/Recent content in Home on Hua (Wally) Xie's Digital Outpost [Site In Progress]Hugo -- gohugo.ioen-us/posts/norm-flow-sbm-james/Mon, 11 Aug 2025 00:00:00 +0000/posts/norm-flow-sbm-james/“A Framework for Variational Inference and Data Assimilation of Soil Biogeochemical Models Using Normalizing Flows” Grateful and relieved. The two emotions that come to the fore when I try to name my feelings associated with this “uni-batch flow” (as this project was nicknamed by its collaborators) manuscript getting a cross the publication finish line at last following the inception of the project in mid-2020 in the depths of COVID lockdown. Last year at this time, I estimated a 5% chance this manuscript would ever see the light of publication day, so I’ve had a substantial catharsis dump over the past few days from the fact this got out at all./posts/2023-modeling-book-chapter-in-soil-microbiology-ecology-biochemistry/Sun, 22 Oct 2023 00:00:00 +0000/posts/2023-modeling-book-chapter-in-soil-microbiology-ecology-biochemistry/Less than two months ago, a book chapter summarizing biogeochemical modeling I worked on with my colleagues Elizabeth Duan, Brian Chung, and my PhD advisor Steve Allison was published in fifth edition of Soil Microbiology, Ecology and Biochemistry (Does Elsevier not use Oxford commas?) as the book’s 16th chapter. I had some fun writing this. The book is available here. A draft version of the chapter can also be found in my thesis./posts/quality-journals/Thu, 02 Mar 2023 00:00:00 +0000/posts/quality-journals/In correspondence with my relatively recent hiring at Kite Pharma, I have sought to learn more about the academic sub-field/sub-domain of Quality Engineering by identifying and scanning through journals associated with the parent domain of Quality. Below is a list of active Quality journals that I have encountered. Obviously, I might have missed some. I filtered out a handful journals that were dead or seemed less reputable. Quality Engineering (ASQ and Taylor & Francis) (ASQ-endorsed) Journal of Quality Technology (ASQ and Taylor & Francis) (ASQ-endorsed) Quality Management Journal (ASQ and Taylor & Francis) (ASQ-endorsed) Technometrics (ASQ, ASA, and Taylor & Francis) (ASQ-endorsed) Quality and Reliability Engineering International (Wiley) Stochastics and Quality Control (De Gruyter) Quality Technology & Quantitative Management (International Chinese Association of Quantitative Management and Taylor & Francis) International Journal of Reliability, Quality, and Safety (World Scientific) International Journal of Lean Six Sigma (Emerald)/posts/normalizing-flows-vs-pinns/Thu, 23 Feb 2023 00:00:00 +0000/posts/normalizing-flows-vs-pinns/With both normalizing flows and physics-inspired neural networks (PINNs) finally making their way from machine learning and physics literature to be applied in biogeochemical model inference problems, I found myself recently thinking about the similarities in both approaches. I have arrived at the notions below, with the general sentiment that normalizing flows can almost be thought of as belonging to a more specific, less flexible subset of PINNs, except for a key difference in optimization objectives./posts/gamma-distribution-exponential-family/Wed, 23 Dec 2020 00:00:00 +0000/posts/gamma-distribution-exponential-family/Note: MathJax 3, Hugo, and Netlify just aren’t playing nice for some reason, so pardon any \(\LaTeX\) spillage. A probability distribution function (PDF) is part of the exponential family if it can be arranged into the form $$ f(x|\theta) = h(x)c(\theta)\exp\left(\sum_{i=1}^kw_i(\theta)t_i(x)\right) $$ where \(\theta\) is the vector of parameters. The shape-scale parameterization of the Gamma distribution PDF takes the form $$ f_X(x) = \frac{1}{\Gamma(k)\beta(k)}x^{k-1}e^{-\frac{x}{\beta}} $$ We use \(\beta\) to notate the rate parameter in the shape-rate parameterization of the Gamma PDF, while \(k\) is the symbol for the scale parameter./posts/matrix-diagonalization-to-solve-linear-ode/Wed, 23 Dec 2020 00:00:00 +0000/posts/matrix-diagonalization-to-solve-linear-ode/Here is a link to some brief PDF notes I wrote previously on the older incarnation of my blog about using matrix diagonalization techniques to solve an example linear ordinary differential equation system modeling some population dynamics./posts/bayesian-approach-to-sbm-evaluation-using-ic-and-cv/Mon, 24 Aug 2020 00:00:00 +0000/posts/bayesian-approach-to-sbm-evaluation-using-ic-and-cv/“A Bayesian approach to soil biogeochemical model evaluation [using information criteria and approximate cross-validation]” This one took a while to get out. The project was started in late 2016 as an offshoot of Adriana Romero-Olivares' soil warming meta-analysis detailed in “Soil microbes and their response to experimental warming over time: A meta-analysis of field studies” and was originally meant to be a section of that paper before becoming its own project./posts/min-chef/Fri, 08 May 2020 00:00:00 +0000/posts/min-chef/Min Chef (民厨) is a pseudo-老北京 (Lao Beijing) restaurant that serves quality variants of authentic Northern Chinese food. Edit3: 民厨 has re-opened as of the latter part of September, 2020! They have a humble website that I wish had their menu in Chinese. But, that’s a minor quib. In my less-humble opinion, Min Chef is probably one of the best Chinese restaurants in California (and by extension, Los Estados Unidos). The chef, whose name I should get at some point, puts a personal flair on traditional 老北京 (Lao Beijing) dishes that are familiar as comfort food for blue-collar Beijingers, such as 炸酱面 and 炸灌肠儿 (note the all important 儿)./about/Mon, 01 Jan 0001 00:00:00 +0000/about/General Bio As part of my meandering, I obtained a PhD from the Mathematical, Computational, and Systems Biology program at UCI as a member of the Allison Lab. Work Resume Before I set up camp in computational science, I used to do some filmmaking. Some of my attempts at visual work remain for posterity. Contact You can reach out to me via one of my emails. I am happy to answer questions about my research and work experiences.