ABSTRACT Background It is important to be able to predict, for each individual patient, the likelihood of later metastatic occurrence, because the prediction can guide treatment plans tailored to a specific patient to prevent metastasis and to help avoid under- or over-treatment. Deep Neural Network (DNN) learning, commonly referred to as deep learning, has become popular due to its success in image detection and prediction, but questions such as whether deep learning outperforms other machine learning methods when using non-image clinical data remain unanswered. Grid search has been introduced to deep learning hyperparameter tunning for the purpose of improving its prediction performance, but the effect of grid search on other machine learning methods are under-studied. In this research, we take the empirical approach to study the performance of deep learning and other machine learning methods when using non-image clinical data to predict the occurrence of breast cancer metastasis (BCM) 5, 10, or 15-years after the initial treatment. We developed DNN models as well as models using 9 other machine learning methods including Naive Bayes (NB), Logistic Regression (LR), Support Vector Machine (SVM), LASSO, Decision Tree (DT), k-Nearest Neighbors (KNN), Random Forrest (RF), AdaBoost (ADB), and XGBoost (XGB). We used grid search to tune hyperparameters for all methods. We then compared the deep learning models to the models trained using the 9 other machine learning methods. Results Based on the mean test AUC results, DNN ranks 6th, 4th, and 3rd when predicting 5-year, 10-year, and 15-year BCM respectively, out of 10 machine learning methods. The top performing methods in predicting 5-year BCM are XGB(1^st), RF(2^nd), and KNN(3^rd). For predicting 10-year BCM the top performers are XGB (1^st), RF(2^nd), and NB(3^rd) . Finally, for 15-year BCM the top performers are SVM (1^st), LR and LASSO (tied for 2^nd), and DNN (3^rd). The ensemble methods RF and XGB outperform other methods when data are less balanced, while SVM, LR, LASSO, and DNN outperform other methods when data are more balanced. Our statistical testing results show that at a significance level of 0.05 DNN overall performs no worse than other machine learning methods when predicting 5-year, 10-year, and 15-year BCM. Conclusions Our results show that deep learning with grid search overall performs at least as well as other machine learning methods when using non-image clinical data. It is interesting to note that some of the other machine learning methods such as XGB, RF, and SVM are very strong competitors of DNN when incorporating grid search. It is also worth noting that the computation time required to do grid search with DNN is way more than that required to do grid search with the other 9 machine learning methods.

ABSTRACT Background Ubiquitination plays an important role in protein post-translational processes and has been found to be involved in a number of regulatory functions including proteasome degradation, DNA repair, transcription, signal transduction, endocytosis, and sorting. As the identification of ubiquitination site is critical to furthering our understanding of the mechanism of ubiquitination, various experimental and machine learning methods have been used to conduct this task. It has been an important but challenging task to improve the accuracy of ubiquitination site prediction. In this research, we explore the possibility of improving the prediction performance of machine learning by incorporating grid search in the training process. Method We developed grid search procedures for each of six widely used machine learning methods including NB, LR, DT, SVM, LASSO, and KNN, and applied them to ubiquitination site prediction using the six PCP datasets that were previously developed. For each of the ML methods, we developed a set of values for each of the tunable hyperparameters available to the method. These sets of values then can be combined to form a large grid of hyperparameter settings, and each of these settings is used in the grid search. We integrated 5-fold cross-validation in grid search to train and test ML models and applied an additional independent validation procedure by conducting a pre-training 80-20 sample split. We evaluated the performance of the six methods by comparing them side by side for each of the six datasets. We also compared the grid search results with the results that were previously published without doing grid search. To optimize the prediction performance, we trained 1.1 million ML models in total through grid search. Results We compared the overall prediction performance of these six methods, as well as their prediction performance when working with balanced vs. imbalanced data, and large-scale vs. small-scale data. From the perspective of dataset, we find that the overall performance of every PCP dataset has been significantly improved in this study compared to the previous study, with the percentage increase of the average AUC of all six datasets ranging from 7.9% (PCP-4) up to 17.0% (PCP-1). From the perspective of method, we find that three out of four methods significantly benefit from grid search comparing to their previously published non-grid search results, with the maximum AUC improvement as high as 47% (LASSO on PCP-5), 43.3% (NB on PCP-1), and 33.7% (SVM on PCP-6). SVM overall ranks number one, followed by KNN as the number two performer based on their average AUCs on all datasets. But these two also ranked the top two (KNN 76 days and SVM 15 days) in terms of the total running time that they need to do grid search. We also find that SVM, KNN, and DT tend to handle small-scale and imbalanced datasets better, while LR, and LASSO are doing well with large-scale and balanced datasets. NB is more sensitive to data imbalance while less sensitive to the size of a dataset. Conclusions Our results show that using grid search has improved the performance of ubiquitination prediction significantly. We find that the performance of a method is closely related to its hyperparameter setting and the type of data it handles. Even though SVM is on average an outperformer, none of the methods can provide the best performance for all datasets. When sufficient computing resources are well accessible, grid search is an effective way to identify both a top performing model for a machine learning method and a suitable machine learning method for a particular dataset.

Background: Risk of metastatic recurrence of breast cancer after initial diagnosis and treatment depends on the presence of a number of risk factors. Although most univariate risk factors have been identified using classical methods, machine-learning methods are also being conducted to tease out non-obvious contributors to a patient’s individual risk of developing late distant metastasis. Bayesian-network algorithms may predict not only risk factors but also interactions among these risks, which consequently lead to metastatic breast cancer. We proposed to apply a previously developed machine-learning method to predict risk factors of 5-, 10- and 15-year metastasis. Methods: We applied a previously validated algorithm named the Markov Blanket and Interactive risk factor Learner (MBIL) on the electronic health record (EHR)-based Lynn Sage database (LSDB) from the Lynn Sage Comprehensive Breast Cancer at Northwestern Memorial Hospital. This algorithm provided an output of both single and interactive risk factors of 5-, 10-, and 15-year metastasis from LSDB. We individually examined and interpreted the clinical relevance of these interactions based on years to metastasis and the reliance on interactivity between risk factors. Results: We found that with lower alpha values (low interactivity score), the prevalence of variables with an independent influence on long term metastasis was higher (i.e., HER2, TNEG). As the value of alpha increased to 480, stronger interactions were needed to define clusters of factors that increased the risk of metastasis (i.e., ER, smoking, race, alcohol usage). Conclusion: MBIL identified single and interacting risk factors of metastatic breast cancer, many of which were supported by clinical evidence. These results strongly recommend the development of further large data studies with different databases to validate the degree to which some of these variables impact metastatic breast cancer in the long term.

Adult neurogenesis involves generation of functional neurons from neural progenitor cells, which have the potential to complement and restore damaged neurons and neural circuits. Therefore, the development of drugs that stimulate neurogenesis represents a promising strategy in stem cell therapy and neural regeneration, greatly facilitating the reconstruction of neural circuits in cases of neurodegeneration and brain injury. Our study reveals that compound A5, previously designed and synthesized by our team, exhibits remarkable neuritogenic activities, effectively inducing neurogenesis in neural stem/progenitor cells (NSPCs). Subsequently, transcriptome analysis using high-throughput Illumina RNA-seq technology was performed to further elucidate the underlying molecular mechanisms by which compound A5 promotes neurogenesis. Notably, comparative transcriptome analysis showed that the up-regulated genes were mainly associated with neurogenesis and the down-regulated genes were mainly concerned with cell cycle progression. Furthermore, we confirmed that compound A5 significantly affected the expression of transcription factors related to neurogenesis and cell cycle regulatory proteins. Collectively, these findings identify a new compound with neurogenic activity and may provide insights into drug discovery for neural repair and regeneration.

Neurogenesis in the adult brain plays a major role in the cognitive ability of animals including learning and memory. Poria cocos (Schw.) Wolf (P. cocos) has been known as a traditional Chinese edible medicinal herb with the potential effect to improve learning and memory. However, the effect mechanisms are still elusive. In this study, significant neuronal differentiation-promoting activities of the ethanol extracts of P. cocos (EEPC) were tested in Neuro-2a cells and mouse cortical neural stem/progenitor cells (NSPCs). Subsequently, 97 compounds of EEPC were identified using UHPLC-Q-Exactive-MS/MS. After investigation of neuronal differentiation-promoting activities of 4 major compounds (Ethyl palmitoleate, L-(-)-Arabitol, Choline and Adenosine), only Choline has significant neuronal differentiation-promoting activity. In summary, we investigated the neuronal differentiation-promoting activity and chemical compositions of EEPC, the study of the neuronal differentiation-promoting effect of ether extract of P. cocos indicated P. cocos’s positive effect on learning and memory functions. This is the first investigation of the neuronal differentiation-promoting effect of ether extract of P. cocos based on similar research references.