Tommi Mäklin

1 Followers
214 Following
74 Posts
I do statistics, metagenomics/bacterial genomics & bioinformatics software development.
Postdoc @ University of Helsinki
Softwarehttps://github.com/tmaklin
This vid about optimizing Mario 64 source code just for the fun of it is coincidentally also a pretty neat example of why/when function inlining and loop unrolling are useful https://youtube.com/watch?v=t_rzYnXEQlE
FIXING the ENTIRE SM64 Source Code (INSANE N64 performance)

Could this bring Luigi back?Patreon: https://www.patreon.com/Kazestuff🎥 https://www.twitch.tv/kazesm64🐦 https://twitter.com/KazeEmanuarMERCH: https://kazem...

YouTube
@rupdecat yep, it's pretty great for the unexpected!

Beating neural approaches to sentence classification for out-of-domain datasets with ... nearest neighbour over *gzip* (finding the ratio between the compressed size of the documents combined vs. smallest compressed size of the inputs being compared).

This is both hilariously simple, and somewhat damning of how the other methods do in this context.

https://aclanthology.org/2023.findings-acl.426/

#computerscience #programming #machinelearning

“Low-Resource” Text Classification: A Parameter-Free Classification Method with Compressors

Zhiying Jiang, Matthew Yang, Mikhail Tsirlin, Raphael Tang, Yiqin Dai, Jimmy Lin. Findings of the Association for Computational Linguistics: ACL 2023. 2023.

ACL Anthology

Hey #bioinformatics , #OpenScience and #computerscience hive minds of mastodon, I have need of your help.

See https://genomic.social/@MrHedmad/110606060559853537

I need a way to make our lab data FAIR without having to explain or use anything very complex. RO-crate does not cut it, for our personal use-case. So I came up with https://github.com/MrHedmad/data-myr

Can anyone take a look and tell me if:
- It is dumb / useless / makes no sense
- There is something identical to it

and any other feedback. Thank you! Love you! xoxoxoxo

Luca Visentin (@[email protected])

A 🧵 [1/n] So, I was thinking about FAIR data. I wanted to start cataloguing our lab's data and make it FAIR, even just locally (with the idea that in the future we can start uploading somewhere). So I wanted to find some software that can bind metadata and data in some way. I found a series of LIMS software that seems to do what I want (e.g. makes protocols, data types, authors, instrument pages and links them all together) [...] #FAIR #OpenScience #help #researchsoftware

genomic.social

@rupdecat the Finnish research HPC maintainers actually built a set of wrapper scripts to handle the filesystem load that individual users' conda installations cause https://github.com/CSCfi/hpc-container-wrapper

It's unfortunate that conda is so incompatible with common HPC setups but something like this seems like an interesting temporary solution.

GitHub - CSCfi/hpc-container-wrapper: Tool to wrap installations into a container designed for use on HPC systems

Tool to wrap installations into a container designed for use on HPC systems - CSCfi/hpc-container-wrapper

GitHub
Wrote a blogthing about how chatgpt is pretty bad at being a self-replicating machine https://maklin.fi/post/computer-science/2023-07-08_llms-and-self-replicating-machines/
Tommi Mäklin

Are large-language models a type of self-replicating machine? Probably, but very lousy ones.

@apposada For computer hardware there's the Free Software Foundation's "Respects your freedom" scheme which is a bit on the extreme side of views on open hardware (https://ryf.fsf.org/) and mainly certifies >10 year old hardware. For phones and gadgets the Fairphone/Pinephone/Purism trio promises 5-year software support and repairability for most of their products.

The communities overlap a lot with the open source ones, so there isn't really any one dedicated to hardware.

Respects Your Freedom Certification | RYF

People on the #FOSS community: the world of Open Source Software is vast an well documented, with numerous past and present examples of communities commited to promote and educate its philosophy and principles. But what about #hardware ? Is there anything similar about the hardware? I’d like to start reading more on sustainable hardware (i.e. devices that can be repaired, that have long term support, software designed to keep supporting them, sustainable materials, etc). Thanks!
Most baffling thing about 'geek culture' is how ultra-conservative it is. People who grew up shouting "hack the planet" grew up to be averse against the smallest changes, from the small scale ("well it works for *me* so why should we change this 15 step setup") to the large ("i refuse to think about the social impacts of my work")
PhD Simulator

A completely random event based text game. Simply make your choice at the beginning of each month and see if you can graduate in time. All outcomes are determined by the random number generator and do not take them seriously. Sometimes the RNG can be brutal :)

Mianzhi Wang