Cophysneurec

If you look at the number of applicants for schools that release data for previous years (Duke, Cornell for example) the number of applicants in the 2021-2022 admission cycle was very much within normal variation. So if the beginning of the pandemic didn't budge numbers too much, I don't think that this years numbers will depart from previous years very much either (aka there should not be a flood of applicants this year).
Anecdotally while there are people who delayed applications because of Covid, in my experience there are also people moved their application up a year for various reasons (I did as well as some other people I know). So it's kind of a wash.

I would probably not mention it. Say something along the lines of "despite struggling to find my way in my first two years of college, I overcame adversity and realized I need to take a different approach. This is why I did far better in the second half, despite having a tougher workload."  Obviously you'll need to wordsmith this and make it sound polished and convincing, but you get the drift."

Other people may have different opinions on this, but I would also be worried about it being judged negatively, and the people on admissions committees are just humans like us, so I would leave it off.
It would be another story if you didn't have a long history of improvement. But lots of people screw up at the beginning of college.  Do you have some research experience and some close relationships with professors to write you letters? These will also help.
I had Bs in calculus and a B- in linear algebra first year of college and it didn't present huge obstacles for me in stats PhD admissions. 
 

Honestly, Twitter was the best resource. I follow PIs whose work I'm interested in to keep up to date but importantly they will retweet when a colleague is starting a lab somewhere. If that lab was interesting to me, I contacted the new PI and expressed interest and asked if they wanted to chat over Skype or in-person at SfN. Out of the PIs (not just new ones) I contacted, roughly half responded and I chatted with most. I chatted with every new PI. I also went to SfN that year and met about 6 or 7 in-person but unfortunately the conference probably won't happen this year (probably virtual). I'm still friendly with a lot of the new PIs I talked to! They really *really* appreciated the earnest interest in them before they even appeared on the department faculty pages. They still come to my posters and retweet papers I've written! 
DM me and I will send you a link to my blog with a ton of intimate details about my application process.

My profile, background, and interests are extremely similar to yours! I have worse grades however but maybe not by much. I had much more extensive research experience. 
GPA 3.1 overall (2.9 in math major/3.0 in biochem major), 3.75 last two years (includes masters in math)
GRE: 167/163/6.0
Post-bacc (Masters): 9 graduate applied math courses: scientific computing, numerical linear algebra, convex optimization, complex analysis, PDEs, dynamical systems, etc
Research experience: 3 years undergrad neuroendocrinology, one third-author IF of 5. 3.5 years post-bacc sys. neuro. unrelated to MS with 5 mid-author papers (IF 5 to 22). 
Programming: 8 years of experience (6 in Python, else in MATLAB). Some professional experience in software development without the title. 1 year consulting on time series forecasting too. (Told you we had similar profiles!)
LoR's: two great and one average. All research advisors.
Papers: 1 3rd (IF 5), 1 2nd (IF 3), 6 mid-author (IF 22 to 5). Many posters several first-author at SfN.
 
Here's how I did for schools:
Rejections: UW, Stanford, Harvard, MIT, CMU/Pitt (PNC), Columbia, NYU, Princeton, UCSF, UCSD
Rejected/Waitlisted after Interview: CMU Bio, BU GPN
Accepted with fellowship: UO neuro (bio dept.), SUNY Stony Brook
 
Frankly, I think your grades are on the cusp of okay but will still get you filtered out from many of the top schools (and you're shooting probably too high). Be sure to network early and often especially with new PIs who will appreciate your interest and be more willing to take on a student. They can send the committee a message saying "so and so is perfect for my lab. Please at least bring them to interview." You'll also want to take a look at direct admit programs. UCSB is one of them and on your list.

This sounds like a great idea. Economics programs hold a ‘math camp’ during the summer before the first year, and I have heard it can be invaluable.
 
I have another thought on this issue, and I want to preface it by saying that creating opportunities for disadvantaged individuals to pursue higher education, elite careers, or what have you, is extremely important and valuable for everybody over the long term. My thought is basically just this: how much of this burden should fall on universities and their faculty? It seems like preferential admission of disadvantaged people can be a source of hope of opportunity and possibility  for the younger generations (particularly helping those who would feel forsaken by birth or by consequence of some event), and those who succeed in the system can later become role models who guide those facing similar difficulties. 
 
I wonder though if creating disruptions at the frontier of research is really the best way to do things. My feeling has been for some time that we need to ramp up free, quality education at the k-12 level with free clubs and activities for all students, better systems to identify gifted students, free daycare programs so that teenagers are not expected to care for younger siblings, free associate degrees and perhaps more. I understand that women tend to face difficulties with differences of communication styles when in majority male environments. Maybe I am blind, but I have not noticed any discrimination towards women in math or science among my peers. It seems to me there is a certain stigma around becoming an engineer or mathematician that evokes a very nerdy numbers obsessed and un-feminine stereotype. But is this stereotype just a function of the subject matter? Is it pernicious in some way? I feel that these career paths also tend to turn off the most masculine men who would not mesh with this stereotype either. I keep hearing about data in Norway showing greater behavioral divides between the genders resulting from greater gender equality, and I really wonder if women face exogenous (others discriminating against them) difficulties with higher math/engineering, or if many women happen to have personalities that don’t always mesh so well with the lifestyle of a math geek or engineering nerd. Sorry for rambling, I’m not trying to impose my view on anyone, but I’m hoping for your thoughts and feedback as my perspective is of course limited.
 
I would just like to add that I think there’s a good chance that women tend to be slightly more gifted in stem areas (based on higher overall college and especially k12 achievement). And I think it would be wonderful for the scientific community of there were more women involved. But even with that, the proportion of women in the medical fields is very high as far as I know. 
To the poster above, please consider the validity of that test. Aside from that, interventions based on such a test have been shown to have net zero or net negative effects. It seems like bunk science to me. Maybe a better measure is needed. 
http://www.hcdi.net/reliability-and-validity-of-implicit-association-test/

So you believe that test-taking ability is the only important indicator of research potential? Did you know that many people with learning disabilities, adhd, or anxiety disorders tend to systematically underperform on tests, regardless of their intelligence, creativity (actually more creative individuals may very well perform worse in a testing environment, all else equal) or research potential? It seems you’ve only thought about yourself in writing this, which is uncharacteristic of a good researcher.

From my experience, STEM subjects requires a lot of time and drilling to grasp foundations and build on previous concepts. As someone who had to work three jobs to pay for college, my socioeconomic situation did not lend itself well to succeeding in STEM. I relied on pulling multiple consecutive all nighters to cram rather than spreading learning over time, which research shows is better for digesting information. 
As a woman who went on to work in industry, I've also experienced blatant discrimination, from superiors preferring to work with a male intern rather than me, a full time employee who owns the subject space with the feedback "they would rather hear this from a man" to a male manager telling me I should "be less direct so people will think you're more approachable." @stemstudent12345 experience with high school class resonated with me. I had wanted to take AP Physics my senior year, having already taken AP chem and bio, and my counselor me girls usually have a hard time in AP Physics and to keep my grades stellar, he moved me out of that class for TA period. I don't share this to complain, only to provide examples of additional external factors that created obstacles for me to do my job or succeed in my career, since we're talking about perspectives and broadening of minds. Generously, maybe none of these examples have anything to do with my gender. Maybe I am way too direct in communication in a business setting. Maybe the audience would rather hear the forecasting model that I build explained by a man. Maybe I would have failed at AP Physics and my counselors saved my GPA. That is how I have to reframe my thinking in order to do the work I care about and spend time and energy dwelling on this instead. I don't doubt that men have problems of their own but sure would be nice to not have these doubts hanging over my head.
 

I'm sorry, I see how my comment came across that way, but I truly didn't mean to imply that you personally didn't value fairness of opportunity. 
I can only speak from my own experiences, which mostly don't contain overt gender discrimination, but I suspect many experiences were subtly gendered nonetheless. For example, when I brought up with an undergraduate professor that I was considering an accelerated masters program in statistics, he encouraged me instead to pursue studying abroad and to consider grad school in a social science field. Now maybe this wasn't about gender at all (this particular professor was very encouraging usually); but I suspect my gender played a part in his response. In high school, when I wanted to take more advanced math classes than what my school offered, my teachers gave me a textbook and after-hours access to the computer lab so I could self-study. One of my male classmates who wanted more advanced classes got the same resources, but also got approved for an independent study where he received one-on-one instruction from a math teacher. Maybe my male classmate pushed harder for the independent study, maybe he was just better at math so the school saw more potential in him, or maybe it was some other factor, but maybe it was about gender. Even thinking back to elementary school, when I did well in math classes or proclaimed that I liked math, many well-meaning adults in my life suggested I could become a K-12 math teacher, rather than suggesting I could become a scientist or an engineer (math teaching is a super honorable and important profession! Don't get me wrong, I just wonder if a young boy who loves math would be told the same thing).
There is also the aspect of microaggressions. In numerous meetings, classes, and seminars, I've seen women's questions brushed off as an annoyance, female Ph.D.s called by their first name in circumstances where their male colleagues were called Doctor, and women interrupted more regularly than their male counterparts. I've seen countless online professor ratings that reduce women to their looks or to their personality, rather than evaluating them the merits of their teaching and fairness of their grading. Like I mentioned in an earlier comment, women are sometimes the ones people first ask to take on unpaid service work, such as helping organize holiday parties or coordinating visit weekend. While these are ostensibly minor issues, I think they contribute to pushing women out of the mathematical sciences and other STEM fields.

It's totally possible that you just have better peers than I do and that they aren't discriminatory! Unfortunately that's not the case in my department. I guess I would say that different numbers of women earning Ph.D.s and becoming professors in STEM fields isn't the only evidence of discrimination in the field, so I don't really find the argument that the discrepancy is due to personality differences compelling. There's a huge body of research on things like implicit bias, interruptions in meetings, subjective credibility of authors/teachers based on gender, etc. (not all of which depends on the Harvard IAT) which I think all important to consider. 

So you're proposing "a college entrance exam (kind of how its done in some foreign countries)" (point 1). And then you said "Nowhere did I suggest people should be evaluated on such exams," referring to timed, closed problems, on strict standards.
So logically, your entrance exams would be untimed, or consist of open problems, or not be standardized. And these exams would be like those in some foreign countries, so supposedly there are countries that operate like this (not just at one program, but some country's programs operate like this). What countries do this?
 Then presumably students would have to take standardized qualifying exams (point 2), because if they are not standardized across programs your (point 3) is entirely nonsensical. So these routine qualifying exams would be untimed, or consist of open problems (based on your own response, since they would be standardized). If your audits do nothing, no program would comply. So you would need to punish them for poor performance by your metrics. How? Funding? How is funding determined when all programs are expected to perform above the same threshold? Do government grants then take into account the compliance rating of a given program? Ok, but this doesn't work. The tests are untimed, remember? So the program can simply instruct students on the exam material during the exam... Or if not, the exams consist of open problems, which makes no sense (timed exams where students are expected to solve open problems in order to stay in the program??). How do you even construct fair exams containing open problems that are standardized by field and timed??
 And schools would be audited for low graduation rates by some overarching body (point 3) so you are advocating for centralized control of the graduate educational system. So many issues with this. Who decides what areas of research in a given field are worth evaluating?  These questions are hard enough at the K-12 level. 
How do you evaluate students on "grant writing" in a standardized way across institutions? If you do not standardize this process, what incentivizes programs to invite audits upon themselves due to low graduation rates? What is comparative advantage?
Exam is a very misleading term as you are using it. Perhaps evaluation would be more appropriate? 
rec letters: based on ability to get along well with superiors and peers, grades, testing, research experience.
GPA: based on aptitude, consistency of work ethic, testing, and whatever else.
Of the three you listed, two reveal much more about an individual than how they perform on tests. My logic never indicated that testing should not be considered in the evaluation of an applicant or progress assessment of a graduate student. I simply pointed out that test scores alone can fail to capture many important facts regarding someone's research potential. 
So far you write like a flopping fish, this way and that, with no clear direction, although any which way you flop you are confined to a space with no practical arguments as Mao Zedong smiles upon you. 

I am well aware that test-taking ability as you seem to define it, is not the most important indicator of research ability. Your statement about those with learning conditions systematically underperforming is valid for those taking highly structured time pressured exams with closed ended problems, designed to be evaluated on a strict set of standards; there are plenty of studies about it. 
Nowhere did I suggest people should be evaluated on such exams, though today it very much is at the undergraduate level. One method for examination is in grant writing/fundraising, which should be a key skill of a researcher. In one of the programs in bioengineering, their qualifying exam consisted of writing a grant proposal in a simulated environment over a semester. The students were then evaluated on how well they were able to convey their ideas, and some could not proceed with the program. This would be one example of a potential "exam." Regardless of learning conditions, poor communication skills can only hurt.

Further, rec letters, GRE, and GPA are one of the biggest factors in admissions already, Typically, faculty prefer to write for students who perform well in their courses (scored well in coursework and made a good impression) - granted I have seen rare occasions when faculty write for poorly performing students (made a good impression). By your logic, do you suggest to remove all metrics based on testing? After all, those with the learning conditions you listed are at a disadvantage already in the current system. My proposed exam strategy, though ill-defined, is not restricted to exams in your narrow definition, and it is ultimately up to the discretion of the university on the content of the exams. 
Testing in the traditional sense is never a good way to assess research ability, and this is well known fact. Gradcafe is an online forum, where people may express ideas in an informal manner, and should never qualify as evidence for research ability. Your inability to discriminate where people state opinions and where research capability is demonstrated, as well as your amiss ad hominem statement about my research ability is highly uncharacteristic of a professional let alone successful researcher.
You're also missing the point too. stemstudent12345 rightly understood it to be a meritocracy based system. Adcoms trying to predict whether students will be successful the way it is done today, is subject to a lot of bias, e.g. being a certain race may cause certain members in the adcoms to view your application more favorably/unfavorably. Using your model analogy, what good is a model that evaluates covariates with a bias? I do not suggest throwing away all covariates, but replacing them with ones that are less subject to bias, and more indicative of merit. Exams take on many forms, and each one should be designed to indicate a student's research potential and likelihood for success, which should be determined by the universities and exam committees themselves. And I've acknowledged that there are resource constraints making this infeasible. 

I think I understand what @TroyBarnes is saying. I think the original post was about AA though, and I think its a difficult topic to address, since everyone thinks they worked hard to get where they are, and rightly so. So for admissions committees to disregard these small nuances is wrong. 
Making it a pure meritocracy does not solve the problem's that AA aims to solve. For example, my uncle worked part time while studying in school to cover life's expenses, while my other uncle had everything paid. They both later applied to the same graduate school with similar academic profiles, but arguable my first uncle worked "harder" since there was more he had to juggle.
On the other hand, admitting for the sake of diversity alone is also wrong. Some jobs use ethnic background as a proxy for AA, but we know its not solely about race. As OP may suggest in the academic setting, it may even get to a point where the department doesn't care for the student's success so long as other students are successful and the DEI quota is met. I'm sorry you're going through that OP, you sacrificed a lot of be where you are now. I hope your department takes note of your plight and does something in your favor about it.

So you believe that test-taking ability is the only important indicator of research potential? Did you know that many people with learning disabilities, adhd, or anxiety disorders tend to systematically underperform on tests, regardless of their intelligence, creativity (actually more creative individuals may very well perform worse in a testing environment, all else equal) or research potential? It seems you’ve only thought about yourself in writing this, which is uncharacteristic of a good researcher.

So you believe that test-taking ability is the only important indicator of research potential? Did you know that many people with learning disabilities, adhd, or anxiety disorders tend to systematically underperform on tests, regardless of their intelligence, creativity (actually more creative individuals may very well perform worse in a testing environment, all else equal) or research potential? It seems you’ve only thought about yourself in writing this, which is uncharacteristic of a good researcher.

Here's a hot take on how I think academic institutions SHOULD operate in an IDEAL world. 

1) Admit any one who wants to attend based on a college entrance exam (kind of how its done in some foreign countries)
2) In specified periodic time intervals, there are qualifying exams to be taken. Those that fail below a certain cutoff will have to leave the school (analogous to PhD exams) 
3) Those that can finish all the coursework and pass all the exams are able to graduate (schools graduate too few/too many students a year should be audited for quality of education)
This is not to say problems with AA and gender bias would disappear, as those with the privilege of accessing resources from a younger age would still benefit - they always will. But this way opens up a larger playing field, where everyone has a chance to succeed, and whether a student can study at an institution is not dictated by a biased admissions committee who decide your capability to succeed based off of a few pieces of paper.
And this way, instead of diversity becomes a moot point, and they would admit you based on your capabilities that you will prove yourself rather.

This is just my hot take, please don't downvote me into oblivion. I understand that there resource constraints that render all of these steps infeasible. But something just doesn't sit right with me in the current way admissions in grad and undergrad are handled. 

Why are you recommending Kent state in all of your comments?

Why are you recommending Kent state in all of your comments?

I know both the applied math and neuroscience programs at UW well. It's always UW because they don't want to be confused with WashU. The applied math and neuro programs have very different approaches to who they choose and both are extremely selective so I'd be very careful. The applied math programs looks for A's in upper-division math courses like intro to analysis or abstract algebra and also that you took graduate level courses and did well. The neuroscience program is like any top neuro program in that they highly value grades but especially research experience and good LoR's. 
UW is highly highly interdisciplinary when it comes to applied math and neuro: it seems like almost half the AMATH faculty there are affiliated with neuroscience. Big names here are Eric Shea-Brown, Raj Rao, Bing Brunton, J. Nathan Kutz, and Adrienne Fairhall among many others. They also have a comp neuro training grant and very active collaborations with the Allen Institute for Brain Science which is every theoreticians dream given the amount of high-quality data they produce.

Great! If you have any other qs feel free to DM me.  I can give you my email address, it'll be easier to talk there.  Maybe depending on your interests, I can suggest some faculty.

This is exactly what I'm thinking at the moment. I'm digging the math more than anything and not super set on any one specialization. In that case, I will start studying for the GREm, and I may very well end up applying to both econ and applied math programs next fall. Thank you so much for your insight!

Ah okay! From my knowledge, it seems that math programs will care much more about test scores/gpa/solid math background, and less about the specifics of your research background.  I can't speak to too many programs, but UC Davis, UNC Chapel Hill,  and UW seem like they have classic programs that people with interest in mathematical biology apply to.  Specifically, I think that NYU would be a great fit for your interests in computational neuro, and I can try to answer some questions about the environment/requirements there if you have any questions!  The math department has tons of faculty with various applied math research interests.

Oh I see. I’m definitely leaning towards applied math programs. I value the interdisciplinary possibilities and quantitative side much more than the particular specialization in neuroscience, although neuro is probably my primary area of interest outside of math itself.
I made another post in this forum about applied math programs after realizing that I would probably want to do computational neuro from a math program. That post has more info on my background and profile.

^^ The reason I say this is because the admission requirements (or desires) will depend heavily on which home department you decide to base yourself in.  I can give some advice on neuro and math programs, but the requirements, I think, will be quite different between the two.  Do you know which department you'd apply to?

Hi! are you applying to specific computational neuroscience programs?  I didn't think that MIT and UW had specific Ph.D. programs in computational neuroscience.  Usually, students base themselves in a home department, and conduct interdisciplinary research or join a specific training grant within the overall program.