All-People-Test-Based Methods for COVID-19 Infectious Disease Dynamics Simulation Model: Towards Citywide COVID Testing.

The conversion rate between asymptomatic infections and reported/unreported symptomatic infections is a very sensitive parameter for model variables that spread COVID-19. This is important information for follow-up use in screening, prediction, prognostics, contact tracing, and drug development for the COVID-19 pandemic. The model described here suggests that there may not be enough researchers to solve all of these problems thoroughly and effectively, and it requires careful selection of what we are doing and rapid sharing of results and models and optimizing modeling simulations with value to reduce the impact of COVID-19. Exploring simulation modeling will help decision makers make the most informed decisions. In order to fight against the "Delta" virus, the establishment of a line of defense through all-people testing (APT) is not only an effective method summarized from past experience but also one of the best means to effectively cut the chain of epidemic transmission. The effect of large-scale testing has been fully verified in the international community. We developed a practical dynamic infectious disease model-SETPG (A + I) RD + APT by considering the effects of the all-people test (APT). The model is useful for studying effects of screening measures and providing a more realistic modelling with all-people-test strategies, which require everybody in a population to be tested for infection. In prior work, a total of 370 epidemic cases were collected. We collected three kinds of known cases: the cumulative number of daily incidences, daily cumulative recovery, and daily cumulative deaths in Hong Kong and the United States between 22 January 2020 and 13 November 2020 were simulated. In two essential strategies of the integrated SETPG (A + I) RD + APT model, comparing the cumulative number of screenings in derivative experiments based on daily detection capability and tracking system application rate, we evaluated the performance of the timespan required for the basic regeneration number (R0) and real-time regeneration number (R0t) to reach 1; the optimal policy of each experiment is available, and the screening effect is evaluated by screening performance indicators. with the binary encoding screening method, the number of screenings for the target population is 8667 in HK and 1,803,400 in the U.S., including 6067 asymptomatic cases in HK and 1,262,380 in the U.S. as well as 2599 cases of mild symptoms in HK and 541,020 in the U.S.; there were also 8.25 days of screening timespan in HK and 9.25 days of screening timespan required in the U.S. and a daily detectability of 625,000 cases in HK and 6,050,000 cases in the U.S. Using precise tracking technology, number of screenings for the target population is 6060 cases in HK and 1,766,420 cases in the U.S., including 4242 asymptomatic cases in HK and 1,236,494 cases in the U.S. as well as 1818 cases of mild symptoms in HK and 529,926 cases in the U.S. Total screening timespan (TS) is 8.25~9.25 days. According to the proposed infectious dynamics model that adapts to the all-people test, all of the epidemic cases were reported for fitting, and the result seemed more reasonable, and epidemic prediction became more accurate. It adapted to densely populated metropolises for APT on prevention.

Envisioning Insight-Driven Learning Based on Thick Data Analytics With Focus on Healthcare.

Detecting and analyzing patient insights from social media enables healthcare givers to better understand what patients want and also to identify their pain points. Healthcare institutions cannot neglect the need to monitor and analyze popular social media outlets such as Twitter and Facebook. To have a study success, a healthcare giver needs to be able to engage with their patients and adapt to their preferences effectively. However, data-driven decision-making is no longer enough, as the best-in-class organizations struggle to realize tangible benefits from their data-driven analytics investments. Relying on simplistic textual analytics that use big data technologies to learn consumer/patient insights is no longer sufficient as most of these analytics utilize sort of bag-of-words counting algorithms. The majority of projects utilizing big data analytics have failed due to the obsession with metrics at the expense of capturing the customer's perspective data, as well as the failure in turning consumer insights into actions. Most of the consumer insights can be captured with qualitative research methods that work with small, even statistically insignificant, sample sizes. Employing qualitative analytics provide some kind of actionable intelligence which acquires understanding to broad questions about the consumer needs in tandem with analytical power. Generating insight, on one hand, requires sound techniques to measure consumers' engagement more precisely and offers depth analytics to the consumer data story. On the other hand, turning relevant insights into actions requires incorporating actionable intelligence across the business by verify hypotheses based on qualitative findings by using web analytics to see if these axioms apply to a large number of customers. The first component of our visionary approach is dedicated to identifying the relationships between constituents of the healthcare pain points as echoed by the social media conversation in terms of sociographic network where the elements composing these conversations are described as nodes and their interactions as links. In this part, conversation groups of nodes that are heavily connected will be identified representing what we call conversation communities. By identifying these conversation communities several consumer hidden insights can be inferred from using techniques such as visualizing conversation graphs relevant to given pain point, conversation learning from question answering, conversations summaries, conversation timelines, conversation anomalies and other conversation pattern learning techniques. These techniques will identify and learn the patient insights without forgetting from the context of conversation communities, are tagged as "thick data analytics". Additionally machine learning methods can be used as assistive techniques to learn from the identified thick data and build models around identified thick data. With the use of transfer learning we also can fine tune these models with the arrival of new conversations. The author is currently experimenting with these seven insights driven learning methods described in this paper with massive geo-located Twitter data to infer the quality of care related to the current COVID-19 outbreak.

Pathogen-Host Analysis Tool (PHAT): an integrative platform to analyze next-generation sequencing data.

SUMMARY: The Pathogen-Host Analysis Tool (PHAT) is an application for processing and analyzing next-generation sequencing (NGS) data as it relates to relationships between pathogens and their hosts. Unlike custom scripts and tedious pipeline programming, PHAT provides an integrative platform encompassing raw and aligned sequence and reference file input, quality control (QC) reporting, alignment and variant calling, linear and circular alignment viewing, and graphical and tabular output. This novel tool aims to be user-friendly for life scientists studying diverse pathogen-host relationships. AVAILABILITY AND IMPLEMENTATION: The project is available on GitHub (https://github.com/chgibb/PHAT) and includes convenient installers, as well as portable and source versions, for both Windows and Linux (Debian and RedHat). Up-to-date documentation for PHAT, including user guides and development notes, can be found at https://chgibb.github.io/PHATDocs/. We encourage users and developers to provide feedback (error reporting, suggestions and comments).

Adaptive Swarm Balancing Algorithms for rare-event prediction in imbalanced healthcare data.

Clinical data analysis and forecasting have made substantial contributions to disease control, prevention and detection. However, such data usually suffer from highly imbalanced samples in class distributions. In this paper, we aim to formulate effective methods to rebalance binary imbalanced dataset, where the positive samples take up only the minority. We investigate two different meta-heuristic algorithms, particle swarm optimization and bat algorithm, and apply them to empower the effects of synthetic minority over-sampling technique (SMOTE) for pre-processing the datasets. One approach is to process the full dataset as a whole. The other is to split up the dataset and adaptively process it one segment at a time. The experimental results reported in this paper reveal that the performance improvements obtained by the former methods are not scalable to larger data scales. The latter methods, which we call Adaptive Swarm Balancing Algorithms, lead to significant efficiency and effectiveness improvements on large datasets while the first method is invalid. We also find it more consistent with the practice of the typical large imbalanced medical datasets. We further use the meta-heuristic algorithms to optimize two key parameters of SMOTE. The proposed methods lead to more credible performances of the classifier, and shortening the run time compared to brute-force method.

Robust High-dimensional Bioinformatics Data Streams Mining by ODR-ioVFDT.

Outlier detection in bioinformatics data streaming mining has received significant attention by research communities in recent years. The problems of how to distinguish noise from an exception and deciding whether to discard it or to devise an extra decision path for accommodating it are causing dilemma. In this paper, we propose a novel algorithm called ODR with incrementally Optimized Very Fast Decision Tree (ODR-ioVFDT) for taking care of outliers in the progress of continuous data learning. By using an adaptive interquartile-range based identification method, a tolerance threshold is set. It is then used to judge if a data of exceptional value should be included for training or otherwise. This is different from the traditional outlier detection/removal approaches which are two separate steps in processing through the data. The proposed algorithm is tested using datasets of five bioinformatics scenarios and comparing the performance of our model and other ones without ODR. The results show that ODR-ioVFDT has better performance in classification accuracy, kappa statistics, and time consumption. The ODR-ioVFDT applied onto bioinformatics streaming data processing for detecting and quantifying the information of life phenomena, states, characters, variables and components of the organism can help to diagnose and treat disease more effectively.

WITHDRAWN: Improving classification of protein binders for virtual drug screening by novel swarm-based feature selection techniques.

This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.

WITHDRAWN: Clinical pathways inference from decision rules by hybrid stream mining and fuzzy unordered rule induction strategy.

This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.

WITHDRAWN: Adaptive Swarm Balancing Algorithms for rare-event prediction in imbalanced healthcare data.

This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.

Evaluation of stream mining classifiers for real-time clinical decision support system: a case study of blood glucose prediction in diabetes therapy.

Earlier on, a conceptual design on the real-time clinical decision support system (rt-CDSS) with data stream mining was proposed and published. The new system is introduced that can analyze medical data streams and can make real-time prediction. This system is based on a stream mining algorithm called VFDT. The VFDT is extended with the capability of using pointers to allow the decision tree to remember the mapping relationship between leaf nodes and the history records. In this paper, which is a sequel to the rt-CDSS design, several popular machine learning algorithms are investigated for their suitability to be a candidate in the implementation of classifier at the rt-CDSS. A classifier essentially needs to accurately map the events inputted to the system into one of the several predefined classes of assessments, such that the rt-CDSS can follow up with the prescribed remedies being recommended to the clinicians. For a real-time system like rt-CDSS, the major technological challenges lie in the capability of the classifier to process, analyze and classify the dynamic input data, quickly and upmost reliably. An experimental comparison is conducted. This paper contributes to the insight of choosing and embedding a stream mining classifier into rt-CDSS with a case study of diabetes therapy.

Real-time clinical decision support system with data stream mining.

This research aims to describe a new design of data stream mining system that can analyze medical data stream and make real-time prediction. The motivation of the research is due to a growing concern of combining software technology and medical functions for the development of software application that can be used in medical field of chronic disease prognosis and diagnosis, children healthcare, diabetes diagnosis, and so forth. Most of the existing software technologies are case-based data mining systems. They only can analyze finite and structured data set and can only work well in their early years and can hardly meet today's medical requirement. In this paper, we describe a clinical-support-system based data stream mining technology; the design has taken into account all the shortcomings of the existing clinical support systems.