Detecting rhythmic spiking through the power spectra of point process model residuals.

Objective: Oscillations figure prominently as neurological disease hallmarks and neuromodulation targets. To detect oscillations in a neuron's spiking, one might attempt to seek peaks in the spike train's power spectral density (PSD) which exceed a flat baseline. Yet for a non-oscillating neuron, the PSD is not flat: The recovery period ("RP", the post-spike drop in spike probability, starting with the refractory period) introduces global spectral distortion. An established "shuffling" procedure corrects for RP distortion by removing the spectral component explained by the inter-spike interval (ISI) distribution. However, this procedure sacrifices oscillation-related information present in the ISIs, and therefore in the PSD. We asked whether point process models (PPMs) might achieve more selective RP distortion removal, thereby enabling improved oscillation detection. Approach: In a novel "residuals" method, we first estimate the RP duration (nr) from the ISI distribution. We then fit the spike train with a PPM that predicts spike likelihood based on the time elapsed since the most recent of any spikes falling within the preceding nr milliseconds. Finally, we compute the PSD of the model's residuals. Main results: We compared the residuals and shuffling methods' ability to enable accurate oscillation detection with flat baseline-assuming tests. Over synthetic data, the residuals method generally outperformed the shuffling method in classification of true- versus false-positive oscillatory power, principally due to enhanced sensitivity in sparse spike trains. In single-unit data from the internal globus pallidus (GPi) and ventrolateral anterior thalamus (VLa) of a parkinsonian monkey -- in which alpha-beta oscillations (8-30 Hz) were anticipated -- the residuals method reported the greatest incidence of significant alpha-beta power, with low firing rates predicting residuals-selective oscillation detection. Significance: These results encourage continued development of the residuals approach, to support more accurate oscillation detection. Improved identification of oscillations could promote improved disease models and therapeutic technologies.

Tailoring time series models for forecasting coronavirus spread: Case studies of 187 countries.

When will the coronavirus end? Are the current precautionary measures effective? To answer these questions it is important to forecast regularly and accurately the spread of COVID-19 infections. Different time series forecasting models have been applied in the literature to tackle the pandemic situation. The current research efforts developed few of these models and validates its accuracy for selected countries. It becomes difficult to draw an objective comparison between the performance of these models at a global scale. This is because, the time series trend for the infection differs between the countries depending on the strategies adopted by the healthcare organizations to decrease the spread. Consequently, it is important to develop a tailored model for a country that allows healthcare organizations to better judge the effect of the undertaken precautionary measures, and provision more efficiently the needed resources to face this disease. This paper addresses this void. We develop and compare the performance of the time series models in the literature in terms of root mean squared error and mean absolute percentage error.

Using machine learning to predict ovarian cancer.

OBJECTIVE: Ovarian cancer (OC) is one of the most common types of cancer in women. Accurately prediction of benign ovarian tumors (BOT) and OC has important practical value. METHODS: Our dataset consists of 349 Chinese patients with 49 variables including demographics, blood routine test, general chemistry, and tumor markers. Machine learning Minimum Redundancy - Maximum Relevance (MRMR) feature selection method was applied on the 235 patients' data (89 BOT and 146 OC) to select the most relevant features, with which a simple decision tree model was constructed. The model was tested on the rest of 114 patients (89 BOT and 25 OC). The results were compared with the predictions produced by using the risk of ovarian malignancy algorithm (ROMA) and logistic regression model. RESULTS: Eight notable features were selected by MRMR, among which two were identified as the top features by the decision tree model: human epididymis protein 4 (HE4) and carcinoembryonic antigen (CEA). Particularly, CEA is a valuable marker for OC prediction in patients with low HE4. The model also yields better prediction result than ROMA. CONCLUSION: Machine learning approaches were able to accurately classify BOT and OC. Our goal is to derive a simple predictive model which also carries a good performance. Using our approach, we obtained a model that consists of just two biomarkers, HE4 and CEA. The model is simple to interpret and outperforms the existing OC prediction methods. It demonstrates that the machine learning approach has good potential in predictive modeling for the complex diseases.

New construction for transversal design.

The study of gene functions requires the development of a DNA library of high quality through much of testing and screening. Pooling design is a mathematical tool to reduce the number of tests for DNA library screening. The transversal design is a special type of pooling design, which is good in implementation. In this paper, we present a new construction for transversal designs. We will also extend our construction to the error-tolerant case.