Neuro PolarBear

I had the PiN interview last week, and I haven't yet had mine for BCS, so maybe ask again in March? Culture is obviously a lot more subjective, but many say MIT is much more competitive and political, which can take some skill to navigate. However, it's hard to know how much these stereotypes hold up, and your experience may certainly vary depending on which lab you end up in.

I've heard that flipping a coin can actually be quite helpful for making decisions like that. If you flip a coin and afterwards find yourself happy/disappointed with how it lands, then you know where to go!

I don't really know what your chances are at those schools, but like I said before I think you would have a shot. Maybe check the survey to see if interviews for all those programs have come out yet?

Where did you apply? Those seem like excellent stats. I think, as you mention, that the only thing that would hold you back would be if your LoR weren't as strong, but I don't see why they wouldn't be given that it sounds like you've accomplished a lot in your lab!

Maybe wait until you visit or get into both first? Also, the two programs have quite different faculty and culture, so I think deciding between them may not be as hard for some people as you might think.

I requested the other date and also haven't gotten an confirmation or response for that yet, so maybe they're still trying to sort it out?

That definitely won't be seen as annoying! PIs are pretty much always happy to share and talk about their work. Also, my school might have access. If you don't hear back feel free to PM me. Or try the #icanhazpaper hashtag on twitter.

I think this is largely a semantic argument. Just as I probably shouldn't have been so quick to take issue with your definition, I don't think you should have been so quick to dismiss mine or to imply that I don't understand the term. Moreover, I think my interpretation falls more in line with common usage. I would definitely be quite hesitant about lumping GECIs, and optical sensors in the same category as optogenetic tools derived from microbial opsins. Given the extent and history of non genetically encoded calcium sensors, it seems easier to me to distinguish tools for monitoring and recording neural activity from those that manipulate and control it. I would also agree that the tools developed by Rich Kramer and Dirk Trauner could indeed by classified as optogenetic tools, but I think calling them as such is potentially misleading, and not as accurate as optical/optogenetic pharmacology or photopharmacology. Moreover, I think many agree with these above sentiments. See for example, the responses to "How do you define optogenetics?" in Nat. Neuro's 10 year anniversary article: http://pyramidal.stanford.edu/publications/Adamantidis2015_NatureNeurosci.pdf Häusser: There’s a broad definition and a narrow definition. The broad definition is rooted in etymology: any approach that combines optical interrogation with genetic targeting qualifies as ‘optogenetic’, and that includes the use of genetically encoded activity sensors. However, most people generally use the term optogenetics to mean the use of probes to manipulate activity, and (as is usual in English) usage normally wins. Schnitzer: Notably, our original intent was to cover both genetically targeted optical control and imaging under a single umbrella term. Nevertheless, I have subsequently always preferred a narrower interpretation of optogenetics that covers only the control approaches and the wonderful field that grew out of Karl’s seminal 2005 paper in Nature Neuroscience; the broader interpretation of optogenetics that includes imaging is so general that, in some respects, it can be vague. My impression is that a substantial majority of the usages of the term optogenetics in the neuroscience literature follows the narrower interpretation. Of course, that's not to say that I wouldn't agree with, as Dick Tsien points out, that such a broad name could easily—and moreover probably should—refer to a larger set of tools, as you suggest. The fact that he still has to make this point, however, would seem to indicate that the broader interpretation is falling out of favor, even if he would prefer its usage. And, yes, I am familiar with the papers that combine these various techniques, as I alluded to in my previous response. These are indeed quite elegant experiments! I do also think my original point still holds about inferring function and causality based on results from optogenetic manipulations. The opposite is also true, as noted by Bence Ölveczky in response to his recent paper: "Our paper cautioning against simplistic over-interpretations is being simplistically over-interpreted by many. Nuance is hard to convey."

Yeah, I think that's a better question. In my opinion, I don't really think the degree you end up getting will make that much of a difference or if one is more advantageous than the other, especially if you plan on doing the same type of research in each program. Obviously what you end up doing for your PhD will matter the most, but maybe some programs are better than others depending on where you want to go or end up after your PhD. Optogenetics seems less likely to give you that data than calcium imaging, especially since it's so far off from the physiological ground truth by pumping neurons full of such high levels of exogenous opsins. In contrast, the most recent deconvolution, demixing, and spike inference statistical methods are getting better and better, as well as imaging methods like SLM microscopy and resonant scanning that enables the imaging of multiple planes and 3D volumes at once with fairly decent spatiotemporal resolution. Photoswitchable tethered ligands for optical pharmacology and voltaic imaging are also promising, but I don't think there has far along as calcium imaging. Though I guess you were maybe referring to some of the more recent closed-loop optogenetics and two-photon imaging / all-optical electrophysiology methods?

In response to your original question and this quote, I think asking how the CNS program at Caltech stands in the neuroscience community is the wrong question to ask since neuroscience and even theoretical neuroscience have been slow to incorporate machine learning and have not yet really embraced a lot of the research in computational neuroscience—even though, as you admit, have decent ties to neuroscience. A lot more of the work on machine learning, neuromorphic engineering, CNNs, etc. has definitely come out of the fields of computer vision, electrical engineering, computer science, and statistics, rather than neuroscience. That said, given your interests, I think you could still find professors there that are good fits, but I'm sure the general neuroscience community is more familiar with Caltech faculty like David Anderson and Markus Meister whose work is much more grounded in biology. The professors that might be best for you are probably less likely to have primary appointments in neuroscience, as mentioned above, so I think it's probably harder to figure out exactly what type of program to apply to. I bet you'll have a better sense after interviews! I'm not as familiar with the more computational side of things, but I'd suggest looking at the faculty at past COSYNE and NIPS meetings. For motor control and machine learning, John Cunningham, who came out of Krishna Shenoy's lab at Stanford, is doing some very interesting work.

Yeah, official email. I received it at 2:30

Just got an invite to UCSF Neuro! Now I've finally heard back from all the programs I applied to.

Maybe we'll hear tomorrow!

Congratulations!

Did your email also ask about your "level of commitment" to Stanford? I know Stanford is a wonderful place—and maybe my top choice if I get accepted— though that seemed like a hard question to answer without sounding like you're just sucking up to them.

I got one of the invites for Stanford neuro. I got a phone call from someone in admissions and she said she'd follow up with an email, but I haven't received that yet. I got the email a few minutes after posting

I'd follow up if you don't hear back by the end of this week.

I haven't either but the coordinator said she would be away for the holidays so we'll probably hear something soon.

Congratulations on your interview to caltech! That's quite an accomplishment. I personally don't really have answers to your questions. To be honest, these are exactly the kind of questions you should should be asking other graduate students during the interview weekend. They will surely have a better perspective on caltech than pretty much any of us here can offer. Academically, caltech is a fabulous place, with some of the top researchers across many different fields. I'd suggest looking more closely at the research of the professors that you're interested in before the interview and then use the interview weekend as an opportunity to answer your other questions about the graduate program's environment.

I don't remember when I submitted my application for MIT, but I submitted all of mine within a week of their deadlines on Dec. 1st. I don't know if other schools do it the same way, but MIT was the only one where we had to specify faculty readers, so maybe it's taking some faculty longer than others to read the applications? Or they could have received more applications to read. I got a call from the professor I put down first in the list of faculty readers. The call from that professor and the official email I received both came later for me than for Edotdl or other people on the survey. The email they sent us after we submitted our application said we wouldn't hear until January, so maybe you'll hear next week!

Unless the professor has strong ties to faculty at the schools you're applying to (is an active collaborator with faculty you want to work with, mentored students that are now professors there, etc.), I don't think the fact that he received his PhD from MIT would really hold that much weight at all. And given that you say they are equally well known in their fields, what matters most is the quality of the letter they will write about YOU. You could contact one of the professors, ask if they'd be able to write you a strong letter of recommendation, and decide what to do based on the response you get. Are you applying this year? If not, you might have a better sense who to ask next fall. What is your relationship to each of these professors? Does one do research that is closer to what you want to do in grad school?

Hmm that's a lot less than other places I've gotten interviews at. But maybe if you use their travel people it might be cheaper or they'll be more likely to reimburse it? Luckily I'm probably just going to take a bus or train there. I put systems as my top choice.

Got mine today! See you there

I already replied in the other thread, but congratulations on all those interviews! I thought UCSF Neuro hasn't sent out invites yet. Did you apply to that program, or Tetrad, or BMS?

I heard from UC Berkeley Neuroscience on Dec. 16th and from Harvard PiN on Dec. 17th. I haven't heard from Stanford yet.