Sadamori Kojaku

Its very hard to type
, and hard to remember the spelling 🫣

I created a tool, snaketail, a snakemake wrapper that fixes workflow and restarts itself automatically when failed.

The idea—feeding the tail (error log) to the head (system input) to self-heal—has practical values to create robust automation system!

skojaku.github.io/snaketail.html

YouTube video by VISUALIUM 鑑賞する科学 漸化式を色々な方法で可視化 | 鑑賞して楽しむ漸化式

This is a beautiful visualization of recurrence relations and eigenvectors. (It’s Japanese so plz turn on auto translation).

I've also seen more and more figures that are apparently generated by generative AIs on preprints, with typos, broken arrows, and inconsistency with the main text body. Found yet another one today 🙃.

ppl should stop using ai-generated diagrams. you know i’m not anti-ai but they’re just not good at this yet!

the problem is that diagrams have a very specific purpose: they’re meant to compress understanding into few key bits. ai vomits out poor approximations that aren’t conceptually compressed

Come and join our Discrete Laplacian workshop in Dresden, Germany 🙌!

With Karel Devriendt, Otto Sumray, and Giulio Zucal, we are organising the workshop in MPI-CBG, 22-25 Jun 2026.
Thanks to the support from Heather Harrington's group at CSBD, MPI!

Abstract ddl: 1 Mar 2026

More details follow 🧵

My daughter isn’t Markovian but my son is (almost) 🙃

New (competition funded) PhD opportunity with me,
@iaciac.bsky.social and @dralgernon.bsky.social
www.findaphd.com/phds/project...
Higher-order networks and animal communication. Suited to someone keen on network science theory/computational modeling and keen to adapt this to ecology & evolution.

Can AI be a good task manager? I tested myself as a weekend project - skojaku.github.io/invisible-cy...

Feed the Beast | Derek Larson AI eats software

Claude code is moving from a coder to a general assistant.

Personally, sending sensitive data to someone's server isn't an option. But w/ ollama "launch" feature, I may do w/ local LLMs. Time for experiment!

(reading while me being fed with a cup of Miso soup)

www.dtlarson.com/feed-the-beast

Thanks!

Scientific production in the era of large language models With the production process rapidly evolving, science policy must consider how institutions could evolve

Thrilled to share our new paper in Science @science.org: “Scientific Production in the era of Large Language Models.”

- LLMs boost productivity, especially for non-native speakers.
- Writing complexity is now "decoupled" from scientific quality.
- LLMs help discover more diverse literature.

Awesome🥳 Big Congrats!!!

A long-overdue interactive version finally done
(Huge thanks to Google Gemini)
Complex Systems Topic Network: Interactive Visualization
bingdev.binghamton.edu/sayama/compl...

We are looking for a PhD student to work with us on network science methods for biomedicine. The student can be enrolled in any graduate program. #NetworkMedicine #ComplexSystems.

GPT Inference (greedy, top-k, beam search, temperature control).

For a thread of community detection, Girvan Newman paper on the modularity, LFR bench, the resolution limit paper, Karrer Newman degree corrected SBMs, Peixoto’s non parametric Bayesian SBMs

word2vec: from the structural linguistic perspective. Written by me. Illustrated by Nano Banana Pro.

🧵1/
A bit late to the party, but I want to introduce a pet project of mine—and my first single-author paper! 🎉

It tackles something that has quietly frustrated me for years: how we measure the similarity of two clusterings/community structures.

Nano Banana Pro unbelievably lowers the entry barrier for people interested in creating short Manga. This blog post describes the recipe (in Japanese). I get this Manga version of my lecture note on the position encoding in transformers, **in the first shot** 😮.

note.com/konho/n/na8d...

海南鶏飯を一日かけて作ったのだけど、子供は食べないばかりかぐちゃぐちゃにされて心が折れた。１０分でできるパスタ出してあげるよ。次から🫠。

I'm looking for a PhD student to join my lab at UAlbany for Fall 2026!

We are data scientists studying the creation, flow, and impact of information. How do scientists collaborate? How does AI shape information access? What drives local innovation?

Want to answer these questions? details below!

🚨 New paper on ArXiv:

“Uncertainty quantification and posterior sampling for network reconstruction”

TL;DR; We present an efficient method to sample the entire ensemble of possible network reconstructions that are compatible with an indirect observation, e.g. a dynamics.

Short thread: 1/N

TLDR: communities are undetectable even if they are because of the variabilities of network topology. We look further into edge weights, showing that a higher variability in edge weights makes communities harder to be detected. Our results inform when to use edge weights and better edge reweighing.

Is #innovation born or made? Why do some places keep innovating while others fall behind? Is innovation the product of cities—or of deeper laws?

Our new paper in npj Complexity explores these questions through the lens of a century of US patent data.🧵👇
nature.com/articles/s44...

Detectability threshold in weighted modular networks We study the necessary condition to detect, by means of spectral modularity optimization, the ground-truth partition in networks generated according to the weighted planted-partition model with two eq...

When are communities detectable in weighted networks? You can find the answer in our latest preprint. Great collaboration with @filipisilva.bsky.social @skojaku.bsky.social arxiv.org/abs/2511.00214

Wanted to create an interactive *public* visualization for networks/embeddings?

I created a minimum GitHub Page template for HeliosWeb visualization. @filipisilva.bsky.social

👉 Demo: shorturl.at/m9CnR
👉 Repo: shorturl.at/HJ2gn
👉 HeliosWeb: shorturl.at/H9bJU

#dataviz #datascience #python

Home page of the Complex Systems Research Exchange website. It reads: Complex Systems Research Exchange (CREx) is an online seminar series aimed at building an international research community in the interdisciplinary field of complex systems, very broadly defined. Our focus is on creating opportunities to hear from early to mid-career researchers about their research, while also serving as a platform for networking and collaboration. We are open to a wide range of research areas including network science, nonlinear dynamics, dynamical systems, computational social science, science of science, machine learning and AI, data science, urban science and human mobility, mathematical biology and ecology, neuroscience, and more. Please subscribe to the mailing list to receive announcements of upcoming seminars. The Zoom link for each seminar will be sent to the mailing list shortly before the seminar. Please reach out to organizers if you are interested in giving a presentation yourself or know someone who would be interested. This seminar series is run on a volunteer basis and is currently organized without funding. Organizers: Jeehye Choi, Takayuki Hiraoka, Inho Hong, Hyewon Kim, Kazuki Nakajima, Ayumi Ozawa, Taekho You

A semi-regular reminder: My colleagues and I are running an interdisciplinary online seminar series called Complex Systems Research Exchange (CREx🦖).
sites.google.com/view/cxrex

Snakemake is essential for reproducible research—it organizes code, and acts as my second brain about code and data relations.

A downside is its maintenance cost. It can be easily convoluted as a project progresses. This tool might resolve that.

arxiv.org/html/2505.02...

I've been playing with Ollama Cloud that has a free cloud Qwen 3 Vision Language model, which is surprisingly good. I put together a small app that automatically renames screenshot files based on their content, which has been super helpful for organizing them.
github.com/skojaku/scre...