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@KenjiEricLee

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Find me at @ kenjilee on ๐ŸŸฆsky. Ph.D. student in the Chand Lab @BU_Tweets . @NIH_NINDS F31 Fellow. @cientificolatin mentor.

Boston, MA
Joined February 2018
Don't wanna be here? Send us removal request.
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
8 months
Tweeprint for those interested! We developed a method, PhysMAP, to identify cell types directly from electrophysiology and show that it interpretably reveals excitatory and inhibitory cell types (PV+ and SST+) of different layers in mouse cortex. 1/8
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
2 years
Flight attendant on the intercom: โ€œthank you for handing me all your poster tubes; there were 19 of them. You can pick them up at the front when you departโ€
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
4 years
@francois18 @cosmojellyfish Highly highly recommend the podcast Offshore by @CivilBeat if you want to delve into a nuanced, contemporary view of Hawaiโ€™i
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
7 months
Congrats to the GRFP winners! unfortunately for most, today they received disappointment. I was rejected from GRFP/CSGF/NDSEG likely because my GPA was awful. Here are the scores for my F31, years later. 1 = best (1 to 9). If youโ€™re good, theyโ€™ll see it eventually; keep at it.
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
4 years
From Bidenโ€™s Campaign Pledge on immigration, โ€œBiden believes that foreign graduates of a U.S. doctoral program should be given a green card with their degreeโ€
@deniswirtz
Denis Wirtz
4 years
We need to staple a green card to every PhD diploma earned by an international student. Trump's executive orders have hurt the reputation of the US for its openness to international scholars. We need to more than repair this calamity and canceling these orders won't suffice.
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
4 years
We are pleased to share our new study from the Chand lab at BU that uses UMAP and graph clustering on single-unit waveforms to identify candidate cell types in monkeys and their potential role in perceptual decision-making.
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@biorxiv_neursci
bioRxiv Neuroscience
4 years
Non-linear Dimensionality Reduction on Extracellular Waveforms Reveals Physiological, Functional, and Laminar Diversity in Premotor ... #biorxiv_neursci
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
4 years
@TonyZador The difference between the U.S. and other nations is absurd. Posting this graph in case some havenโ€™t seen it before.
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
2 years
At long last! First in vivo Neuropixels recording.
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
3 years
Chand Labโ€™s first neuron!! โšก๏ธโšก๏ธ๐Ÿง 
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
3 years
Super excited to announce our manuscript out in @eLife ! We developed an analysis, WaveMAP, combining graph clustering, UMAP, and interpretable ML. When applied to extracellular spikes, it uncovers cell type diversity hidden by feature-based methods 1/14
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
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Sometimes neurons will tell you *exactly* what theyโ€™re up to, no analysis needed :)
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
6 months
Delighted to see that grades will no longer be considered! If youโ€™ve done enough to get into a PhD program, they shouldnโ€™t be taken into account given theyโ€™re no predictive of grad school success.
@NIHgrants
Extramural Research
6 months
๐Ÿ“ขNIH is pleased to announce revisions to the fellowship application and review process for grant submission deadlines on or after 1/25/25. The goal is to improve the chances that the most promising fellowship candidates will be consistently identified.
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
3 years
It's a bit of a strong statement and I'm confused as to why the non-preservation of ambient distances is held up as some knock against UMAP when the UMAP paper explicitly eschews this. It doesn't preserve ambient distances because it's not supposed to!
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@lpachter
Lior Pachter
3 years
It's time to stop making t-SNE & UMAP plots. In a new preprint w/ Tara Chari we show that while they display some correlation with the underlying high-dimension data, they don't preserve local or global structure & are misleading. They're also arbitrary.๐Ÿงต
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
2 years
It was nice to finally go viral at least once before the meteor hit. Follow me at @kenji @fediscience .org I guess! For the interested, this was the Delta red eye out of San Diego to Boston on the last day of @SfNtweets . The attendant was very happy to help despite it being 10 pm!
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
11 months
Really really important work by Max Shinn to shine a light on how PCA can show oscillatory components from noise. A definite must-read for anyone in neuroscience. Phantom oscillations in principal component analysis | PNAS
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
4 years
@littleidiotgirI Who could forget this work of art?
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
7 months
BU is now threatening to dock the pay of striking grad students. My standard of living has actively decreased since starting my PhD but your support would go a long way towards helping us get back to a more stable living situation. Thank you and please RT!
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
1 year
This seems to me like itโ€™s just what happens when you apply PCA to noise: the top PCs resemble harmonics. Same issue is that one high-profile fMRI paper that showed harmonics over brain surface.
@mthiboust
Matthieu Thiboust
1 year
Cortical activity is made of rhythmic patterns of various frequencies. It resonates when stimulated at specific frequencies. Interestingly, resonant standing waves in the gamma band correspond to a spatial pattern of around 1mm (~ size of a functional cortical module?)
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
2 years
If you're headed to Cosyne this week, stop by and see what our lab has been working on! (also lmk if you're interested in hitting the local climbing gym!)
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
1 year
Finally here!! We were too scared to open the real box for a photo. Thank you @imec_int for the first sale of 4.5 cm NHP Neuropixels!
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
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New paper from Chand lab! We use multimodal graph combination to identify cell types in several areas of mouse ctx from ephys alone. Verified via optotagging. Building towards a future with cell types in every recording. Tweeprint when im not at Cosyne!
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
1 year
Why is this framed as โ€œprofessors vs. studentsโ€? As if, students are selfishly eating up lab costs and not instead giving up their 20โ€™s. If we want to tell students the โ€œreal costsโ€ we need to be transparent about graduate outcomes and talk about lost income opportunity costs.
@pauldauenhauer
Paul J. Dauenhauer
1 year
I honestly think @cenmag should do a story on this every year to provide all of the students real details on the actual costs associated with research and graduate school. Let's communicate the real situation
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
3 years
@gvanrossum Sapiens and Guns, Germs, and Steel sound great and all but theyre really just narratives spun out of scant to no evidence. Anthropologists sort of hate both books. is made of academics and they have a great reading list on the sidebar
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๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
2 years
From Cosyneโ€™s opening session: โ€œPillow lab won Cosyne this year as the only lab with 5 abstracts accepted!โ€ Me in the back: ๐Ÿค”๐Ÿซ 
@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
2 years
If you're headed to Cosyne this week, stop by and see what our lab has been working on! (also lmk if you're interested in hitting the local climbing gym!)
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
2 years
Waiting at the terminal post-SfN for a red eye to Boston and seeing people working on their Cosyne abstracts is stressing me the fuck out
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
2 years
Maybe not controversial but if youโ€™re interested in neuroscience, donโ€™t apply to neuro PhD programs. Theyโ€™re too ridiculously selective; go for affiliated programs. Also, no one cares about your double major or classes, volunteer in a lab 20 hours a week and youโ€™re set.
@MrJoeMilliano
Joe Milliano
2 years
Which of your STEM education related opinions would get you in this position?
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
6 years
@doristsao Welp. Just got into grad school and was so thankful to have my poor undergrad grades behind me but now I guess I can go back to worrying for the next 10 years.
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@KenjiEricLee
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@Metabo_Dave Iโ€™m one of the students who responded and these numbers are no surprise at all. I took way more issue that he seems to use it as an argument that studentโ€™s shouldnโ€™t advocate for greater stipends because it increases costs. Why not put the pressure on admins or founders instead?
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
3 years
@benoitbruneau @drbstewart Neither densities nor original Euclidean distances are preserved under this nonlinear dimensionality reduction. Therefore, velocity and distributional overlap donโ€™t make sense to compute.
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
4 years
@francois18 @cosmojellyfish @CivilBeat This is the most popular Iโ€™ve ever been! Check out my soundcloud!
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
5 years
Thanks to @univpugetsound for featuring me! Big thanks also to the PI's ( @SiddBits , Jรฉrรดme Lecoq, and @chandmuse ) and institutions ( @HBAEagles , @univpugetsound , @UW , @AllenInstitute , @BU_Tweets ) who've supported/believed in me! I should've put a better plot on the computer . . .
@univpugetsound
Univ. of Puget Sound
5 years
Logger Kenji Lee โ€™15 is intent on improving the treatment of neurological disorders. Today, heโ€™s a doctoral student at @BU_Tweets , teaching computers to understand the brainโ€™s commands so he can build better prosthetics: INNOVATE #LikeALogger . #PSsuccess
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
3 years
Time to play some โ€œDeepLabCutโ€ and some โ€œKilosort3โ€. ๐Ÿ˜ฌ
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
3 years
Love studying at coffeeshops in Boston/Cambridge: every laptop has up at least one of (a) Mendeley, (b) a manuscript in progress, or (c) a python/Matlab window.
@kaia_mattioli
Dr. Kaia Mattioli
3 years
i am at a restaurant and there is a man showing a woman at the bar a full blown PowerPoint of his research on transmembrane proteins?????? this is TOO BOSTON
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๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
1 year
We're excited to put out this protocol (now in @STARProtocols ) on how to use WaveMAP on your waveform dataset! It's been very bracing to see others use our tool and hope this manuscript will provide an entry point for others hoping to use it.
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
3 years
@Meliseymo Yup. Imo assessing the โ€œresearch potentialโ€ of late UG/early grad students off of a 2 page proposal is futile and ends up reinforcing existing inequities (I.e. GPA+prestigious undergrad+mentors who can help write good proposals). Itโ€™s a subsidy for already wealthy top schools!
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
4 years
@KateWassum (Incentive) structures in academia: how grants are evaluated; peer review process; how tenure packages are evaluated; what do hiring searches look for/how to appeal to industry; responsibilities/expectations of a PI; subfield-specific ecosystem of labs, conferences, and journals
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๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
1 year
Our updated manuscript with new DLPFC data that is consistent with predictions from our multi-area RNN model is now out and being reviewed at eLife! Congrats to @MichaelKleinman , PI's @JonathanCKao & Chand Chandrasekaran, @TianWang0318 , @ColeeCarr , and others!
@biorxivpreprint
bioRxiv
1 year
A cortical information bottleneck during decision-making #bioRxiv
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
9 months
I mean, for a PhD advisor, I would argue the mentor is one of the only things to consider and the research topic is almost entirely irrelevant.
@Johanna_A_Joyce
Johanna Joyce
9 months
You cannot underestimate all the positive and long-term benefits of having a great mentor. One could argue this is at least as important as the research topic. Do choose wisely.. #NationalMentoringMonth
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
2 years
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
8 months
Lisbon is looking amazing but bring your walking shoes! I was not ready for these cobblestone hills but I am ready for #Cosyne2024 .
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๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
3 years
@ATinyGreenCell @kaia_mattioli Ugh except I have literally done this on a date with a girl at a bar in Cambridge at the aptly named Miracle of Science. In all fairness, it was on my phone and she asked. She also showed me her manuscript on arXiv. There was no second date.
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
8 months
Come see work from the Chand lab (co-led by @TianWang0318 and I) on how the computational geometry of multiple tasks is preserved during decision making across macaque DLPFC and RNNs! Poster 2-016
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
2 years
Exciting things are happening!!!!
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
2 years
Got this fortune the other day and today it came true! Thank you #Cosyne2023 !
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
5 years
Thrilled to announce Iโ€™ll be attending Boston University in the Fall for a PhD in neuro! A big thank you to all who helped namely @matchings , @DrJigsaww , @adriana_et_al , @lucylai_ , @SiddBits , and others not on Twitter! And of course, @chandmuse for welcoming me to his lab!
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๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
1 year
Just published from the Chand lab! Congrats to all the co-authors on their hard work!!! 22 supplementary figures ๐Ÿ˜›
@PierreOBoucher
Pierre Boucher
1 year
New paper from the Chand lab! Initial conditions combine with sensory evidence to induce decision-related dynamics in premotor cortex
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
1 year
@pauldauenhauer Somewhat uncharitable but this easily reads as "You PhD students should feel lucky you're getting paid at all!"
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
4 years
@KateWassum Also all the computer things that are used in research but aren't taught in CS for life sciences classes such as linux, terminals, VCS, documentation, data standards (NWB), code reproducibility, real-time programming (NI or Simulink). Pretty much
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
6 years
@heysciencesam I use an iPhone app called CVSimulator to make sure all my figures are still clear for a variety of types of color-blindness
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
2 years
Is it possible for an animal to be *too* good at a task? Not session averaged! Perfect curves over only 300 trials! He focuses better than I do . . .
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
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@matsci_mikayla I have heard of faculty negotiating for one in their offer package lol. Explaining that if they want you to attend hoodings, they better be the ones to buy it for you
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
2 years
I was inspired by Krishnaโ€™s work as a freshman; some kids knew every football player and the teams they played on, I had scientist genealogies. I remember deeply wanting to be on this branch and, a decade later, there I am! Grateful for Krishna and grateful to be a part of things
@SussilloDavid
David Sussillo
2 years
Who was @shenoystanford ? The change in conversation from neuron to population, the development of dynamics in neuroscience, the advance of BMI to help humans with profound illness. But mentorship and care for his neuroscience family, as he would say, that was deepest Krishna.
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
5 years
Back home for break and decided to explore the park behind my house for the first time.
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
11 months
Boston people know this probability is, in fact, rather high
@NatlParkService
National Park Service
11 months
Your chances of being hunted by a turkey are low, but never zero.
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๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
1 year
@Metabo_Dave I get that it's hard to be a PI and have to watch the costs of doing science increase with no commensurate increase in funding but it's also hard to be a student experiencing the costs-of-living increases with no stipend adjustment. I take issue with valuing science over people.
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
2 years
Seconds from Disaster #neuroscience #SfN2022
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
3 years
I thought this way esp. as an UG/grad student in app. math. This changed after working in exp. labs for 7 years. I was ignorant about how complicated it all was until I started collecting data myself. I thought "complex math" would make sense of "complex data". I was very wrong.
@DavidAMarkowitz
David A. Markowitz
3 years
Last week, a prominent computational neuroscientist suggested to me that in 20 years we may look back and realize we already had all the experimental data needed to understand computation in the brain in 2022, but institutional failures held us back. Do others agree?
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
9 months
I've started to leave my phone (sometimes laptop) at work, even over the weekend. Biggest changes I noted: #1 I could literally read again like sit with a book for hours. #2 contentedness just to sit "doing nothing"; my mind is just so much quieter, commuting became meditation.
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
5 years
Awesome to see the Brain Observatory paper now out there! This was what I worked on for the past three years and the team effort of dozens of individuals at the Allen Institute. Congrats to all involved!
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
11 months
Once again beating a dead horse and saying taking a few years off before a PhD was the best decision ever. The Allen Institute matched contributions at 50% *up to the federal limit*. I put away $50k after tax and am halfway done for retirement after only 3 years!
@sciliz
A scientific lizard ๐Ÿงฌ๐ŸฆŽ
11 months
If you fill your Roth IRA for 10 years at the beginning of your career, and get 7% real returns, and never contribute another dime during 30 additional working years, we're talking $670k at retirement. 10 years in your 20s is worth so much more than 10 years in your 30s.
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
3 years
Cool results! Very gratifying to see people using Brain Observatory data; makes all those countless hours in the dark worth it ๐Ÿฅฒ
@achristensen56
Amy Christensen
3 years
My paper with @jpillowtime analyzing the Allen brain observatory Ca2+ imaging dataset is finally out! #tweetprint to follow
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
4 years
Please retweet! Come see what weโ€™ve been working on in my first year at our labโ€™s *first* poster, โ€œRevealing cell types in vivo via dimensionality reduction and graph clustering of spike waveformsโ€ (P380 @ 3:00 PM EST on 1/11). #SfNConnectome21
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
3 years
Yes this is why I worked for four years before a PhD through with an employer with a great match (50% to federal limit on a Roth 401k). Investing a modest amount of money that early is enough to retire on without even putting anything else in! So many students donโ€™t realize this.
@jordanjosbecker
Jordan Becker
3 years
1/ Most institutions do not offer 401k/403b plans to graduate students. This results in considerable loss to an already underpaid and undervalued workforce.
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
11 months
@WhySharksMatter Itโ€™s because we have to ask why he feels the need to address this to grad students? If itโ€™s a PSA, why not direct this to postdocs on the market? He tells on himself here
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
4 years
Mention in passing to grandma that I โ€œwrote a paper for schoolโ€ and now this
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
6 years
@doubleshelixpod @jpillowtime This was helpful but I think many of the questions were a bit too ... pointed? I donโ€™t think a grad student is likely to say what frustrates them about their PI outright; maybe instead asking them what sorts of qualities a grad student needs to succeed in that lab?
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
4 years
Iโ€™d never met someone with a PhD until I got to college. I donโ€™t think Iโ€™m gonna make it to faculty yโ€™all.
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
3 years
To summarize, it's unfair to criticize UMAP for something that it explicitly states it does not do (ambient distance preservation). In fact, this lack of ambient dist. preservation it's key to why UMAP works! Overall, this is a good awareness piece even if I disagree on the tone.
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
2 years
Come check out work from Chand lab (and collaborators @MichaelKleinman @JonathanCKao ) at our first SfN! We show, through neurophysiology and modeling, how PFC areas coordinate during decision-making. Also how we find cell types using Neuropixels/WaveMAP in macaque V1. Please RT!
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
7 months
One thing I didnโ€™t expect about monkey training/shaping was how individualized motivating them is: time of day, juice type, snack breaks, nap breaks, timeout length, secondary rewards, stochastic rewards, whether they like even the experimenter etc. very fun & very challenging!
@msokoletsky
Michael Sokoletsky
7 months
Mouse training is an art form, but there is one tenet I stand by: they naturally go from being hypermotivated to not motivated, and while you may control this to an extent by adjusting reward-to-punishment ratio, it's best to sort trials into states (e.g. Ashwood et al. 2022).
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
2 years
So I usually go a little stir crazy on my plane rides home but this time I had my F31 revision to work on; this time, more than anything, I was annoyed the flight had ended so soon! Even the couple across the aisle commented โ€œyou stared at a stack of papers the whole 11 hoursโ€
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
3 years
A lesson that needs to be taught to all grad students EARLY not just to understand how much they could be getting but also to understand the long-term opportunity costs of academia. Especially for quantitative types, this number is in the *millions* of dollars.
@kayteeflick
Kaytee Flick
3 years
PhDs must be recruiters' favorites for salary negotiations - we are so used to being underpaid and underappreciated and don't know our market worth at all.
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
3 years
Utterly floored that our lab's method was used in analyzing the first (?) human neuropixels recordings. Kudos to the team! Sincerely, I'm honored to have been able to be some small part of this historic effort. Another point on the board for UMAP!
@ACPaulk
Angelique C Paulk
3 years
Really proud to share our preprint on the work, and lessons learned, in using Neuropixels to understand the human brain with an incredible team. @EricMTrautmann @sergeydoestweet @MGHNeurosurg @MGHNeurology @shenoystanford @RMarkRichardson @MGH_CNTR
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
1 year
@pauldauenhauer And that's great for you! However, it is also important to realize that, as a mentor, not all students have that luxury. In fact, >90% don't. I too am grateful to be in a PhD program but gratitude doesn't keep a roof over my head.
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
6 years
This drained me emotionally, in the best of ways (like listening to Mahler). Besides being an incisive critique of the rot in Academia, both structural and specific, it's a sublime piece of writing. Maybe @theorygurl can write a take-down of life science?
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
4 years
UMAP got me my first first-authored manuscript in my first year! I canโ€™t overstate how useful it would be for so many neuroscientists but hasnโ€™t yet for no better reason than that they donโ€™t understand it. Read this thread (or DM me) if you donโ€™t!
@leland_mcinnes
Leland McInnes
4 years
The latest version of umap-learn is now out. Version 0.5 includes some major new features, including ParametricUMAP, DensMAP, AlignedUMAP, model composition, and model updating. Thank you to everyone who contributed! 1/14
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
4 years
I did *not* move all the way to Boston just for my family in Hawaii to get the vaccine before me! ๐Ÿ˜ก enjoy huffing that raw air.
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
4 years
Ugh why is there always a line outside of Trader Joeโ€™s
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
10 months
Anyone else headed to #Cosyne2024 ? I, uh, got my poster rejected but Lisbon is too good to pass up!
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
5 years
@gottapatchemall @neuromusic Algernon is that you?
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
2 years
@sabrinastronomy 1000%. I took 4 years post-bacc to build a nest egg and pay for loans and Iโ€™m relatively privileged financially (parents paid most of my tuition). People shaming others for going into industry have generational privilege and it shows
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
5 years
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
2 years
Quite frankly, I find this graph disgustingly racist. 1) Selectively disaggregating Asians and only showing those that are high-income but omitting/erasing others that are less so like Hmong, Cambodians, etc.
@paulg
Paul Graham
2 years
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
2 years
@EpiEllie Letโ€™s just say that after seeing Brookline public health fit a Gaussian to times series data (to show COVID was no longer a problem), I donโ€™t exactly have a lot of trust in their data-driven decision-making. Will leave an email though!
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
3 years
For a very long time Iโ€™ve been asking people for a guide to extracellular Ephys and the best reading out there was always โ€œthe Axon Guideโ€. Hereโ€™s what I wish I had years ago!
Quick ephys test: โšก๏ธ2 identical devices start acquiring at the exact same time & frequency. Why are they not synchronized? โšก๏ธWhen should you not connect GND and REF? โšก๏ธWhat happens inside a headstage? Drawing a blank or just want to know more? You're in luck! (1/6)
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
1 year
Thanks to Alex and the CCN for an amazing time!!! The institute and people (and food) were ๐Ÿคฉ. Not sure why I decided to mirror @emdupre_ โ€™s pose lmao
@ItsNeuronal
Alex Williams
1 year
Just wrapped up the @FlatironCCN Junior Theoretical Neuroscientist Workshop. Very grateful to have the opportunity to host this impressive cohort. We had a glimpse of the future and it looks bright!
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
1 year
When the mouse supremacists tell you that all of primate literature is suspect due to not accounting for uninstructed movements:
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@NatureNeuro
Nature Neuroscience
1 year
In primates, activity in visual cortex is minimally driven by spontaneous body movements. These results confirm the functional specialization of primate visual processing and contrast with findings in mice.
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
4 years
@mortenbc58 @ReichlinMelnick Not just โ€œinvolvement in American cultureโ€; immigrants and visitors are an essential component of what America is. Without them, there is no American culture.
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
2 years
Priced out of my Brookline apartment and, to rub salt in the wound, I just found out it's being filled with a bunch of MathWorks devs. #BostonGradSchoolLife
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
4 years
@ZombieFoodllc @cosmojellyfish Absolutely not but itโ€™s a common mistake to make. Hawaiian is a demonym reserved for those with indigenous ancestry. Itโ€™s a respect thing: Iโ€™m always a โ€œlocalโ€ but never โ€œHawaiianโ€ or โ€œnativeโ€ because I know Iโ€™m on annexed land.
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
3 years
@KaoLeeYang1 Without commenting on how oppression is defined and if itโ€™s a prerequisite for a particular definition of being โ€œunderrepresentedโ€ by the HHMI, the NIH and US Census consider Hmong (among other Asian ethnicities) to be underrepresented in the life sciences. Link below.
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
2 years
I have literally had a conversation too loudly at the climbing gym about my research and then gotten into an argument with a stranger about whether to use UMAP. I love Boston.
@shtriana
Sergio Triana
2 years
Peak Boston/Cambridge, there are UMAPs and Volcano plots in the train ads ๐Ÿ˜‚๐Ÿค“
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
2 years
@andpru Relatedly, I tell undergrads interested in neuro to pick a single major in math/applied math/data science and volunteer in a neuro lab 20 hours a week.
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
3 years
@ebblackwood @drdevangm Iโ€™ve always understood this in the context of being inclusionary towards techs and undergrads.
@vectorgen
Jason Rasgon
6 years
30. Authorship is cheap. Err on the side of inclusion, especially for technicians and undergrads
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
3 years
thus it shouldn't be "never use UMAP" but instead "if your latent dimensionality is far from the projected one, be careful interpreting it". This *doesn't* mean UMAP isn't useful for transcriptomics, only that the projected space can't serve as a map in the most literal sense.
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
9 months
I always find freely-behaving macaque studies so impressive and this is no exception! Now what I really want to know is how hard was it to train them to wear mobile eye trackers.
@Melissa_Franch
Melissa Franch
9 months
After 2 rounds of applying to graduate programs and 6 years of experimental and computational effort, I am incredibly grateful to present my dissertation work and first, first-author paper on social learning in freely moving macaques, out today in Nature!
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
11 months
I loved my time โ€œtime offโ€ but yes, Iโ€™ve started to see admits with first-authorships whereas speaking to friends who did PhDs a decade ago, any authorship was rare. Anon grad program this year (not mine) got a thousand apps for what might be 20 offers. Things getting out of hand
@drugmonkeyblog
Drug Monkey
11 months
@martinowk Now all of a sudden it is getting harder and harder to get into grad programs without first author pubs, plural. and "experience". postbacc and postbacc-like tech positions are moving from rare to advantageous and are heading towards obligatory.
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
9 months
Growing up I definitely took Hawaii for granted. This place was always just โ€œthat quiet park down the streetโ€.
@cathsimard_
CATH Simard
9 months
QT your most viral artwork
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
1 year
It's always a struggle to embed into 2D but UMAP/t-SNE/LE all do a pretty great job (it's clearest in UMAP) identifying the latent dim! I bumped up the Zipf dim. to make it easier visualize but all methods do very well. Can you guess what number I chose?
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@tiagopeixoto
Tiago Peixoto
1 year
How about this set if 10โถ x 10-dimensional points sampled i.i.d. from a Zipf distribution? Does the manual say anything about that? Keep increasing the number of points, and watch the medusa get more interesting. Friends don't let friends interpret UMAP plots.
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@KenjiEricLee
๐Š๐ž๐ง๐ฃ๐ข ๐‹๐ž๐ž
3 years
Contributing an intuitive guide to the steps of UMAP I made for our lab's paper. Follow the blue squares up until B vi.
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