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Software Architecture

Contents - Infrastructural Aspects of Software Component (in association with Robot)
   (1) Device Interface
   (2) Waveform Analyses
   (3) Hemodynamics
   (4) Medical Statistics
   (5) Machine Learning
- Projects in association with Software Architecture
- License Policy in the Long-Term Future

Infrastructural Aspects of Software Component top

Each component will be the basis upon which other components can be built. This circulative data flow in the architecture diagram will eventually contribute to the development of other components synergistically. In other words, when considering the final overall goal of this software project as facilitating the data flow according to the software architecture, one part of the development will benefit the other part of the research.

The hemodynamic workbench software will be implemented to provide the following infrastructural functionalities: (1) To receive signals from the hemodynamic instrument; (2) To extract necessary information by wavelet analyses; (3) To understand the data according to the hemodynamic model and simulation; (4) To provide medical statistics; (5) To perform an action by reinforcement of the learning process.

(1) Device Interface top

Device driver interface component will enable the software to access raw data directly from a device. Biomedical companies seem to welcome the idea of enabling third parties to write software for their devices, which is exemplified by 3M providing an SDK (Software Development Kit) to allow people to write software for its Bluetooth stethoscope. However, my ultimate goal will be to make one step further by implementing the kernel-level device driver that would connect devices more fundamentally (as compared to existing SDK) and, therefore, to establish an integrative and flexible hemodynamic workbench.
    Some EKG classification articles (Lee, 2013) (Lihuang, 2010) relied exclusively on the MIT-BIH arrhythmia database or the standard test material to evaluate their arrhythmia detection algorithms. However, to the best of our knowledge, the difficulty of acquiring additional new raw EKG dataset due to the absence of open-source device interface for EKG instrument may be at least partially attributed to those researchers's having to work exclusively on MIT-BIH arrhythmia database. Therefore, if this software can receive the EKG raw stream over a WiFi or USB connection from instruments, future engineers can acquire additional test materials by collecting further raw EKG data alongside with corresponding EKG diagnoses, directly.
    Nonetheless, companies would be cautious about opening their device protocols for my implementing the kernel-level device interface, since doing so might change the company's marketing strategies and policies. Therefore, continuous improvement of Project nGene.org® in the long-term to gain agreement concerning its clinical pragmatism and to embrace clinicians' needs by providing an easy-to-write environment for their own scripts will have to be prioritized over this kernel component.

(2) Waveform Analyses top

"(2) Waveform Analyses" component pre-processes the raw wavelet data directly from the devices via the "(1) Device interface" component. In order to handle the raw wavelet dataset, such as EKG, lung and heart sounds, etc., two core algorithms have been chosen to be common denominating features: Independent Component Analysis (ICA) separates the mixed wavelets, whereas Support Vector Machine (SVM) classifies things after being trained.
    Its benefit can be illustrated by how this feature may change the existing flow. These machine-learning components can be used tentatively, until a more precise implementation of the classification for wavelets is implemented later in the point of time. For example, machine-learning algorithms for classifying EKG would be no match for a manually-written conditional statements implemented according to the Sokolow-Lyon Criteria for left ventricular hypertrophy (LVH) (Sokolow, 1949), as it would be nonsensical for training SVM to distinguish whether the summation of the S wave in V1 and the R wave in V5 or V6 is greater than, specifically, 35mm or not for LVH. However, until the manually-implemented code is developed according to certain criteria, it may be better to employ machine-learning features to accommodate wavelets in order to accelerate research and development in the meanwhile.
    For an example of embedding this software into the educational CPR kit mentioned above, the AED (Automated External Defibrillation) algorithm requires distinguishing normal EKG from various arrhythmia cases. However, since the MIT-BIH "arrhythmia" database does not have normal EKG dataset, the "(1) Device Interface" component can be used to collect a normal EKG raw dataset. Once normal EKG data with diagnoses are accumulated, then the SVM algorithm can be trained to classify whether it should be defibrillated, synchronized cardioversion, non-shockable, and normal, until the development of a more accurate manually-programmed classifying algorithm.

(3) Hemodynamics top

Project nGene.org® intends to facilitate research on the hemodynamic model, not only to better understand the physiology, and but also to gain further insights into improving the model. There are numerous equations published already and in the future and it may be too late if we just wait for the echocardiography manufacturing engineer to implement the module for the equation we need. Unless it is open-sourced, it cannot possibly follow the speed of insights during research. Yale Neuron is open-sourced with GUI for simulating neuron network; however, in my opinion, no matter how flexibly a software architect may implement its GUI, it cannot be on a par with the flexibility and creativity of new equations and insights of clinicians in the future.
    Therefore, Project nGene.org® tries to circumvent this problem by integrating R script so that clinicians can add their equations to test those features during echocardiographic measurements on the flies. At the same time, I believe that the success of earning popularity depends on how easy and generic it is for clinicians to add and modify the source code. Since clinicians do not have time to spend on learning, it is very important to make it very intuitive to make them willing to invest their time. I think that clinicians will invest their time only if they can get it intuitively.

(4) Medical Statistics & (5) Machine Learning top

"(4) Medical Statistics" is something that I do, not as a destination, but as a necessary step. To put it straightforwardly, the ultimate goal is "(5) Machine Learning". "(5) Machine Learning" component is pushed back on the priority list in the Masterplan Chart, because the software is designed to provide the following different types of dataset for the machine-learning algorithms: (i) Directly from hardware via the kernel program part, "(1) Device Interface"; (ii) Indirectly processing the wavelets raw data from instruments, "(2) Waveform Analyses"; (iii) Parsing and processing articles, especially meta-analysis and survival curve data, "(4) Medical Statistics", via a semantic web.
    The semantic web is a very suitable piece for medicine due to several reasons: (1) It is very flexible to integrate other semantic webs together, such that it can be used as a knowledge database with numerical information. (2) This numerical information with a network form can be fed into Bayesian-based machine learning. (3) Meta-Analysis is one of the forms of very specialized information that are available in the domain of medicine, and getting the hazard ratio from the survival curve for meta-analysis was, in my opinion, the most difficult methodology and the most challenging technical barrier when building a semantic web database.

Projects in association with Software Architecture top

This masterplan chart illustrates where each study finds a place in the attempts to implement the hemodynamic software. Each component of the software architecture represents a horizontal layer for corresponding individual projects which are illustrated with inter-dependencies across different layers. Please note that there are two big themes of this software, which are kernel programming and artificial intelligence. Research and theses will have been tightly intertwined with hemodynamics, as illustrated in the masterplan chart.

[Molecular Biology] Protocol to evaluate infection level by ECMO

(1) A previous study (Kurundkar, 2010)

LTA detected by Western blot over time incurred by ECMO

(2) Frank's Protocol.io (2015)

[Programming] a Python-based tool to measure Echocardiographic Indices (2016)

Measuring and Analyzing Echocardiographic Hemodynamic Indices (Prototype)

EchoRuler.py is a python script designed to measure the time and distance on the printouts from echocardiography. Instead of using a physical ruler, this software takes the scanned image of the echocardiographic printout, performs the calibration for time and distance initially, and then computes the actual time and distances per calibrations in return.

Illustration of computing the actual distances considering the concentric distance field by EchoRuler.py:

With respect to the LV eccentricity index, two diameters on the left ventricular cavity can be drawn at the level of the papillary muscle, for which EchoRuler.py will compute the actual distances considering the concentric distance field. Similarly, regarding the acceleration time, you can draw a line to measure the acceleration time, ejection time, and RR-interval.

[Meta-Analysis] Survival benefits of pulmonary resection for tuberculosis (2017)

[Meta-Analysis] Robotic vs laparoscopic surgery (2018)

Roh HF, Nam SH, Kim JM (2018) Robot-assisted laparoscopic surgery versus conventional laparoscopic surgery in randomized controlled trials: A systematic review and meta-analysis. PLoS ONE 13(1): e0191628. https://doi.org/10.1371/journal.pone.0191628 © 2018 Roh et al.

[Hemodynamics] A logistic-based systolic model for a pulmonary circulation (2018)

Induced (1) Logistic-based systolic model on pulmonary circulation

Proposed (2) for PAP estimation by PAcT of Echocardiography

Its relevant material: (3) Hemodynamic simulator (Prototype in 2016)

[Programming] Wavelet analyses on raw datasets (2019)

Independent Component Analysis (ICA) - Actual sample output

The ICA algorithm had been demonstrated to separates mixed sounds from lung and heart sounds upon chest auscultation (Chien, 2006), and fetal and maternal heart sounds upon fetal auscultation (Porcaro, 2006). This infrastructural package includes a whole source code for this procedure where two randomly chosen real heart sounds from "Heart Sound & Murmur Library" webpage are mixed and then separated, accordingly:

Support Vector Machine (SVM) for EKG - Actual sample output

The SVM algorithm classifies LVH, RVH, and QT elongation of multiple EKG categories. After the SVM algorithm is trained to learn EKG categories based upon min and max voltage and QT duration (time), the algorithm is asked to classify new EKG cases into one of those categories learned beforehand, whose output will be displayed in a two-dimensional space using Multi-Dimensional Scaling (MDS).

[Meta-Analysis] ECMO of time-to-event data in cardiopulmonary disease in adults (2020)

License Policy in the Long-Term Future top

This software has not been designed as an end-product, but will be eventually implemented to be "an infrastructure" on which other people can write their own programming scripts. However, so far, its license policy to host and adopt a third party's published source code modification on Project nGene.org® has been rather limited, since Project nGene.org® has its own long-term milestones, and having manpower to handle and manage other works may increase inner-communication complexity and confusion. In the future, Project nGene.org® would be developed and determined to be ready to embrace the work of clinicians and engineers. Then, its policy will then be modified to more openly accommodate a third party's contribution.


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Project nGene.org® is a registered trademark.