Calibrated prediction intervals for polygenic scores across diverse contexts.

Polygenic scores (PGS) have emerged as the tool of choice for genomic prediction in a wide range of fields. We show that PGS performance varies broadly across contexts and biobanks. Contexts such as age, sex and income can impact PGS accuracy with similar magnitudes as genetic ancestry. Here we introduce an approach (CalPred) that models all contexts jointly to produce prediction intervals that vary across contexts to achieve calibration (include the trait with 90% probability), whereas existing methods are miscalibrated. In analyses of 72 traits across large and diverse biobanks (All of Us and UK Biobank), we find that prediction intervals required adjustment by up to 80% for quantitative traits. For disease traits, PGS-based predictions were miscalibrated across socioeconomic contexts such as annual household income levels, further highlighting the need of accounting for context information in PGS-based prediction across diverse populations.

Robust QRS detection based on simulated degenerate optical parametric oscillator-assisted neural network.

Accurately detecting the depolarization QRS complex in the ventricles is a fundamental requirement for cardiovascular disease detection using electrocardiography (ECG). In contrast to traditional signal enhancement algorithms, emerging neural network approaches have shown promise for QRS detection because of their generalizability on complex data. However, the inevitable noise present during ECG recording leads to a decrease in the performance of neural networks. To enhance the robustness and performance of neural network-based QRS detectors, we propose a simulated degeneration unit (SDU)-assisted convolutional neural network (CNN). An SDU simulates the physical degeneration process of interfering optical pulses, which can effectively suppress in-band noise. Through comprehensive performance evaluations on three open-source databases, the SDU-enhanced CNN-based approach demonstrated better performance in detecting QRS complexes than other recently reported QRS detectors. Furthermore, real-world noise injection tests indicate that the optimal noise robustness boundary for the CNN equipped with SDU is 167-300% higher than that for the CNN without SDU.

Revolutionary Potential of ChatGPT in Constructing Intelligent Clinical Decision Support Systems.

Recently, Chatbot Generative Pre-trained Transformer (ChatGPT) is recognized as a promising clinical decision support system (CDSS) in the medical field owing to its advanced text analysis capabilities and interactive design. However, ChatGPT primarily focuses on learning text semantics rather than learning complex data structures and conducting real-time data analysis, which typically necessitate the development of intelligent CDSS employing specialized machine learning algorithms. Although ChatGPT cannot directly execute specific algorithms, it aids in algorithm design for intelligent CDSS at the textual level. In this study, besides discussing the types of CDSS and their relationship with ChatGPT, we mainly investigate the benefits and drawbacks of employing ChatGPT as an auxiliary design tool for intelligent CDSS. Our findings indicate that by collaborating with human expertise, ChatGPT has the potential to revolutionize the development of robust and effective intelligent CDSS.

Enhancing Performance of Convolutional Neural Network-Based Epileptic Electroencephalogram Diagnosis by Asymmetric Stochastic Resonance.

Epilepsy is a chronic disorder that leads to transient neurological dysfunction and is clinically diagnosed primarily by electroencephalography. Several intelligent systems have been proposed to automatically detect seizures, among which deep convolutional neural networks (CNNs) have shown better performance than traditional machine-learning algorithms. Owing to artifacts and noise, the raw electroencephalogram (EEG) must be preprocessed to improve the signal-to-noise ratio prior to being fed into the CNN classifier. However, because of the spectrum overlapping of uncontrollable noise with EEG, traditional filters cause information loss in EEG; thus, the potential of classifiers cannot be fully exploited. In this study, we propose a stochastic resonance-effect-based EEG preprocessing module composed of three asymmetrical overdamped bistable systems in parallel. By setting different asymmetries for the three parallel units, the inherent noise can be transferred to the different spectral components of the EEG through the asymmetric stochastic resonance effect. In this process, the proposed preprocessing module not only avoids the loss of information of EEG but also provides a CNN with high-quality EEG of diversified frequency information to enhance its performance. By combining the proposed preprocessing module with a residual neural network, we developed an intelligent diagnostic system for predicting seizure onset. The developed system achieved an average sensitivity of 98.96% on the CHB-MIT dataset and 95.45% on the Siena dataset, with a false prediction rate of 0.048/h and 0.033/h, respectively. In addition, a comparative analysis demonstrated the superiority of the developed diagnostic system with the proposed preprocessing module over other existing methods.

Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph.

BACKGROUND: Optical maps record locations of specific enzyme recognition sites within long genome fragments. This long-distance information enables aligning genome assembly contigs onto optical maps and ordering contigs into scaffolds. The generated scaffolds, however, often contain a large amount of gaps. To fill these gaps, a feasible way is to search genome assembly graph for the best-matching contig paths that connect boundary contigs of gaps. The combination of searching and evaluation procedures might be "searching followed by evaluation", which is infeasible for long gaps, or "searching by evaluation", which heavily relies on heuristics and thus usually yields unreliable contig paths. RESULTS: We here report an accurate and efficient approach to filling gaps of genome scaffolds with aids of optical maps. Using simulated data from 12 species and real data from 3 species, we demonstrate the successful application of our approach in gap filling with improved accuracy and completeness of genome scaffolds. CONCLUSION: Our approach applies a sequential Bayesian updating technique to measure the similarity between optical maps and candidate contig paths. Using this similarity to guide path searching, our approach achieves higher accuracy than the existing "searching by evaluation" strategy that relies on heuristics. Furthermore, unlike the "searching followed by evaluation" strategy enumerating all possible paths, our approach prunes the unlikely sub-paths and extends the highly-probable ones only, thus significantly increasing searching efficiency.