A Novel Patient Similarity Network (PSN) Framework Based on Multi-Model Deep Learning for Precision Medicine

A Patient Similarity Network (CHDmap) to Predict Outcomes After Congenital Heart Surgery: Development and Validation Study

Background

Although evidence-based medicine proposes personalized care that considers the best evidence, it still fails to address personal treatment in many real clinical scenarios where the complexity of the situation makes none of the available evidence applicable. "Medicine-based evidence" (MBE), in which big data and machine learning techniques are embraced to derive treatment responses from appropriately matched patients in real-world clinical practice, was proposed. However, many challenges remain in translating this conceptual framework into practice.

Objective

This study aimed to technically translate the MBE conceptual framework into practice and evaluate its performance in providing general decision support services for outcomes after congenital heart disease (CHD) surgery.

Methods

Data from 4774 CHD surgeries were collected. A total of 66 indicators and all diagnoses were extracted from each echocardiographic report using natural language processing technology. Combined with some basic clinical and surgical information, the distances between each patient were measured by a series of calculation formulas. Inspired by structure-mapping theory, the fusion of distances between different dimensions can be modulated by clinical experts. In addition to supporting direct analogical reasoning, a machine learning model can be constructed based on similar patients to provide personalized prediction. A user-operable patient similarity network (PSN) of CHD called CHDmap was proposed and developed to provide general decision support services based on the MBE approach.

Results

Using 256 CHD cases, CHDmap was evaluated on 2 different types of postoperative prognostic prediction tasks: a binary classification task to predict postoperative complications and a multiple classification task to predict mechanical ventilation duration. A simple poll of the k-most similar patients provided by the PSN can achieve better prediction results than the average performance of 3 clinicians. Constructing logistic regression models for prediction using similar patients obtained from the PSN can further improve the performance of the 2 tasks (best area under the receiver operating characteristic curve=0.810 and 0.926, respectively). With the support of CHDmap, clinicians substantially improved their predictive capabilities.

Conclusions

Without individual optimization, CHDmap demonstrates competitive performance compared to clinical experts. In addition, CHDmap has the advantage of enabling clinicians to use their superior cognitive abilities in conjunction with it to make decisions that are sometimes even superior to those made using artificial intelligence models. The MBE approach can be embraced in clinical practice, and its full potential can be realized.

Constructing gene similarity networks using co-occurrence probabilities

Gene similarity networks play important role in unraveling the intricate associations within diverse cancer types. Conventionally, gauging the similarity between genes has been approached through experimental methodologies involving chemical and molecular analyses, or through the lens of mathematical techniques. However, in our work, we have pioneered a distinctive mathematical framework, one rooted in the co-occurrence of attribute values and single point mutations, thereby establishing a novel approach for quantifying the dissimilarity or similarity among genes. Central to our approach is the recognition of mutations as key players in the evolutionary trajectory of cancer. Anchored in this understanding, our methodology hinges on the consideration of two categorical attributes: mutation type and nucleotide change. These attributes are pivotal, as they encapsulate the critical variations that can precipitate substantial changes in gene behavior and ultimately influence disease progression. Our study takes on the challenge of formulating similarity measures that are intrinsic to genes' categorical data. Taking into account the co-occurrence probability of attribute values within single point mutations, our innovative mathematical approach surpasses the boundaries of conventional methods. We thereby provide a robust and comprehensive means to assess gene similarity and take a significant step forward in refining the tools available for uncovering the subtle yet impactful associations within the complex realm of gene interactions in cancer.

Empowering Patient Similarity Networks through Innovative Data-Quality-Aware Federated Profiling

Continuous monitoring of patients involves collecting and analyzing sensory data from a multitude of sources. To overcome communication overhead, ensure data privacy and security, reduce data loss, and maintain efficient resource usage, the processing and analytics are moved close to where the data are located (e.g., the edge). However, data quality (DQ) can be degraded because of imprecise or malfunctioning sensors, dynamic changes in the environment, transmission failures, or delays. Therefore, it is crucial to keep an eye on data quality and spot problems as quickly as possible, so that they do not mislead clinical judgments and lead to the wrong course of action. In this article, a novel approach called federated data quality profiling (FDQP) is proposed to assess the quality of the data at the edge. FDQP is inspired by federated learning (FL) and serves as a condensed document or a guide for node data quality assurance. The FDQP formal model is developed to capture the quality dimensions specified in the data quality profile (DQP). The proposed approach uses federated feature selection to improve classifier precision and rank features based on criteria such as feature value, outlier percentage, and missing data percentage. Extensive experimentation using a fetal dataset split into different edge nodes and a set of scenarios were carefully chosen to evaluate the proposed FDQP model. The results of the experiments demonstrated that the proposed FDQP approach positively improved the DQ, and thus, impacted the accuracy of the federated patient similarity network (FPSN)-based machine learning models. The proposed data-quality-aware federated PSN architecture leveraging FDQP model with data collected from edge nodes can effectively improve the data quality and accuracy of the federated patient similarity network (FPSN)-based machine learning models. Our profiling algorithm used lightweight profile exchange instead of full data processing at the edge, which resulted in optimal data quality achievement, thus improving efficiency. Overall, FDQP is an effective method for assessing data quality in the edge computing environment, and we believe that the proposed approach can be applied to other scenarios beyond patient monitoring.

Composition of caching and classification in edge computing based on quality optimization for SDN-based IoT healthcare solutions

This paper proposes a novel approach that uses a spectral clustering method to cluster patients with e-health IoT devices based on their similarity and distance and connect each cluster to an SDN edge node for efficient caching. The proposed MFO-Edge Caching algorithm is considered for selecting the near-optimal data options for caching based on considered criteria and improving QoS. Experimental results demonstrate that the proposed approach outperforms other methods in terms of performance, achieving decrease in average time between data retrieval delays and the cache hit rate of 76%. Emergency and on-demand requests are prioritized for caching response packets, while periodic requests have a lower cache hit ratio of 35%. The approach shows improvement in performance compared to other methods, highlighting the effectiveness of SDN-Edge caching and clustering for optimizing e-health network resources.