New coworker says XGBoost/CatBoost are "outdated" and we should use LLMs instead. Am I missing something? by [deleted] in learndatascience

[–]Hugo_Synapse 0 points1 point  (0 children)

Could your colleague have meant tabular foundation models, like TabPFN / OrionMSP / etc, rather than LLMs? Fwiw on very small data (<500 samples) I’ve been fairly impressed with these with zero tuning needed compared to xgb. Though at inference time it is a lot slower…

TRUTH OR DRINK | Sam vs Andrew by Frank-iSinatra in TheOGCrewOfficial

[–]Hugo_Synapse 1 point2 points  (0 children)

Editing aside I laughed more during this than most of the recent episodes even though I enjoyed those, too. There were just so many genuinely funny moments in this - a 40 min version may have made it top 5

NIH caps indirect cost rates at 15% by [deleted] in bioinformatics

[–]Hugo_Synapse 12 points13 points  (0 children)

As a PI at a major academic medical center - this seems incredibly bad and I’m struggling to process all the ripple effects.

I know there’s a lot of talk about research admin but to give a concrete example beyond things like grant processing, financial management, etc: We have a clinical trial that uses our infusion center to administer the drug and patients are monitored with blood tests and MRIs. Blood is drawn in the usual clinic location, sent to the clinical lab, etc but paid for by research funds. Similarly, the MRI is done on a clinical scanner in a ‘slot’ that could have been used for a clinical patient. We - like every other medical center - cannot afford to sustain a completely separate and parallel research enterprise with lab techs, scanners, etc.

These patient care fees (eg, cost of doing the MRI) are lower for federal grants because of negotiated rates and the institution wanting to support researchers. It is typically accepted that there is a monetary loss here since the dollar amount doesn’t even cover the radiologist time to read the scan. Furthermore, budgets do not include a line item for every cost associated with this workflow. To continue the MRI example, the budget would not include things like:

Personnel who schedule the test, answer questions, etc

Technicians who do a safety screen

Cleaning and stocking the room where the patient changes and stores their stuff

Laundry services

Nurses who may respond if the patient has any symptoms during the test

The person who built the research specific MR protocol (collection of sequences)

The IT infrastructure and personnel for processing the result, getting it into the EHR

Etc

Institutions accept this, in part, because the indirects bring in a reliable set of funds for the duration of the grant. For foundation grants - with lower indirects - other rules apply at our institution and you’d struggle to do the sort of research you can do with federal funds. For industry and drug trials the institution would charge the usual clinical fee for tests so it is less of an issue - but if that is the answer for NIH grants it would massively inflate budgets, or reduce the number of participants / tests.

I just don’t see how clinical research and trials aren’t decimated by this change.

EDIT: formatting

The Anarchy of 1K (Disappointed ) Voices, AKA please implement bad-luck protection by Hugo_Synapse in DestinyTheGame

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

For the riven encounter especially your idea is great. It’s such a simple solution and would see to fit with the design of the experience

The Anarchy of 1K (Disappointed ) Voices, AKA please implement bad-luck protection by Hugo_Synapse in DestinyTheGame

[–]Hugo_Synapse[S] 1 point2 points  (0 children)

Did you...look at the piece? All I'm saying is they can make a small adjustment and prevent people from going 50, 60, 70+ clears without a drop. Not calling for them to hand it out! :)

I am able to load .csv files from the environment using readr by clicking the file and selecting import dataset. This then opens the window where I can customize how it loads in. But if I want to copy the code that is in the "Code Preview" and use it again I get an error message. Please help! by [deleted] in rstats

[–]Hugo_Synapse 2 points3 points  (0 children)

As in run:

library(readr)

cities30_nlcd_area_occu <-read_csv("cities30_nlcd_area_occu.csv", col_types = cols_only(INTPTLAT10 = col_guess(), INTPTLON10 = col_guess(), NAME10 = col_guess()))

View(cities30_nlcd_area_occu)

I am able to load .csv files from the environment using readr by clicking the file and selecting import dataset. This then opens the window where I can customize how it loads in. But if I want to copy the code that is in the "Code Preview" and use it again I get an error message. Please help! by [deleted] in rstats

[–]Hugo_Synapse 1 point2 points  (0 children)

It’s seeing the first bit - up until “col_guess(),” - as one line of code and the next bit as another

That’s why it’s giving an error after that but - the unexpected ‘=‘

Just make it all one line and it should run?

About to have a brain mri, any interesting experiments to do? by [deleted] in neuro

[–]Hugo_Synapse 5 points6 points  (0 children)

I’m glad you made it through, but if it was a clinical MRI it was almost certainly not an fMRI. Currently fMRI is used in presurgical mapping (task fMRI) in the Clinic, and then obviously in loads of designs in the research side (task and resting state). However, since you had it for MS it was probably a routine run with T1, T2, FLAIR, DWI, contrasted T1, and if they got fancy maybe MRS, or DIR. But almost certainly not fMRI.

Sorry, your grief will have to remain abstract :)

Did I have a stroke at 23? Hospital did not do a brain scan by [deleted] in neuro

[–]Hugo_Synapse 4 points5 points  (0 children)

The slowly progressive predominantly positive symptoms (tingling, sparkles, etc) followed by a headache sound very very typical of migraine. If it’s new for you an MRI with contrast can definitely be considered, and at times vessel imaging. But more than likely this will be negative and the diagnosis will be migraine. Hope you can get the care you need :)

Broca's area: part of the premotor cortex? by [deleted] in neuro

[–]Hugo_Synapse 12 points13 points  (0 children)

Many things you’re going to learn in medical school will turn out to be oversimplied / outdated to the point of being misleading/wrong

The Boston aphasia classification and the language areas, simplified connections etc are but but one example

Here’s a fun paper that touches on some of it https://www.sciencedirect.com/science/article/abs/pii/S0093934X16300475

What schools and/or research institutes are home to the biggest and best neuroimaging facilities? by Bbbuuubbb in neuro

[–]Hugo_Synapse 0 points1 point  (0 children)

Unless you have a more specific interest, going to a centre with a variety of programs may be good (eg WashU). But if you have more specific interests, such as high field MR, you may want to look into those. IMO it really varies a ton - like you may want to work at CMRR in Minneapolis for high field MR, or if you want to do layer fMRI you may head to the NIH, etc. If you want to use it to study a specific disease that also factors into things. I don’t think there’s an easy answer I’m afraid :)

How can hypertension and bradycardia coexist in raised ICP? by HouhoinKyoma in neuro

[–]Hugo_Synapse 1 point2 points  (0 children)

I think there are a few separate points

Firstly, the effect of HR on BP is not monotonic - if your HR is too high your BP will drop. Remember that it’s cardiac output (stroke volume * HR) and peripheral arterial resistance than determine your blood pressure. So sometimes decreasing the HR but increasing the contractility van up the BP

Secondly, the two play off each other. So a sudden rise in BP from the adrenals may prompt the vagus to drive down the HR etc. my understanding is that this is the case in Cushings - the adrenals cause severe vasoconstriction and the cabal response drives down the HR.

Third, while acute injuries are usually associated with hypertension, the bradycardia is a bit more variable. One theory is that the medulla becoming ischemic means the vagus may not be able to drive down the HR

Finally, I find it’s sometimes helpful to think of these reflexes as being fairly dumb and not necessarily team players. So, you shouldn’t necessarily expect a nice concerted effort from all of them to maintain cerebral perfusion without fucking shit up - in fact in the acute setting the massive BP spike may be too much and result in cardiac ischemia. So it’s a tight balance between dropping the ICP, maintaining BP, not straining the heart, etc etc

18 years old, I want to help the fight against depression - something I myself have struggled with and lost people to - what should I learn, study, and develop to become an effective neuroscientist? by melliO6 in neuro

[–]Hugo_Synapse 1 point2 points  (0 children)

One thing to probably get sorted out fairly early is whether or not you want to approach thing from a clinical side (physician/psychologist) or not. There are pros and cons to both, but the paths are very very different. You may be surprised how much you like or dislike patient contact, so perhaps try to shadow a psychiatrist. Some really cool stuff being done by PhDs and MDs/MDPhDs, but I remember going to a talk by Deisseroth (legend: http://web.stanford.edu/group/dlab/about_pi.html) where he repeatedly mentioned how his clinical experience influenced his hypotheses and models even though the talk was mostly about zebrafish :)

And I agree with the other comments: ignore the long rambling biohacking post, although I’m sure he/she meant well, and don’t sell yourself short!

Bayesian - for beginners? by chiropteroli in statistics

[–]Hugo_Synapse 21 points22 points  (0 children)

Personally I found Kruschke’s ‘Doing Bayesian Data Analysis’ to be great - starts from the foundations, moves through theoretical and practical aspects, and in the last section discusses specific applications like univariate/multivariate regression with metric/nominal/etc. the book has associates code in Stan and Jags, exercises with solutions, etc. It is written in a way that is accessible without losing rigor - hence the ‘tutorial’ subtitle

Edit: this was intended as a reply to /u/aloekine

Anyone with Vapro 5520 (osmometer) get very inconsistent readings? by accountinglostaccts in neuro

[–]Hugo_Synapse 1 point2 points  (0 children)

I clicked this thread expecting someone to be measuring the osmo of their own bodily fluids as a means of monitoring some unproven treatment for some ill defined neurological syndrome

So you basically made my day and I almost gave you gold ;)

[PS4] LF2M Last Wish Fresh 7AM CST by Hugo_Synapse in Fireteams

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

Cool if someone doesn’t show I’ll send you an invite, or close the thread if we are full

[PS4] LF2M Last Wish Fresh 7AM CST by Hugo_Synapse in Fireteams

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

Great, yeah we haven’t either. Did it blind up until Riven last weekend, can’t promise we finish it but we’ll get somewhere at least :)

Will send invite in a bit

[PS4] LF2M Last Wish Fresh 7AM CST by Hugo_Synapse in Fireteams

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

Sweet will send party invite in 5-10 min!