Swarm Learning for decentralized and confidential clinical machine learning.
Ontology highlight
ABSTRACT:
SUBMITTER: Warnat-Herresthal S
PROVIDER: S-EPMC8189907 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:In recent years, comprehensive learning particle swarm optimization (CLPSO) has attracted the attention of many scholars for using in solving multimodal problems, as it is excellent in preserving the particles' diversity and thus preventing premature convergence. However, CLPSO exhibits low solution accuracy. Aiming to address this issue, we proposed a novel algorithm called LILPSO. First, this algorithm introduced a Lagrange interpolation method to perform a local search for the global best point (gbest). Second, to gain a better exemplar, one gbest, another two particle's historical best points (pbest) are chosen to perform Lagrange interpolation, then to gain a new exemplar, which replaces the CLPSO's comparison method. The numerical experiments conducted on various functions demonstrate the superiority of this algorithm, and the two methods are proven to be efficient for accelerating the convergence without leading the particle to premature convergence.
| S-EPMC4849747 | biostudies-literature
Project description:Gene expression profiles were generated from 199 primary breast cancer patients. Samples 1-176 were used in another study, GEO Series GSE22820, and form the training data set in this study. Sample numbers 200-222 form a validation set. This data is used to model a machine learning classifier for Estrogen Receptor Status. RNA was isolated from 199 primary breast cancer patients. A machine learning classifier was built to predict ER status using only three gene features.
2013-01-01 | E-GEOD-29210 | biostudies-arrayexpress
Project description:BackgroundTo accelerate healthcare/genomic medicine research and facilitate quality improvement, researchers have started cross-institutional collaborations to use artificial intelligence on clinical/genomic data. However, there are real-world risks of incorrect models being submitted to the learning process, due to either unforeseen accidents or malicious intent. This may reduce the incentives for institutions to participate in the federated modeling consortium. Existing methods to deal with this "model misconduct" issue mainly focus on modifying the learning methods, and therefore are more specifically tied with the algorithm.Basic proceduresIn this paper, we aim at solving the problem in an algorithm-agnostic way by (1) designing a simulator to generate various types of model misconduct, (2) developing a framework to detect the model misconducts, and (3) providing a generalizable approach to identify model misconducts for federated learning. We considered the following three categories: Plagiarism, Fabrication, and Falsification, and then developed a detection framework with three components: Auditing, Coefficient, and Performance detectors, with greedy parameter tuning.Main findingsWe generated 10 types of misconducts from models learned on three datasets to evaluate our detection method. Our experiments showed high recall with low added computational cost. Our proposed detection method can best identify the misconduct on specific sites from any learning iteration, whereas it is more challenging to precisely detect misconducts for a specific site and at a specific iteration.Principal conclusionsWe anticipate our study can support the enhancement of the integrity and reliability of federated machine learning on genomic/healthcare data.
| S-EPMC10017272 | biostudies-literature
Project description:ImportanceThe development of artificial intelligence (AI)-based melanoma classifiers typically calls for large, centralized datasets, requiring hospitals to give away their patient data, which raises serious privacy concerns. To address this concern, decentralized federated learning has been proposed, where classifier development is distributed across hospitals.ObjectiveTo investigate whether a more privacy-preserving federated learning approach can achieve comparable diagnostic performance to a classical centralized (ie, single-model) and ensemble learning approach for AI-based melanoma diagnostics.Design, setting, and participantsThis multicentric, single-arm diagnostic study developed a federated model for melanoma-nevus classification using histopathological whole-slide images prospectively acquired at 6 German university hospitals between April 2021 and February 2023 and benchmarked it using both a holdout and an external test dataset. Data analysis was performed from February to April 2023.ExposuresAll whole-slide images were retrospectively analyzed by an AI-based classifier without influencing routine clinical care.Main outcomes and measuresThe area under the receiver operating characteristic curve (AUROC) served as the primary end point for evaluating the diagnostic performance. Secondary end points included balanced accuracy, sensitivity, and specificity.ResultsThe study included 1025 whole-slide images of clinically melanoma-suspicious skin lesions from 923 patients, consisting of 388 histopathologically confirmed invasive melanomas and 637 nevi. The median (range) age at diagnosis was 58 (18-95) years for the training set, 57 (18-93) years for the holdout test dataset, and 61 (18-95) years for the external test dataset; the median (range) Breslow thickness was 0.70 (0.10-34.00) mm, 0.70 (0.20-14.40) mm, and 0.80 (0.30-20.00) mm, respectively. The federated approach (0.8579; 95% CI, 0.7693-0.9299) performed significantly worse than the classical centralized approach (0.9024; 95% CI, 0.8379-0.9565) in terms of AUROC on a holdout test dataset (pairwise Wilcoxon signed-rank, P < .001) but performed significantly better (0.9126; 95% CI, 0.8810-0.9412) than the classical centralized approach (0.9045; 95% CI, 0.8701-0.9331) on an external test dataset (pairwise Wilcoxon signed-rank, P < .001). Notably, the federated approach performed significantly worse than the ensemble approach on both the holdout (0.8867; 95% CI, 0.8103-0.9481) and external test dataset (0.9227; 95% CI, 0.8941-0.9479).Conclusions and relevanceThe findings of this diagnostic study suggest that federated learning is a viable approach for the binary classification of invasive melanomas and nevi on a clinically representative distributed dataset. Federated learning can improve privacy protection in AI-based melanoma diagnostics while simultaneously promoting collaboration across institutions and countries. Moreover, it may have the potential to be extended to other image classification tasks in digital cancer histopathology and beyond.
| S-EPMC10851139 | biostudies-literature
Project description:INTRODUCTION:Adverse event (AE) under-reporting has been a recurrent issue raised during health authorities Good Clinical Practices (GCP) inspections and audits. Moreover, safety under-reporting poses a risk to patient safety and data integrity. The current clinical Quality Assurance (QA) practices used to detect AE under-reporting rely heavily on investigator site and study audits. Yet several sponsors and institutions have had repeated findings related to safety reporting, and this has led to delays in regulatory submissions. Recent developments in data management and IT systems allow data scientists to apply techniques such as machine learning to detect AE under-reporting in an automated fashion. OBJECTIVE:In this project, we developed a predictive model that enables Roche/Genentech Quality Program Leads oversight of AE reporting at the program, study, site, and patient level. This project was part of a broader effort at Roche/Genentech Product Development Quality to apply advanced analytics to augment and complement traditional clinical QA approaches. METHOD:We used a curated data set from 104 completed Roche/Genentech sponsored clinical studies to train a machine learning model to predict the expected number of AEs. Our final model used 54 features built on patient (e.g., demographics, vitals) and study attributes (e.g., molecule class, disease area). RESULTS:In order to evaluate model performance, we tested how well it would detect simulated test cases based on data not used for model training. For relevant simulation scenarios of 25%, 50%, and 75% under-reporting on the site level, our model scored an area under the curve (AUC) of the receiver operating characteristic (ROC) curve of 0.62, 0.79, and 0.92, respectively. CONCLUSION:The model has been deployed to evaluate safety reporting performance in a set of ongoing studies in the form of a QA/dashboard cockpit available to Roche Quality Program Leads. Applicability and production performance will be assessed over the next 12-24 months in which we will develop a validation strategy to fully integrate our model into Roche QA processes.
| S-EPMC6689279 | biostudies-other
Project description:AI is a broad concept, grouping initiatives that use a computer to perform tasks that would usually require a human to complete. AI methods are well suited to predict clinical outcomes. In practice, AI methods can be thought of as functions that learn the outcomes accompanying standardized input data to produce accurate outcome predictions when trialed with new data. Current methods for cleaning, creating, accessing, extracting, augmenting, and representing data for training AI clinical prediction models are well defined. The use of AI to predict clinical outcomes is a dynamic and rapidly evolving arena, with new methods and applications emerging. Extraction or accession of electronic health care records and combining these with patient genetic data is an area of present attention, with tremendous potential for future growth. Machine learning approaches, including decision tree methods of Random Forest and XGBoost, and deep learning techniques including deep multi-layer and recurrent neural networks, afford unique capabilities to accurately create predictions from high dimensional, multimodal data. Furthermore, AI methods are increasing our ability to accurately predict clinical outcomes that previously were difficult to model, including time-dependent and multi-class outcomes. Barriers to robust AI-based clinical outcome model deployment include changing AI product development interfaces, the specificity of regulation requirements, and limitations in ensuring model interpretability, generalizability, and adaptability over time.
| S-EPMC8786279 | biostudies-literature
Project description:BACKGROUND:Clinical narratives represent the main form of communication within health care, providing a personalized account of patient history and assessments, and offering rich information for clinical decision making. Natural language processing (NLP) has repeatedly demonstrated its feasibility to unlock evidence buried in clinical narratives. Machine learning can facilitate rapid development of NLP tools by leveraging large amounts of text data. OBJECTIVE:The main aim of this study was to provide systematic evidence on the properties of text data used to train machine learning approaches to clinical NLP. We also investigated the types of NLP tasks that have been supported by machine learning and how they can be applied in clinical practice. METHODS:Our methodology was based on the guidelines for performing systematic reviews. In August 2018, we used PubMed, a multifaceted interface, to perform a literature search against MEDLINE. We identified 110 relevant studies and extracted information about text data used to support machine learning, NLP tasks supported, and their clinical applications. The data properties considered included their size, provenance, collection methods, annotation, and any relevant statistics. RESULTS:The majority of datasets used to train machine learning models included only hundreds or thousands of documents. Only 10 studies used tens of thousands of documents, with a handful of studies utilizing more. Relatively small datasets were utilized for training even when much larger datasets were available. The main reason for such poor data utilization is the annotation bottleneck faced by supervised machine learning algorithms. Active learning was explored to iteratively sample a subset of data for manual annotation as a strategy for minimizing the annotation effort while maximizing the predictive performance of the model. Supervised learning was successfully used where clinical codes integrated with free-text notes into electronic health records were utilized as class labels. Similarly, distant supervision was used to utilize an existing knowledge base to automatically annotate raw text. Where manual annotation was unavoidable, crowdsourcing was explored, but it remains unsuitable because of the sensitive nature of data considered. Besides the small volume, training data were typically sourced from a small number of institutions, thus offering no hard evidence about the transferability of machine learning models. The majority of studies focused on text classification. Most commonly, the classification results were used to support phenotyping, prognosis, care improvement, resource management, and surveillance. CONCLUSIONS:We identified the data annotation bottleneck as one of the key obstacles to machine learning approaches in clinical NLP. Active learning and distant supervision were explored as a way of saving the annotation efforts. Future research in this field would benefit from alternatives such as data augmentation and transfer learning, or unsupervised learning, which do not require data annotation.
| S-EPMC7157505 | biostudies-literature
Project description:Conventional microwave imagers usually require either time-consuming data acquisition, or complicated reconstruction algorithms for data post-processing, making them largely ineffective for complex in-situ sensing and monitoring. Here, we experimentally report a real-time digital-metasurface imager that can be trained in-situ to generate the radiation patterns required by machine-learning optimized measurement modes. This imager is electronically reprogrammed in real time to access the optimized solution for an entire data set, realizing storage and transfer of full-resolution raw data in dynamically varying scenes. High-accuracy image coding and recognition are demonstrated in situ for various image sets, including hand-written digits and through-wall body gestures, using a single physical hardware imager, reprogrammed in real time. Our electronically controlled metasurface imager opens new venues for intelligent surveillance, fast data acquisition and processing, imaging at various frequencies, and beyond.
| S-EPMC6403242 | biostudies-other
Project description:Machine learning methods, particularly neural networks trained on large datasets, are transforming how scientists approach scientific discovery and experimental design. However, current state-of-the-art neural networks are limited by their uninterpretability: despite providing accurate predictions, they cannot describe how they arrived at their predictions. Here, using an ``interpretable-by-design'' approach, we present a neural network model that provides insights into RNA splicing, a fundamental process in the transfer of genomic information into functional biochemical products. Although we designed our model to emphasize interpretability, its predictive accuracy is on par with state-of-the-art models. To demonstrate the model's interpretability, we introduce a visualization that, for any given exon, allows us to trace and quantify the entire decision process from input sequence to output splicing prediction. Importantly, the model revealed novel components of the splicing logic, which we experimentally validated. This study highlights how interpretable machine learning can advance scientific discovery.
2022-10-01 | GSE200096 | GEO
Project description:We focused on building models that incorporated transcription factor (TF)-DNA interaction data for 12 members of the Auxin Response Factor (ARF) family from soybean as assessed by DNA Affinity Purification and sequencing (DAP-seq).
2023-06-01 | GSE193400 | GEO