Role of Optimization in RNA-Protein-Binding Prediction.

RNA-binding proteins (RBPs) play an important role in regulating biological processes, such as gene regulation. Understanding their behaviors, for example, their binding site, can be helpful in understanding RBP-related diseases. Studies have focused on predicting RNA binding by means of machine learning algorithms including deep convolutional neural network models. One of the integral parts of modeling deep learning is achieving optimal hyperparameter tuning and minimizing a loss function using optimization algorithms. In this paper, we investigate the role of optimization in the RBP classification problem using the CLIP-Seq 21 dataset. Three optimization methods are employed on the RNA-protein binding CNN prediction model; namely, grid search, random search, and Bayesian optimizer. The empirical results show an AUC of 94.42%, 93.78%, 93.23% and 92.68% on the ELAVL1C, ELAVL1B, ELAVL1A, and HNRNPC datasets, respectively, and a mean AUC of 85.30 on 24 datasets. This paper's findings provide evidence on the role of optimizers in improving the performance of RNA-protein binding prediction.

Adaptive infrared patterns for microscopic surface reconstructions.

PURPOSE: Multi-zoom microscopic surface reconstructions of operating sites, especially in ENT surgeries, would allow multimodal image fusion for determining the amount of resected tissue, for recognizing critical structures, and novel tools for intraoperative quality assurance. State-of-the-art three-dimensional model creation of the surgical scene is challenged by the surgical environment, illumination, and the homogeneous structures of skin, muscle, bones, etc., that lack invariant features for stereo reconstruction. METHODS: An adaptive near-infrared pattern projector illuminates the surgical scene with optimized patterns to yield accurate dense multi-zoom stereoscopic surface reconstructions. The approach does not impact the clinical workflow. The new method is compared to state-of-the-art approaches and is validated by determining its reconstruction errors relative to a high-resolution 3D-reconstruction of CT data. RESULTS: 200 surface reconstructions were generated for 5 zoom levels with 10 reconstructions for each object illumination method (standard operating room light, microscope light, random pattern and adaptive NIR pattern). For the adaptive pattern, the surface reconstruction errors ranged from 0.5 to 0.7 mm, as compared to 1-1.9 mm for the other approaches. The local reconstruction differences are visualized in heat maps. CONCLUSION: Adaptive near-infrared (NIR) pattern projection in microscopic surgery allows dense and accurate microscopic surface reconstructions for variable zoom levels of small and homogeneous surfaces. This could potentially aid in microscopic interventions at the lateral skull base and potentially open up new possibilities for combining quantitative intraoperative surface reconstructions with preoperative radiologic imagery.