Vy Bui

Vy Bui, Hang Yu, Karthik Kantipudi et al.

Backpropagation with gradient descent is a common optimization strategy employed by most neural network architectures in machine learning. However, finding optimal hyperparameters to guide training has proven challenging. While it is widely acknowledged that selecting appropriate parameters is crucial for avoiding overfitting and achieving unbiased outcomes, this choice remains largely based on empirical experiments and experience. This paper presents a new probabilistic framework for the learning rate, a key parameter in stochastic gradient descent. The framework develops classic Bayesian statistics into a double-Bayesian decision mechanism involving two antagonistic Bayesian processes. A theoretically optimal learning rate can be derived from these two processes and used for stochastic gradient descent. Experiments across various classification, segmentation, and detection tasks corroborate the practical significance of the theoretically derived learning rate. The paper also discusses the ramifications of the proposed double-Bayesian framework for network training and model performance.

Thanh Nguyen, Vy Bui, Anh Thai et al.

Fluorescence microscopy plays a vital role in understanding the subcellular structures of living cells. However, it requires considerable effort in sample preparation related to chemical fixation, staining, cost, and time. To reduce those factors, we present a virtual fluorescence staining method based on deep neural networks (VirFluoNet) to transform fluorescence images of molecular labels into other molecular fluorescence labels in the same field-of-view. To achieve this goal, we develop and train a conditional generative adversarial network (cGAN) to perform digital fluorescence imaging demonstrated on human osteosarcoma U2OS cell fluorescence images captured under Cell Painting staining protocol. A detailed comparative analysis is also conducted on the performance of the cGAN network between predicting fluorescence channels based on phase contrast or based on another fluorescence channel using human breast cancer MDA-MB-231 cell line as a test case. In addition, we implement a deep learning model to perform autofocusing on another human U2OS fluorescence dataset as a preprocessing step to defocus an out-focus channel in U2OS dataset. A quantitative index of image prediction error is introduced based on signal pixel-wise spatial and intensity differences with ground truth to evaluate the performance of prediction to high-complex and throughput fluorescence. This index provides a rational way to perform image segmentation on error signals and to understand the likelihood of mis-interpreting biology from the predicted image. In total, these findings contribute to the utility of deep learning image regression for fluorescence microscopy datasets of biological cells, balanced against savings of cost, time, and experimental effort. Furthermore, the approach introduced here holds promise for modeling the internal relationships between organelles and biomolecules within living cells.