L. Raymer

Symposium of Student Research, Scholarship, and Creative Activities Materials

Most computational predictive models are specifically trained for a single toxicity endpoint. Since more than 1300 toxicity assays have been reported in the TOXCAST dashboard, achieving high coverage over this growing number of toxicity endpoints remains challenging. Furthermore, single-endpoint models lack the ability to learn dependencies between endpoints, such as those targeting similar biological pathways, which may be used to boost model performance. In this study, we characterize the performance of 3 multi-label classification (MLC) models, namely Classifier Chains (CC), Label Powersets (LP) and Stacking (SBR), on Tox21 challenge data. These MLC models employ the Problem Transformation approach, which is …

Iamhappy: Towards An Iot Knowledge-Based Cross-Domain Well-Being Recommendation System For Everyday Happiness, Amelia Gyrard, Amit Sheth

Kno.e.sis Publications

Nowadays, healthy lifestyle, fitness, and diet habits have become central applications in our daily life. Positive psychology such as well-being and happiness is the ultimate dream of everyday people’s feelings (even without being aware of it). Wearable devices are being increasingly employed to support well-being and fitness. Those devices produce physiological signals that are analyzed by machines to understand emotions and physical state. The Internetof Things (IoT) technology connects (wearable) devices to the Internet to easily access and process data, even using Web technologies (aka Web of Things).

We design IAMHAPPY, an innovative IoT-based well-being recommendation system to encourage every …

Comparative Mito-Genomic Analysis Of Different Species Of Genus Canis By Using Different Bioinformatics Tools, Ume Rumman, Ghulam Sarwar, Safia Janjua, Fida Muhammad Khan, Fakhra Nazir

Journal of Bioresource Management

In the current study, the mitochondrial genes sequence for COI, Cyt b and 16s rRNA of seven species found in different parts of the world were retrieved from NCBI Gene Bank while, PCR products of COI, Cyt b and 16s rRNA genes obtained from C. lupus and C.aureus present in Pakistan were sequenced and aligned for comparison. The phylogenetic analysis of mitochondrial COI, Cyt b and 16s rRNA genes showed almost the same results for the extant species of genus Canis. 16s rRNA revealed C. latrans, C. lycaon and C. simensis showed close phylogenetic relation with each other. …

Question Answering For Suicide Risk Assessment Using Reddit, Amanuel Alambo, Usha Lokala, Ugur Kursuncu, Krishnaprasad Thirunarayan, Amelia Gyrard, Randon S. Welton, Jyotishman Pathak, Amit P. Sheth

Kno.e.sis Publications

Mental Health America designed ten questionnaires that are used to determine the risk of mental disorders. They are also commonly used by Mental Health Professionals (MHPs) to assess suicidality. Specifically, the Columbia Suicide Severity Rating Scale (C-SSRS), a widely used suicide assessment questionnaire, helps MHPs determine the severity of suicide risk and offer an appropriate treatment. A major challenge in suicide treatment is the social stigma wherein the patient feels reluctance in discussing his/her conditions with an MHP, which leads to inaccurate assessment and treatment of patients. On the other hand, the same patient is comfortable freely discussing his/her mental …

Empathi: An Ontology For Emergency Managing And Planning About Hazard Crisis, Manas Gaur, Kaeedeh Shekarpour, Amelia Gyrard, Amit P. Sheth

Kno.e.sis Publications

In the domain of emergency management during hazard crises, having sufficient situational awareness information is critical. It requires capturing and integrating information from sources such as satellite images, local sensors and social media content generated by local people.
A bold obstacle to capturing, representing and integrating such heterogeneous and diverse information is lack of a proper ontology which properly conceptualizes this domain, aggregates and unifies datasets. Thus, in this paper, we introduce empathi ontology which conceptualizes the core concepts describing the domain of emergency managing and planning of hazard crises.
Although empathi has a coarse-grained view, it considers the necessary …

Adaptive Knowledge Networks: A Time Capsule, Swati Padhee, Anurag Illendula, Amit Sheth, Krishnaprasad Thirunarayan, Valerie L. Shalin

Kno.e.sis Publications

❖ Real world events are dynamic in nature Periodic events e.g. US Presidential Election Non-periodic events e.g. Cyclone Idai

❖ Need for real-time predictive analysis, trend analysis, spatio-temporal decision making, public opinion analysis for events.

❖ Current state-of-the-art curates dynamic knowledge graph from structured text.

❖ We propose creating an Adaptive Knowledge Network from incoming real-time multimodal spatio-temporally evolving data.

Automatic Identification Of Individual Drugs In Death Certificates, Soon Jye Kho, Amit Sheth, Olivier Bodenreider

Kno.e.sis Publications

Background:

Establishing trends of drug overdoses requires the identification of individual drugs in death certificates, not supported by coding with the International Classification of Diseases. However, identifying drug mentions from the literal portion of death certificates remains challenging due to the variability of drug names.

Objectives:

To automatically identify individual drugs in death certificates.

Methods:

We use RxNorm to collect variants for drug names (generic names, synonyms, brand names) and we algorithmically generate common misspellings. We use this automatically compiled list to identify drug mentions from 703,106 death certificates and compare the performance of our automated approach to that of …

Building Iot Based Applications For Smart Cities: How Can Ontology Catalogs Help?, Amelia Gyrard, Antoine Zimmermann, Amit P. Sheth

Kno.e.sis Publications

The Internet of Things (IoT) plays an ever-increasing role in enabling smart city applications. An ontology-based semantic approach can help improve interoperability between a variety of IoT-generated as well as complementary data needed to drive these applications. While multiple ontology catalogs exist, using them for IoT and smart city applications require significant amount of work. In this paper, we demonstrate how can ontology catalogs be more effectively used to design and develop smart city applications? We consider four ontology catalogs that are relevant for IoT and smart cities: 1) READY4SmartCities; 2) linked open vocabulary (LOV); 3) OpenSensingCity (OSC); and 4) …

Using Electronic Health Records To Characterize Prescription Patterns: Focus On Antidepressants In Nonpsychiatric Outpatient Settings, Joseph J. Deferio, Tomer T. Levin, Judith Cukor, Samprit Banerjee, Rozan Abdulrahman, Amit P. Sheth, Neel Mehta, Jyotishman Pathak

Kno.e.sis Publications

Objective

To characterize nonpsychiatric prescription patterns of antidepressants according to drug labels and evidence assessments (on-label, evidence-based, and off-label) using structured outpatient electronic health record (EHR) data. Methods

A retrospective analysis was conducted using deidentified EHR data from an outpatient practice at a New York City-based academic medical center. Structured “medication–diagnosis” pairs for antidepressants from 35 325 patients between January 2010 and December 2015 were compared to the latest drug product labels and evidence assessments. Results

Of 140 929 antidepressant prescriptions prescribed by primary care providers (PCPs) and nonpsychiatry specialists, 69% were characterized as “on-label/evidence-based uses.” Depression diagnoses were associated …

Poster: Privacy-Preserving Boosting With Random Linear Classifiers, Sagar Sharma, Keke Chen

Kno.e.sis Publications

We propose SecureBoost, a privacy-preserving predictive modeling framework, that allows service providers (SPs) to build powerful boosting models over encrypted or randomly masked user submit- ted data. SecureBoost uses random linear classifiers (RLCs) as the base classifiers. A Cryptographic Service Provider (CSP) manages keys and assists the SP’s processing to reduce the complexity of the protocol constructions. The SP learns only the base models (i.e., RLCs) and the CSP learns only the weights of the base models and a limited leakage function. This separated parameter holding avoids any party from abusing the final model or conducting model-based attacks. We evaluate …

Creating Real-Time Dynamic Knowledge Graphs, Swati Padhee, Sarasi Lalithsena, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

Augmented Personalized Health: Using Semantically Integrated Multimodal Data For Patient Empowered Health Management Strategies, Amit P. Sheth, Hong Y. Yip, Utkarshani Jaimini, Dipesh Kadariya, Vaikunth Sridharan, R. Venkataramanan, Tanvi Banerjee, Krishnaprasad Thirunarayan, Maninder Kalra

Kno.e.sis Publications

Healthcare as we know it is in the process of going through a massive change from:

1. Episodic to continuous

2. Disease-focused to wellness and quality of life focused

3. Clinic-centric to anywhere a patient is

4. Clinician controlled to patient empowered

5. Being driven by limited data to 360-degree, multimodal personal-public-population physical-cyber-social big data-driven URL: https://mhealth.md2k.org/2018-tech-showcase-home

Towards Practical Privacy-Preserving Analytics For Iot And Cloud Based Healthcare Systems, Sagar Sharma, Keke Chen, Amit P. Sheth

Kno.e.sis Publications

Modern healthcare systems now rely on advanced computing methods and technologies, such as IoT devices and clouds, to collect and analyze personal health data at unprecedented scale and depth. Patients, doctors, healthcare providers, and researchers depend on analytical models derived from such data sources to remotely monitor patients, early-diagnose diseases, and find personalized treatments and medications. However, without appropriate privacy protection, conducting data analytics becomes a source of privacy nightmare. In this paper, we present the research challenges in developing practical privacy-preserving analytics in healthcare information systems. The study is based on kHealth - a personalized digital healthcare information system …

Knowledge-Enabled Personalized Dashboard For Asthma Management In Children, Vaikunth Sridharan, Revathy Venkataramanan, Dipesh Kadariya, Krishnaprasad Thirunarayan, Amit Sheth, Maninder Kalra

Kno.e.sis Publications

Introduction: Childhood Asthma is a significant public health concern worldwide. Effective management of childhood asthma requires close monitoring of disease triggers, medication compliance and symptom control. The recent growth of the Internet of Things (IoT) based devices has enabled continuous monitoring of patients. kHealth-Asthma is a knowledge-enabled semantic framework consisting of IoT enabled sensors to record patient symptoms, medication usage and their environment. For each patient, 29 diverse parameters with 1852 data points are collected daily. kHealthDash platform enables real-time visual analysis at an individual and cohort level over such high volume, high variety data.

Methods: The kHealth kit was …

Iot-Enhanced Human Experience, Amit P. Sheth, Biplav Srivastava, Florian Michahelles

Kno.e.sis Publications

The two articles in this special section represent ongoing Internet of Things applications in the context of Europe trying to make solutions usable to people in daily times.

Metrics For Evaluating Quality Of Embeddings For Ontological Concepts, Faisal Alshargi, Saeedeh Shekarpour, Tommaso Soru, Amit P. Sheth

Kno.e.sis Publications

Although there is an emerging trend towards generating embeddings for primarily unstructured data and, recently, for structured data, no systematic suite for measuring the quality of embeddings has been proposed yet. This deficiency is further sensed with respect to embeddings generated for structured data because there are no concrete evaluation metrics measuring the quality of the encoded structure as well as semantic patterns in the embedding space. In this paper, we introduce a framework containing three distinct tasks concerned with the individual aspects of ontological concepts: (i) the categorization aspect, (ii) the hierarchical aspect, and (iii) the relational aspect. Then, …

"What's Ur Type?" Contextualized Classification Of User Types In Marijuana-Related Communications Using Compositional Multiview Embedding, Ugur Kursuncu, Manas Gaur, Usha Lokala, Anurag Illendula, Krishnaprasad Thirunarayan, Raminta Daniulaityte, Amit P. Sheth, Budak Arpinar

Kno.e.sis Publications

With 93% of pro-marijuana population in US favoring legalization of medical marijuana, high expectations of a greater return for Marijuana stocks, and public actively sharing information about medical, recreational and business aspects related to marijuana, it is no surprise that marijuana culture is thriving on Twitter. After the legalization of marijuana for recreational and medical purposes in 29 states, there has been a dramatic increase in the volume of drug-related communication on Twitter. Specifically, Twitter accounts have been established for promotional and informational purposes, some prominent among them being American Ganja, Medical Marijuana Exchange, and Cannabis Now. Identification and characterization …

Personalized Prediction Of Suicide Risk For Web-Based Intervention, Amanuel Alambo, Manas Gaur, Ugur Kursuncu, Krishnaprasad Thirunarayan, Jeremiah Schumm, Jyotishman Pathak, Amit P. Sheth

Kno.e.sis Publications

Across the United States, suicide is the second leading cause of death for people aged between 15 and 34, and younger people are more prone to mental health problems, suicidal thoughts, and behaviors. For instance, 80% of patients with Borderline Personality Disorder have suicide-related behaviors, and between 4-9% of them commit suicide. Moreover, the social stigma associated with mental health issues and suicide deter patients from sharing their experiences directly with others. In such a situation, social media that provides a free and open forum for voluntary expression can provide insights into suicide ideation and self-destructive behavior.

Reddit is a …

Poster: Image Disguising For Privacy-Preserving Deep Learning, Sagar Sharma, Keke Chen

Kno.e.sis Publications

No abstract provided.

Feasibility Of Recording Sleep Quality And Sleep Duration Using Fitbit In Children With Asthma, Amit Sheth, Hong Y. Yip, Utkarshani Jaimini, Dipesh Kadariya, Vaikunth Sridharan, Revathy Venkataramanan, Tanvi Banerjee, Krishnaprasad Thirunarayan, Maninder Kalra

Kno.e.sis Publications

Sleep disorders are common in children with asthma and are increasingly implicated in poor asthma control. Smart wearables such as the Fitbit wristband allow monitoring of users’ sleep duration and quality in their natural surroundings. However, the utility and efficacy of using such wearable devices to monitor sleep in pediatric patients with asthma have not been well-established. Thus, the objective of this study is to demonstrate the feasibility of recording sleep quality and sleep duration using Fitbit in children with asthma.

Khealth: A Personalized Healthcare Approach For Pediatric Asthma, Utkarshani Jaimini, Hong Y. Yip, Revathy Venkataramanan, Dipesh Kadariya, Vaikunth Sridharan, Tanvi Banerjee, Krishnaprasad Thirunarayan, Maninder Kalra, Amit Sheth

Kno.e.sis Publications

Can we assess the asthma control level, determine vulnerability, and medication compliance for a patient? Can we understand the causal relationship between the asthma symptom and possible factors responsible for it? Can we reduce the number of asthma attacks through continuous monitoring of the patient’s health condition?

“How Is My Child’S Asthma?” Digital Phenotype And Actionable Insights For Pediatric Asthma, Utkarshani Jaimini, Krishnaprasad Thirunarayan, Maninder Kalra, Revathy Venkataramanan, Dipesh Kadariya, Amit Sheth

Kno.e.sis Publications

Background: In the traditional asthma management protocol, a child meets with a clinician infrequently, once in 3 to 6 months, and is assessed using the Asthma Control Test questionnaire. This information is inadequate for timely determination of asthma control, compliance, precise diagnosis of the cause, and assessing the effectiveness of the treatment plan. The continuous monitoring and improved tracking of the child’s symptoms, activities, sleep, and treatment adherence can allow precise determination of asthma triggers and a reliable assessment of medication compliance and effectiveness. Digital phenotyping refers to moment-by-moment quantification of the individual-level human phenotype in situ using data from …

Personalized Health Knowledge Graph, Amelia Gyrard, Manas Gaur, Saeedeh Shekarpour, Krishnaprasad Thirunarayan, Amit Sheth

Kno.e.sis Publications

Our current health applications do not adequately take into account contextual and personalized knowledge about patients. In order to design “Personalized Coach for Healthcare” applications to manage chronic diseases, there is a need to create a Personalized Healthcare Knowledge Graph (PHKG) that takes into consideration a patient’s health condition (personalized knowledge) and enriches that with contextualized knowledge from environmental sensors and Web of Data (e.g., symptoms and treatments for diseases). To develop PHKG, aggregating knowledge from various heterogeneous sources such as the Internet of Things (IoT) devices, clinical notes, and Electronic Medical Records (EMRs) is necessary. In this paper, we …

Khealth Digital Personalized Healthcare Technology For Pediatric Asthma, Utkarshani Jaimini, Hong Y. Yip, Revathy Venkataramanan, Dipesh Kadariya, Vaikunth Sridharan, Tanvi Banerjee, Krishnaprasad Thirunarayan, Maninder Kalra, Amit Sheth

Kno.e.sis Publications

Episodic:Traditional Clinician Centric Healthcare

Questions to be answered:

1.Can we reduce the number of asthma attacks through continuous monitoring of the patient's health condition?

2.Can we predict the asthma attack based on the data collected from the patient?

3.Can we predict the asthma vulnerability score for a patient?

4.Can we predict the asthma severity level of a patient?

5.Can we understand the casual relationship between the asthma symptom and the possible factors responsible for it?

Discovering Explanatory Models To Identify Relevant Tweets On Zika, Roopteja Muppalla, Michele Miller, Tanvi Banerjee, William L. Romine

Kno.e.sis Publications

Zika virus has caught the worlds attention, and has led people to share their opinions and concerns on social media like Twitter. Using text-based features, extracted with the help of Parts of Speech (POS) taggers and N-gram, a classifier was built to detect Zika related tweets from Twitter. With a simple logistic classifier, the system was successful in detecting Zika related tweets from Twitter with a 92% accuracy. Moreover, key features were identified that provide deeper insights on the content of tweets relevant to Zika. This system can be leveraged by domain experts to perform sentiment analysis, and understand the …

A Knowledge Graph Framework For Detecting Traffic Events Using Stationary Cameras, Roopteja Muppalla, Sarasi Lalithsena, Tanvi Banerjee, Amit Sheth

Kno.e.sis Publications

With the rapid increase in urban development, it is critical to utilize dynamic sensor streams for traffic understanding, especially in larger cities where route planning or infrastructure planning is more critical. This creates a strong need to understand traffic patterns using ubiquitous sensors to allow city officials to be better informed when planning urban construction and to provide an understanding of the traffic dynamics in the city. In this study, we propose our framework ITSKG (Imagery-based Traffic Sensing Knowledge Graph) which utilizes the stationary traffic camera information as sensors to understand the traffic patterns. The proposed system extracts image-based features …

Eassistant: Cognitive Assistance For Identification And Auto-Triage Of Actionable Conversations, Hamid R. Motahari Nezhad, Kalpa Gunaratna, Juan Cappi

Kno.e.sis Publications

The browser and screen have been the main user interfaces of the Web and mobile apps. The notification mechanism is an evolution in the user interaction paradigm by keeping users updated without checking applications. Conversational agents are posed to be the next revolution in user interaction paradigms. However, without intelligence on the triage of content served by the interaction and content differentiation in applications, interaction paradigms may still place the burden of information overload on users. In this paper, we focus on the problem of intelligent identification of actionable information in the content served by applications, and in particular in …

What Are People Tweeting About Zika? An Exploratory Study Concerning Its Symptoms, Treatment, Transmission, And Prevention, Michele Miller, Tanvi Banerjee, Roopteja Muppalla, William L. Romine, Amit Sheth

Kno.e.sis Publications

Background: In order to harness what people are tweeting about Zika, there needs to be a computational framework that leverages machine learning techniques to recognize relevant Zika tweets and, further, categorize these into disease-specific categories to address specific societal concerns related to the prevention, transmission, symptoms, and treatment of Zika virus.

Objective: The purpose of this study was to determine the relevancy of the tweets and what people were tweeting about the 4 disease characteristics of Zika: symptoms, transmission, prevention, and treatment.

Methods: A combination of natural language processing and machine learning techniques was used to determine what people were …