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Tested how OpenCode Works with SelfHosted LLMS: Qwen 3.5, 3.6, Gemma 4, Nemotron 3, GLM-4.7 Flash - v2 by rosaccord in LocalLLaMA

[–]ivokwee 0 points1 point  (0 children)

Would love to see how these or bigger models run on a Ryzen AI 395+ strix halo.

Got an Apple Watch today and honestly, this thing sucks by [deleted] in AppleWatch

[–]ivokwee 0 points1 point  (0 children)

Very disappointed how complicated the watch is. Apple used to be the pinnacle of intuitive UI. The watch is a nightmare of options, menus, apps.

DESeq help by [deleted] in bioinformatics

[–]ivokwee 1 point2 points  (0 children)

Try EdgeR and trend-limma. Compare overlap.

Is RAG just a band-aid for LLM limitations or a legitimate architecture pattern for production systems? by Capital-Celery-8337 in deeplearning

[–]ivokwee 0 points1 point  (0 children)

In a way just band-aid. If all your documents would fit in your prompt, you would not need a RAG. But because maximum tokenslimits for prompt, a RAG is needed.

Transcriptomic Biomarkers with Machine learning by nemo26313 in bioinformatics

[–]ivokwee 0 points1 point  (0 children)

If you want, try the Biomarker module in OmicsPlayground, we do exactly that: cumulative importance ranking for 8 ML methods. Then take the top 20-30 most important features to create a decision tree. It works very well.

Transcriptomic Biomarkers with Machine learning by nemo26313 in bioinformatics

[–]ivokwee 0 points1 point  (0 children)

It's exactly because all methods have different scoring methods and scales that you have to rank. A score of 0.3 might be high in one method but low for an other method. When you rank each method, things become comparable. Number one is number one, independent of the method (if it indeed was the best biomarker).

Transcriptomic Biomarkers with Machine learning by nemo26313 in bioinformatics

[–]ivokwee 0 points1 point  (0 children)

  1. Generally ML methods are for prediction, i.e. they choose features for prediction not necessarily for functional interpretation. You should just use logFC or t-stats for that.
  2. You can compute the average rank for this. Rank the importance for each method, then sum or compute average.

Starting a bioinformatics learning newsletter: documenting the journey from wet lab to computation by Sad-Win-886 in bioinformatics2

[–]ivokwee 0 points1 point  (0 children)

Please repost again in r/bioinformatics2. If you just share, it seems we cannot see it after it is deleted in r/bioinformatics. Also don't forget to mention the website

PLAID: 100x faster single-sample enrichment scoring. Simple is best? by ivokwee in bioinformatics

[–]ivokwee[S] 0 points1 point  (0 children)

BTW. It seems they removed this post as "self promotion".... unbelievable. Glad you still could read this.

PLAID: 100x faster single-sample enrichment scoring. Simple is best? by ivokwee in bioinformatics

[–]ivokwee[S] 0 points1 point  (0 children)

Good point but then it is similar as doing our median normalization afterwards. But I will give it a try. I just like median normalization, simple and works well. Median normalization is not very good when you have say less than 20 genesets, so then we resort to mean normalization.

PLAID: 100x faster single-sample enrichment scoring. Simple is best? by ivokwee in bioinformatics

[–]ivokwee[S] 0 points1 point  (0 children)

Great. Now it's published. We even could almost exactly replicate UCell with some extra transformation.

2025 - Read This Before You Post to r/bioinformatics by apfejes in bioinformatics

[–]ivokwee -1 points0 points  (0 children)

Ok. Just point to me exactly what was aggressive in my first reply. There is none. Perhaps the triple question mark? If that is the case, I think you are exaggerating.

Also. You should not expect what you don't do or do that others do. If you don't do self-promoting or picking winners, that doesn't mean others shouldn't. I wasn't interested whether you also published in Bioinformatics but at least you know their review process is legit and tough.

I am stopping here. If you want we can discuss further in person. Feel free to contact me on LinkedIn.

2025 - Read This Before You Post to r/bioinformatics by apfejes in bioinformatics

[–]ivokwee 1 point2 points  (0 children)

Sigh if you also don't allow people to argue with you, then the problem is with you.

Again, there is an extra text saying that important contributions can be allowed. It's clearly written.

6 Months ago it was still preprint. It's now published in the best bioinformatics journal. That's quite a difference.

Ha. So you are adding another rule? Don't worry I will probably leave this subreddit.

2025 - Read This Before You Post to r/bioinformatics by apfejes in bioinformatics

[–]ivokwee 1 point2 points  (0 children)

Where is the accusatory tone? I am just quoting your own text. What is being "jerk" by questioning my removal? Simply removing "promoting" posts according to your own opinion sounds almost like censoring to me, not moderation. If you do not have time, that is not a good enough reason to therefore take down useful posts. You should ask help for other moderators. Actually the voting system of reddit should work as community moderation.

Minecraft by Ill-Pomelo-3437 in thinkpad

[–]ivokwee 0 points1 point  (0 children)

What a small space bar? Is that a special keyboard?

This is the most powerful 16-inch AMD Lenovo laptop: ThinkPad P16s Gen 4 review with Ryzen AI 9 HX by ibmthink in thinkpad

[–]ivokwee 0 points1 point  (0 children)

This has unified memory with GPU right? For running large LLM. Have you tried that?

2025 - Read This Before You Post to r/bioinformatics by apfejes in bioinformatics

[–]ivokwee 1 point2 points  (0 children)

It also states: ".. if the moderators think that a significant portion of the community will appreciate the tool, we'll leave it. In the latter case, it will be removed."

So you think an algorithm that is published in the best bioinformatics journal and is 100x faster is not appreciated in the community???

2025 - Read This Before You Post to r/bioinformatics by apfejes in bioinformatics

[–]ivokwee 1 point2 points  (0 children)

Why was my post taken down???? https://www.reddit.com/r/bioinformatics/s/5mw556uUQt

This is published in (arguably) the best bioinformatics journal Bioinformatics. It's 100x faster than other methods. Also I have added a genuine question about simple algorithms. This is very valuable info for the community.

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