Marcin Cieslik

[Marcin Cieslik @i000]

@anshulkundaje @PracheeAC @WalentekLab To me this discussion is just on which side of the Gartner hype cycle one is more comformtable at. Those who ride the upswing are more risk tolerant and need more capital so benefit from hype. Those in the wake benefit from rigor as they compete on deliverables not visions.

[Marcin Cieslik @i000]

@jrkelly The difference is that from the very start (i.e. 1973 Asilomar) biotech remains a regulated industry. There are also harsher limits to scaling biology (reaction kinetics, cell size, indeterminism); these are real barriers which, IMHO, clamp biotech to a comparatively small niche.

[Marcin Cieslik @i000]

@jrkelly I understood your IBM metaphor to be on productivity gains not cost savings. But I find it a bit loose, computers didn't just make compute cheaper, they resulted in the creation of completely new goods and services. A new IT economy; what would be the new lab-automation economy?

[Marcin Cieslik @i000]

@anshulkundaje I am not saying it is an excuse. But it is a finite system. Increasing salaries without increasing budgets will: 1) decrease the total # of scientists, 2) increase the competition for funding - to maintain lab sizes, and 3)in my opinion overall favor big labs. Maybe its all good.

[Marcin Cieslik @i000]

@anshulkundaje Perhaps not necessarily, but the ones I know do. I also say this from personal experience doing a post-doc in such a lab.

[Marcin Cieslik @i000]

@jrkelly @gama_search What is a fair price depends on the efficiency on the industry. Given its aging and ailing population US would be silly not to import safe/effective drugs from efficient economies + allow medicare/aid to fully negotiate prices to have the same levarage on pharma as other nations.

[Marcin Cieslik @i000]

@silvirouskin Circular tRNAs?

[Marcin Cieslik @i000]

@BoWang87 I find your argument of reasoning vs narrating really insightful. Too often we hear about the promise of AI to discover biological knowledge, as opposed to generating hypotheses. The impact of AI will have to be on how biology is practiced, not generating a de-novo Bio GrokPedia.

[Marcin Cieslik @i000]

@deAlmeida_BP @instadeepai Taken at face value these data are at odds with published literature which showed that long contexts are needed to model interactions between promoters and regulatory elements to model 'integrated' outputs. Do you have any ideas how this works?

[Marcin Cieslik @i000]

@deAlmeida_BP @instadeepai Thanks! Figs 3G and A.9C are intriguing. They suggest that long context >8kb offers almost no benefit for NTv3 on predicting functional tracks. But how is this possible e.g. for RNA-seq where a 8kb window will rarely cover the promoter. /1

[Marcin Cieslik @i000]

@msikic @anshulkundaje AIxbio follows the same trajectory as systems biology. sysbio failed to deliver on its grand promise, yet ultimately became an essential part of how biology is done. Same for AIxBio it will both fail miserably and transform fundamentally.

[Marcin Cieslik @i000]

@owl_posting I once met some pharma project managers getting hammered in the middle of the week in a suburban dive bar in Hershey Pennsylvania. Big WTF. They must worked for auxolith. ;)

[Marcin Cieslik @i000]

@owl_posting @ronalfa @NOETIK_ai I will definitely read those! It seems fair to speculate that spatial FM, being a much better fit for DL, will be of higher value then squeezing ranked gene names into transformer architectures. Perhaps especially when fine-tune for discovery from small sample sizes. But overall?

[Marcin Cieslik @i000]

@ronalfa @NOETIK_ai @owl_posting You have shown that a FM can make plausible predictions - this is nice, hypothesis generation is important, and I am with you on the importance of looking at human tissues for biomarkers. But it is a far cry from the claims above.

[Marcin Cieslik @i000]

@ronalfa @NOETIK_ai @owl_posting Sure, I checked it out. Do you refer to the STK11/KRAS study? It seems like nice set of results, but it does not show that the FM was: necessary and improved over baselines. It shows no exp. validation for "Target A". Has no comparison to supervised approaches.

[Marcin Cieslik @i000]

@adamfeuerstein @ScottAdamsSays Such a bad take. Lack of evidence is not evidence of absence. Response rates are highly variable including Pluvicto. Whether either drug does anything for him is anyone's guess.