TOC {:toc} Objective Build the software environment for Scientific Computing Data Analysis and Deep Learning for a GPU enabled Linux work station. This post majorly summarizes the tools and references for building up a Linux Working Environment. I’ll update the errors and trouble shooting notes as I encounter them.
Jul 25, 2019
DeepLabCut Trouble Shooting @(Ponce Lab) TOC {:toc} Install DLC Windows machine, follow the steps in install tutorial to establish the whole conda environment in the machine. Fail at first step Many of us just fail at first step, some error message like
Jul 2, 2019
Motivation Although there are a millennium of methods for neural and behavioral signal recording, the questions asked about the neural data is ususally less diverse. Ultimately, everything is number and we process numbers with algorithm.
Jul 1, 2019
TOC {:toc} Problem Setting The original problem of non-negative matrix factorization is simple, if the dissimarity $D(A\|HW)$ between original matrix and reconstructed one is L2 distance than, $$ argmin_{H,W} \|A-HW\|_F^2, \\ s.t.\ W\succeq0, H\succeq0 $$The non-negative constraint applies element-wise.
Jun 25, 2019
TOC {:toc} Constrained CMA-ES Algorithm Target CMA-ES is originally used in unconstrained optimization. To adapt it into constrained optimization and we have to handle the boundary in some way. So how could it handle this geometric boundary?
Jun 20, 2019
TOC {:toc} 最近在阅读1，是以为记。 Objective of Algorithm 目标 Belief Propagation算法想解决的是Markov随机场，Bayes网络等图模型的边缘概率估计，以及求解最可能的状态的问题。 有许多名字称呼这一General的算法，如sum-product, max-product, min-sum, Message Passing等，属于更general的Message Passing算法范畴。 同时这一算法可以说是一种通用框架或者philosophy，因此在不同结构的模型中有许多著名的特例，这些具体算法也有各自的名字(如前向后向算法，Kalman Filter等等) 对于统计学习问题，通常会区分模型与算法，模型设定一些假设，抽象现实的某个方面，建立问题的结构；而算法求解问题(很多时候是转化为优化问题来求解)。在这个post中将要介绍的Belief Propagation算法，属于后者，但为了理解他，我们首先需要理解他对应的模型，即概率图模型。 Graphical Models： What relates graph to probability? 第一次接触概率图模型的人（像我）都会问，概率和图这两者有什么关系呢？ 我们知道图是一种直观的表征事物之间二元关系的方法通常由$(\mathcal V, \mathcal E)$定点和边组成。在概率图模型中，顶点通常代表随机变量，而边代表随机变量之间的关系。
May 18, 2019
Larval zebrafish is a tiny vertebrate, really suitable for circuit study, as its translucency. Gross Anatomy Data Zebrafish brain explorer @ Harold Burgess Lab Cell Type Data Comprehensive Identification and Spatial Mapping of Habenular Neuronal Types Using Single-Cell RNA-Seq Standard Brain
Apr 18, 2019
Note on Automatic 3D Instance Segmentation Pipeline In this note I try to summarize several recent works on Automatic 3D Instance Segmentation, with most direct application to saturated reconstruction of neural morphology in an imaging volume (mostly scanning Electral Microscopy, but seems it can be generalized into other imaging modality), which is one of the most important method of high-throughput connectomics1.
Dec 9, 2018
How to automatically analyze behavior video? DeepLabCut is a powerful tool to rapidly1 train a neural network (based on ResNet) to track keypoints on movement videos, esp. those of moving human or animals. Thus this is a game changing tool for all kind of behavior quantification for neuroscience and psychology researchers (can be applied to nearly any behavioral science topic, e.g. motor learning, motor control, facial expression, social interaction…). The workflow is relatively simple and it scarcely takes time after the network have been trained, and the video analysis can be done automatically. Because of this it’s really favorable to the reserchers doing long term ecological video recording.
Nov 17, 2018
Overview Objective: Build a online blog. Most preferably Posts can be written in Markdown, which is the format of most of my notes. Math formula (in Latex syntax) and equation rendering are Solution
Sep 10, 2018