Adaptive Double Self-Organizing Map for Clustering Gene Expression Data

This thesis presents a novel clustering technique known as adaptive double self- organizing map (ADSOM) that addresses the issue of identifying the correct number of clusters. ADSOM has a flexible topology and performs clustering and cluster visualization simultaneously, thereby requiring no a priori knowledge about the number of clusters. ADSOM combines features of the popular self-organizing map with two- dimensional position vectors, which serve as a visualization tool to decide the number of clusters. It updates its free parameters during training and it allows convergence of its position vectors to a fairly consistent number of clusters provided that its initial number of nodes is greater than the expected number of clusters. A novel index is introduced based on hierarchical clustering of the final locations of position vectors. The index allows automated detection of the number of clusters, thereby reducing human error that could be incurred from counting clusters visually. The reliance of ADSOM in identifying the number of clusters is proven by applying it to publicly available gene expression data from multiple biological systems such as yeast, human, mouse, and bacteria

MineNav: An Expandable Synthetic Dataset Based on Minecraft for Aircraft Visual Navigation

We propose a simply method to generate high quality synthetic dataset based on open-source game Minecraft includes rendered image, Depth map, surface normal map, and 6-dof camera trajectory. This dataset has a perfect ground-truth generated by plug-in program, and thanks for the large game's community, there is an extremely large number of 3D open-world environment, users can find suitable scenes for shooting and build data sets through it and they can also build scenes in-game. as such, We don't need to worry about manual over fitting caused by too small datasets. what's more, there is also a shader community which We can use to minimize data bias between rendered images and real-images as little as possible. Last but not least, we now provide three tools to generate the data for depth prediction ,surface normal prediction and visual odometry, user can also develop the plug-in module for other vision task like segmentation or optical flow prediction.Comment: 6 pages,10 figure

Artificial non-Abelian lattice gauge fields for photons in the synthetic frequency dimension

Non-Abelian gauge fields give rise to nontrivial topological physics. Here we develop a scheme to create an arbitrary SU(2) lattice gauge field for photons in the synthetic frequency dimension using an array of dynamically modulated ring resonators. The photon polarization is taken as the spin basis to implement the matrix-valued gauge fields. Using a non-Abelian generalization of the Harper-Hofstadter Hamiltonian as a specific example, we show that the measurement of the steady-state photon amplitudes inside the resonators can reveal the band structures of the Hamiltonian, which show signatures of the underlying non-Abelian gauge field. These results provide opportunities to explore novel topological phenomena associated with non-Abelian lattice gauge fields in photonic systems

XScan: An Integrated Tool for Understanding Open Source Community-Based Scientific Code

Many scientific communities have adopted community-based models that integrate multiple components to simulate whole system dynamics. The community software projects’ complexity, stems from the integration of multiple individual software components that were developed under different application requirements and various machine architectures, has become a challenge for effective software system understanding and continuous software development. The paper presents an integrated software toolkit called X-ray Software Scanner (in abbreviation, XScan) for a better understanding of large-scale community-based scientific codes. Our software tool provides support to quickly summarize the overall information of scientific codes, including the number of lines of code, programming languages, external library dependencies, as well as architecture-dependent parallel software features. The XScan toolkit also realizes a static software analysis component to collect detailed structural information and provides an interactive visualization and analysis of the functions. We use a large-scale community-based Earth System Model to demonstrate the workflow, functions and visualization of the toolkit. We also discuss the application of advanced graph analytics techniques to assist software modular design and component refactoring