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Paul Harrison

@paulfharrison.bsky.social
459 followers 128 following 101 posts

Bioinformatician at Monash University, Melbourne, Australia. I also use mastodon: @pfh@mastondon.online mastodon.online/@pfh My homepage is: logarithmic.net/pfh On Twitter I was: @paulfharrison

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Paul Harrison @paulfharrison.bsky.social · 20/09/2026
Saw an interesting video of a Go player analyzing an AlphaGo Zero game. He didn't much care for it, as the play style was incomprehensible. He was however more satisfied by a game by a more recent and superior Go engine. So human incomprehensibility seems to have at most marginal benefit to Go play.
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Paul Harrison @paulfharrison.bsky.social · 24/08/2026
x <- c(rep(0,19),1) cor.test(x,x, method="...something rank-based and exact...") Surely the p value is no smaller than 1/20, but I have tried a variety of packages and they are all hopelessly optimistic. :-(
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Frank Harrell @f2harrell.bsky.social · 23/06/2026
#Statistics thought of the day: At the heart of much nonsense research lies data analysis (including machine learning) of a complexity that the effective sample size cannot support: hbiostat.org/hdata #StatsSky
hbiostat.org
Challenges of High-Dimensional Data Analysis
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Paul Harrison @paulfharrison.bsky.social · 10/06/2026
I'm greatly appreciating this series of videos about biological modelling with Karthik Raman. I started with the flux-balance models, but now I'm going back to the beginning. www.youtube.com/playlist?lis...
youtube.com
Computational Systems Biology | IIT Madras - YouTube
"This lecture series, part of the ""Computational Systems Biology"" course, focuses on the mathematical modeling of biological systems. It introduces various...
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Wolfgang Huber @wkhuber.bsky.social · 29/05/2026
Thanks to input from @helucro.bsky.social, Daria Lazic, Hugo Gruson, Artür Manukyan and many others, there is now a whole new level of maturity and ease-of-use for spatial omics data, see helenalc.github.io/SpatialData....
helenalc.github.io
csama – SpatialData
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Paul Harrison @paulfharrison.bsky.social · 04/05/2026
"The cow is homeostatic for blood-temperature ... If, however, a sensitive temperature-recorder be inserted in the brain and then a stream of ice-cold air driven past the animal the temperature rises without any preliminary fall." The cow must have a model. pespmc1.vub.ac.be/books/Conant...
pespmc1.vub.ac.be
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Paul Harrison @paulfharrison.bsky.social · 05/04/2026
I've recently been exploring an Ornstein-Uhlenbeck SDE model of scRNA-Seq and Perturb-Seq. It's a simplistic model, but is enough to encounter many concrete problems that come up in stochastic models, such as parameter identifiability. Some rough slides here. logarithmic.net/2026/sde/sde...
logarithmic.net
A Simple SDE Model from Yeast Perturb-Seq
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Paul Harrison @paulfharrison.bsky.social · 29/12/2025
Minor theme this year: There's a rough right number of files to split datasets into. For my data, on the order of 100s of files. Too few, can't process in parallel. Want to be writing in parallel now! Too many, filesystems go slow or break, especially network/cloud storage. HPC team becomes sad.
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Jayani Lakshika @jayanigamage.bsky.social · 07/12/2025
Shared my talk “Visualise your fitted non-linear reduction model in high-dimensional space” at ASC2025, Curtin University, Perth. Great conversations, great people, and so much inspiration. ✨ Slides: jayani-asc2025.netlify.app #ASC2025 #Statistics #DataScience #Visualisation
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Paul Harrison @paulfharrison.bsky.social · 29/11/2025
I'm trying using background workers in Shiny. Pattern: Cache results on disk. On a cache miss, launch-and-forget a background worker, tell Shiny to invalidate later, and throw an error for Shiny to display. Workers use file locks to avoid doubling up work. App remains responsive! #R #Shiny
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Jovana Maksimovic @jovmaksimovic.bsky.social · 26/11/2025
It's not just because @torstenseemann.bsky.social is a bioinformatics legend but this may be my favourite #abacbs2025 poster because I'm a #trek tragic 🖖
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Jovana Maksimovic @jovmaksimovic.bsky.social · 25/11/2025
Congrats @lonsbio.bsky.social on being awarded the inaugural @abacbs.bsky.social Nick Wong Community Building Award at #abacbs2025! @hdashnow.bsky.social was absolutely right - you really are the Ted Lasso of Australian bioinformatics and computational biology 😃
media.tenor.com
a man pointing to a sign that says believe
ALT: a man pointing to a sign that says believe
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Julia Evans @b0rk.jvns.ca · 20/10/2025
just added the MEGA TERMINAL CHEAT SHEET from "The Secret Rules of the Terminal" to our list of posters at wizardzines.com#posters
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Paul Harrison @paulfharrison.bsky.social · 11/10/2025
Pondering k-Nearest Neighbor density estimation. There's some subtlety making the density smooth and integrate to 1. Here is a simple scheme: - Assign each point a radius from the distance to its kth nearest neighbor. - The density is the sum of a set of Gaussian splats with those radii.
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Paul Harrison @paulfharrison.bsky.social · 26/08/2025
"... a fundamental question that often remains overlooked is whether or not model parameters can be confidently estimated from the available data."
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Ming Tommy Tang @tommytang.bsky.social · 06/08/2025
Heatmap in ggplot2 yunuuuu.github.io/ggalign/ind... I always use complexheatmap, but this seems to be a good alternative if you want to stay within the ggplot
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Paul Harrison @paulfharrison.bsky.social · 03/08/2025
Happened to pick up "The Lancet Handbook of Essential Concepts in Clinical Research" (Schulz and Graves). A short read and surprisingly excellent. You can really tell that the authors have seen it all. www.elsevierhealth.com.au/essential-co...
elsevierhealth.com.au
Essential Concepts in Clinical Research: 2nd edition | Kenneth Schulz | ISBN: 9780702073946 | Elsevier Australia Bookstore
This practical guide speaks to two audiences: those who read and those who conduct research. Clinicians are medical detectives by training. For each patient, they assemble clinical clues to establish ...
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Paul Harrison @paulfharrison.bsky.social · 27/07/2025
uvx demakein I've finally updated my wind instrument design program to Python 3. It only took me 10 years to get around to. I was pleased to find there is now a fairly solid python library for 3D boolean operations (manifold3d). github.com/pfh/demakein
A picture of a 3D printed whistle in front of a 3D printer.
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Paul Harrison @paulfharrison.bsky.social · 11/07/2025
grug brain bioinformatician not trust maximum a posteriori estimate. big brained bioinformatics shaman develop map estimate. danger! noise demon hide deeper in data! grug prefer count matrix. grug know what to do when have count matrix.
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Robert Aboukhalil @robert.bio · 10/06/2025
Excited to announce our first interactive article on sandbox.bio, about genomic ranges: sandbox.bio/concepts/gen... Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!
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MACSYS @macsys.bsky.social · 23/06/2025
🚨 Exciting PhD Opportunities with MACSYS! The MACSYS team at Monash University is offering multiple fully funded #PhD scholarships for students eager to explore the cutting edge of computational biology, microbiology, and systems modelling. 👉More info/apply: macsys.org/monash-phd-s...
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Kim-Anh Lê Cao @mixomics.org · 23/06/2025
👩‍💻 We’re hiring! Lê Cao Lab at Uni Melbourne @mig-unimelb.bsky.social needs an R dev to power the next-gen of mixOmics 🚀 Love #RStats, #Bioconductor & multi-omics? Help expand mixOmics, run workshops & publish cutting-edge methods. Apply: unimelb.wd105.myworkdayjobs.com/en-US/UoM_Ex...
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Davis McCarthy @davisjmcc.bsky.social · 16/06/2025
📢 PostDoc opportunity in our Bioinformatics & Cellular Genomics lab at SVI! 🧬 You’d join a welcoming, supportive, and brilliant team. Why not spend a few years in Melbourne and be part of something exciting? Apply here: www.seek.com.au/job/84737876 #ScienceCareers #PostDoc #Bioinformatics
seek.com.au
Research Officer - Bioinformatics Job in Fitzroy, Melbourne VIC - SEEK
Seeking a Postdoc to develop computational toolkits to enable large-scale studies of single-cell and spatial 'omics and statistical genetics
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Paul Harrison @paulfharrison.bsky.social · 18/05/2025
I continue to be astounded at the number of compositional data analysis packages that will happily report differential abundance of individual species. Did they not understand the concept of compositional data? How is it possible to publish methods with this premise?
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Paul Harrison @paulfharrison.bsky.social · 03/05/2025
Normalization and log transformation of log count data. Pseudocounts, library size adjustment, Centered Log Ratios (CLR), Variance Stabilizing Transformation, and all that. Many variations on a similar task. Here's something I haven't seen done:
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Paul Harrison @paulfharrison.bsky.social · 22/04/2025
Random 2d Turing Machines make interesting patterns. pointersgonewild.com/2012/12/31/t...
pointersgonewild.com
Turing Drawings
Turing Drawings
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Paul Harrison @paulfharrison.bsky.social · 16/04/2025
An experimental design I've seen this three times in different contexts in the last couple of years. The RNA-Seq DE analysis turns out to be non-obvious: You apply treatment X to one group of subjects and treatment Y to another group. You have samples from before and after the treatment.
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Ming Tommy Tang @tommytang.bsky.social · 02/04/2025
🧵 PCA is everywhere in bioinformatics—but did you know it’s just SVD in disguise? 1/ If you've done bioinformatics, you've likely used PCA. But did you know Singular Value Decomposition (SVD) is at its core? Let’s break it down. 👇
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Paul Harrison @paulfharrison.bsky.social · 09/03/2025
Happy little accidents...
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Paul Harrison @paulfharrison.bsky.social · 08/03/2025
I'm really liking this course on generative diffusion models. They seem to have boiled many years of confusing development of ideas down to a simple approach. diffusion.csail.mit.edu
Generation of samples can be adjusted to output samples that are very clearly distinguishable as members of the desired class.
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Paul Harrison @paulfharrison.bsky.social · 05/03/2025
Monash University is considering the use of AI assisted assessment. Implementation planned to begin in semester 2 of this year. www.monash.edu/learning-tea...
monash.edu
Programmatic Assessment and AI Review (PAAIR)
You are here:
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Paul Harrison @paulfharrison.bsky.social · 23/02/2025
Comparison of optimization and sampling from a distribution defined by an energy function. I use a continuous version of the Ising model spin lattice energy. First, optimization from a random initial state using gradient descent with momentum, using the SGD optimizer in PyTorch.
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Paul Harrison @paulfharrison.bsky.social · 13/02/2025
I think I'm a little bit in love with the withr package in R. Similar to "with" in Python, you can guarantee to properly clean up when using a resource such as a connection to a file, a temporary directory, or a temporary global setting change. withr.r-lib.org
withr.r-lib.org
Run Code With Temporarily Modified Global State
A set of functions to run code with safely and temporarily modified global state. Many of these functions were originally a part of the devtools package, this provides a simple package with limited de...
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Ming Tommy Tang @tommytang.bsky.social · 10/02/2025
Bash Strict Mode: Stop Silent Failures in Your Scripts 🧵 1/ Ever had a Bash script fail silently, leading to hours of debugging? Bash doesn't fail by default—it keeps running even after errors. Here's how to fix it with strict mode. 👇
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Paul Harrison @paulfharrison.bsky.social · 10/02/2025
I've been playing with a Langevin Dynamics sampler as an optimizer in PyTorch -- SGD with momentum and noise. It's a remarkably simple algorithm for sampling from a distribution (approximately). Should eliminate over-fitting, and can also be used for generative tasks.
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Scott Fairchild🍁 @sithvicious.bsky.social · 20/01/2025
Trying to bring some old family photos back to life with g.i.m.p and its truly amazing resynthesizer add-on created by @paulfharrison.bsky.social getting some pretty good results. Takes me a few hours per photo, but is super satisfying…
Picture of my father drinking coffee on his break, working at the sears photo lab 1965 dark suit and a half smile.Picture of my father drinking coffee on his break, working at the sears photo lab 1965 dark suit and a half smile. but with scratches and cracks in the photo.
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Davide Risso @davi1893.bsky.social · 21/01/2025
This is long overdue, but over the winter break we were finally able to write up our sgdGMF paper: arxiv.org/abs/2412.20509 We present a stochastic gradient descent method that allows to efficiently and very quickly estimate latent factors for, e.g., dimensionality reduction of single-cell data
arxiv.org
Stochastic gradient descent estimation of generalized matrix factorization models with application to single-cell RNA sequencing data
Single-cell RNA sequencing allows the quantitation of gene expression at the individual cell level, enabling the study of cellular heterogeneity and gene expression dynamics. Dimensionality reduction ...
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Dr Di Cook @visnut.bsky.social · 06/01/2025
If I were to do some virtual half-day workshops this year, what topics and depths might be useful?
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Paul Harrison @paulfharrison.bsky.social · 26/12/2024
I've been watching the 2023 Statistical Rethinking lecture series by Richard McElreath. These cover a complete approach to statistics based on causal reasoning and Bayesian analysis. They are excellent, highly recommend. www.youtube.com/playlist?lis...
youtube.com
Statistical Rethinking 2023 - YouTube
See full course materials and topical outline here: https://github.com/rmcelreath/stat_rethinking_2024
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Ming Tommy Tang @tommytang.bsky.social · 24/12/2024
10/ TL;DR: ✔️ Under the null, p-values are uniform (flat distribution). ✔️ A "spike near 0" suggests true effects. ✔️ A "U-shape" signals artifacts—time to troubleshoot. Plot your p-values. They’ll tell you more than you think! Have questions? Let’s chat 👇
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Australian BioCommons @ausbiocommons.bsky.social · 06/12/2024
☎️ calling #SingleCell researchers in 🇦🇺! Join our last community meeting for the year Hear from @lgmartelotto.bsky.social and @swbioinf.bsky.social and chat all things single cell or #SpatialOmics! www.biocommons.org.au/events/sc-sp... #bioinformatics #lifescience
Flyer advertising the quarterly single cell and spatial omics meeting. All welcome!
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Paul Harrison @paulfharrison.bsky.social · 05/12/2024
Some years ago I wrote some code that produced a bad plot. I then had to endure multiple people having to explain my bad plot in seminars.
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The Carpentries @carpentries.carpentries.org · 02/12/2024
Starting today, The Carpentries will be active on BlueSky! 🥳 We'll continue to maintain our Mastodon (hachyderm.io/@thecarpentr...) and our LinkedIn (www.linkedin.com/company/the-...) accounts, and the content we post on here will be the same as the content we post on Mastodon. Excited to be here!
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Paul Harrison @paulfharrison.bsky.social · 27/11/2024
I just ran my 1.5 hour HTML+SVG+JavaScript+D3 workshop at ResBaz Victoria 2024. Touched on hopefully most of the important ideas needed for an interactive web-based data visualization. #resbaz #resbazvic #resbazvic2024 pfh.github.io/jsfoot/
pfh.github.io
HTML, Javascript, SVG, D3: a foot in the door
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Dr Di Cook @visnut.bsky.social · 21/11/2024
Our paper "A Plot is Worth a Thousand Tests: Assessing Residual Diagnostics with the Lineup Protocol" has appeared in issue 3 of JCGS, www.tandfonline.com/doi/full/10.... . It is open access for now, but if you ever have problems accessing you'll find the preprint at doi.org/10.48550/arX...
tandfonline.com
A Plot is Worth a Thousand Tests: Assessing Residual Diagnostics with the Lineup Protocol
Regression experts consistently recommend plotting residuals for model diagnosis, despite the availability of many numerical hypothesis test procedures designed to use residuals to assess problems ...
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Dr Di Cook @visnut.bsky.social · 19/11/2024
I've begun a statistical graphics starter pack at go.bsky.app/EMb8xWf . Please help me find more people or feeds to add to this pack. #rstats #visualisation #statistics 📈
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Dr Andrew Lonsdale @lonsbio.bsky.social · 19/11/2024
Great 'cos I just started this one. go.bsky.app/NmhwfbN
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Paul Harrison @paulfharrison.bsky.social · 18/11/2024
Pondering FDR control. Procedures like BH represent a certain policy, which can be confirmed to work by simulation for any given number of true discoveries. The actually achieved FDR guarantee is the FDR obtained in the worst case.
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Eugene Valkov @eugenevalkov.bsky.social · 19/02/2024
Our collaborative work with Narry Kim on the kinetics of mRNA poly(A) tail shortening. Led by Young-suk Lee, who established his own lab while the work was in progress, and Yevgen Levdansky in my lab. #RNASky #RNABiology www.nature.com/articles/s41...
nature.com
Deadenylation kinetics of mixed poly(A) tails at single-nucleotide resolution - Nature Structural & Molecular Biology
Here, using mathematical modeling and an in vitro deadenylation system, the authors quantitatively demonstrate the effect of non-adenosines in the poly(A) tail and exemplify how tail sequence regulate...
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Paul Harrison @paulfharrison.bsky.social · 15/11/2024
Something that should exist: geom_principal_curve() If x and y have a symmetric relationship, eg both x and y are noisy measurements of an underlying hidden variable, geom_smooth will under-estimate the slope, just like linear regression.
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