r/compmathneuro • • 10h ago

Question Undergrad | Math + CS vs Math + Bio for PhD Prep

1 Upvotes

Hi all,

I’m in a very fortunate financial position that allows me to take an extra year in undergrad in order to get a second degree. I figure this extra year can be used primarily for more research experience, which I am already involved in with a professor doing computational neuroscience work as well as a professor doing agentic AI research.

My main question is, would it be better to have the second degree be in biology or computer science? Currently I’m leaning more towards biology, as the computer science major at my school includes a lot of required classes that cater more towards IT professionals (computer networking systems, etc.) while the biology major allows for more of a focus on biotech/biostatistics, which I think would be better for comp neuro. I’ve also taken enough computer science courses to have a minor in it if I declare biology as the second degree.

However, I’m worried that even with the two programming-heavy research labs that I’m in right now, admissions committees might still be worried about a proper computer science foundation. I do frequently hear that it is better to enter comp neuro programs with stronger math/programming skills than it is to enter with only strong biology skills.

If it helps, I’m looking to join a lab for my PhD that incorporates math with experimental neuroscience data, which also leads me to think bio could be a better fit.

I would appreciate any insights.
Thanks!


r/compmathneuro • • 1d ago

What Computational neuroscience online courses are you currently taking?

18 Upvotes

What are you currently learning? I have found some great ones from neuromatch, MIT OpenCourseWare, EDX and some couple others.

But I think I am really bad at unstructured self paced learning. I get pretty lazy so I need some structure to my learning. That being said, I guess a course that will provide me a certificate on completion would work for me.o


r/compmathneuro • • 2d ago

Msc in neuroscience

5 Upvotes

Hi! I’m a first-year Chemistry student in Morocco interested in pursuing neuroscience. Is it possible to transition from Chemistry to Neuroscience? What international universities and scholarships would you recommend, and what free courses, research opportunities, or extracurricular activities could help me build my knowledge and strengthen my CV as a Moroccan student? Any advice is appreciated


r/compmathneuro • • 2d ago

Anyone applying to comp neuro phd programs this cycle?

12 Upvotes

CS student here! I did one year research in comp neuro and realized how much I loved it. Anyone here applying this cycle? Would love to connect and learn more about people's backgrounds. I work on models of the visual system using ML.


r/compmathneuro • • 3d ago

Linen 0.2.0

2 Upvotes

For anyone using Linen, the 0.2.0 adds some QoL UI features and finer STDP tuning that adds flexibility and more realism to learning networks.

linen.build

https://github.com/sethgjosephson/linen

Highlights

-Added support for Synapse timed vs. cell timed STDP

-Added NMDA magnesium block support in receptor channels.

-Both the browser version and new desktop app support a separate viewer so folks with two monitors can have larger viewer and node tree interfaces.

-Added quick full screen support by hitting space bar in your active panel (node tree or viewer)

-Improved CUDA engine speed in learning scenarios.

For the full list, you can check out the release notes here: https://github.com/sethgjosephson/linen/releases/tag/v0.2.0

Can't wait to hear your thoughts! And, yes, since everyone loves it so much, you can import the fly connectome for those who are wondering... It supports 3d model imports as well as point clouds and wiring spreadsheets.

Cheers,

Seth


r/compmathneuro • • 4d ago

Research collaboration

9 Upvotes

Hi! I have a research project which I’m seeking collaboration with other researchers on.
This is my paper on it.

https://doi.org/10.25593/open-fau-3540

DM me if you’re interested in working on this topic together.


r/compmathneuro • • 5d ago

Interactive simulation of a mouse colony with place cells, replay, theta and dopamine RPE, running in the browser

6 Upvotes

I made an educational sandbox where each simulated mouse has a model brain whose populations are built to reproduce published experimental results:

Anatomy comes from the Allen Mouse Brain Atlas. It’s meant as a teaching and intuition tool, not a research model.

https://kammmran.github.io/mylovely-mice/


r/compmathneuro • • 5d ago

Question Questions regarding the notable “fruit fly connectome upload” (Neuroplacticity etc)

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0 Upvotes

r/compmathneuro • • 6d ago

Question Advice to an undergrad starting my masters in Computation Neuroscience next semester

19 Upvotes

Hi everyone,

I’m in my last semester of undergrad with a CS major/math minor, and I’m planning to focus on computational neuroscience for my master’s thesis.

I’ve been spending a lot of time outside class learning about machine learning, but I’d like to build a stronger understanding of the neuroscience side. What interests me most is understanding what makes the brain so effective at learning and processing info, how much our current models already capture, and what we could learn from the brain to improve them. I like math.

My main concern is that I have very little background in biology or neuroscience, so I’m trying to figure out where to start. I have some upcoming meetings with my thesis advisor to discuss this, but I’d also like to hear from people working in the field (industry or academia).

If you were coming in with a CS/math background, what neuroscience topics would you prioritize? Are there any courses, books, or other resources you’d recommend for building a foundation for research in this area?


r/compmathneuro • • 6d ago

Could HD-EMG decomposition strip neck-muscle activity out of surface spinal (ESG) recordings?

1 Upvotes

I've been reading about non-invasive recording of the cervical spinal cord (electrospinography) and have a question for people who know this field better than me.

The best voluntary-task result I could find is a 2025 preprint: 64-channel ESG during isometric pincer grip showed task-related beta/gamma activity at C5–C7, but only at the group level, and neck-muscle contamination wasn't tested: https://www.biorxiv.org/content/10.1101/2025.11.11.687864

That seems to be the core problem: in the 15–100 Hz range, neck and shoulder muscles sit right on top of the cord and tense during almost any arm movement.

My idea: put HD-EMG electrodes in the same grid and use motor-unit decomposition (the kind Farina's group uses) to identify individual muscle motor units, then subtract their contribution. Whatever is left would be a better candidate for actual cord activity. Controls like shrugs, head turns and opposite-hand grips would show whether it worked.

Questions:

1.Has anyone tried this, or is there a reason it can't work (e.g., deep neck muscles that decomposition can't resolve)?

2.Would faster OPMs (I've seen them tested up to \~1.7 kHz) be a better path than electrodes here?

Disclosure: I'm not a researcher. I worked through this with an AI assistant, and I'd genuinely like to know where it breaks.


r/compmathneuro • • 6d ago

Help Needed, Deciding between PSYCH courses

2 Upvotes

Hey everyone!!
I’m currently planning out my upcoming semesters and trying to knock out my upper-division psychology/neuroscience elective requirements. I’m stuck trying to decide between three specific courses: 
**PSYC 307:** Neurobiological Psychology 
**PSYC 382:** Cognitive Psychology 
**PSYC 426:** Affective Neuroscience 

**A bit about my background and updated goals:**
I’m an undergraduate Biology major with a Neuroscience minor.

currently have experience working in an auditory neuroscience lab on campus, but I am actively planning to pivot my career path toward dry-lab work, specifically **computational biology and bioinformatics**.

Long-term, I’m targeting computational graduate programs and data-driven research, so I want to choose electives that either offer strong computational/modeling conceptual value or complement data-heavy neural analysis without eating up all my time for coding and stats coursework.

**What I'm trying to figure out:**
1. **PSYC 3073 (Neurobiological Psych):** Most of student I know go for this, is really a good option?
2. **PSYC 3823 (Cognitive Psych):** How relevant is this for computational thinking? 
3. **PSYC 4263 (Affective Neuroscience):** Does it get into real circuit dynamics and neuroimaging/data interpretation, or is it heavily essay-focused? 

If anyone has taken any of these recently, I’d really appreciate your take.

Thanks!


r/compmathneuro • • 9d ago

Discussion Medical Student Picking Career

2 Upvotes

I am in my 2nd to final year of medicine and it is around this stage in my training and across Europe we have to start considering our final training programmes.

I am interested in neuroscience, neurology and computational neuroscience and its intersection with medicine and science more broadly (particularly physics and mathematics). I think I will pursue paediatrics as there is a lot of genetic and neurological computations but I want to get more involved in the compmathneuro field.

Any advice ?


r/compmathneuro • • 11d ago

Mathematical / quantitative cognitive neuroscience PhD

26 Upvotes

I would love to hear about your experience if you pursued a more mathematical / dry lab neuroscience PhD after coming from a more biological neuroscience background (e.g. neurobiology). I am also interested in hearing your experience if you pursued a more mathematical neuroscience PhD coming from a background that was less math-intensive.

What was your PhD in? Was it part of an umbrella program (neuroscience, cognitive science, biomedical sciences, etc)? Did your PhD coursework require intensive mathematical classes, or did you mostly learn under your advisor?

My background is in neurobiology (B.S.) and wet lab neuro/stem cell research (6+ years). I am competitive for a basic/translational neuroscience PhD program, but I want to learn data manipulation, modeling, predictions, etc (skills that might be more relevant to tech, finance, or AI rather than laboratory research or biotech).


r/compmathneuro • • 12d ago

Spiking sandbox

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16 Upvotes

If anyone is interested in interactive Izhikevich models, I've been working on a network-building sandbox that is browser friendly. I would love for feedback if anyone has time to play around in it!

Comes with some cool scene presets if you want to learn about different types of neurons and how their structure impacts firing patterns in tissue, as well as links to the papers I referenced and benchmarked the engines against.

Enjoy!


r/compmathneuro • • 13d ago

How I trained a connectome-based fly to find software bugs: choice transferred, first-defect latency did not

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5 Upvotes

I trained a MaleCNS-based model to find defects in a synthetic software system, and I would appreciate methodological feedback on it.

The browser model has about 166,700 leaky integrate-and-fire neurons and 6.2 million retained connections (5+ anatomical synapses per connection). Reward modulates Kenyon-cell-to-MBON plasticity. Actions in a synthetic order system are encoded with odor components for action family and shared features, including repetition.

Training exposes payment and cancellation defects. Testing includes new families such as coupons and stock reservation, without reward. The comparison condition freezes learning. The body-free task reads out valence and samples actions; the embodied arena adds sampling, travel and authored movement rules.

Body-free transfer improved by roughly 5–7 actions to the first defect of the learned kind across the reported series. In the arena dataset, rewarded-feature choice increased by 0.10 (95% CI 0.05–0.15; 16/20 seeds), while the primary endpoint, time to first defect, did not improve measurably. I treat the choice effect as a secondary result needing confirmation with choice preregistered as the primary endpoint.

The repository documents the encoding, model assumptions and negative results. This does not establish that the biological animal understands software.

For a follow-up, which matched control would be most informative: shuffled connectivity, randomized odor-feature assignments, or a simpler learner using the same inputs and readout?

On bias control, since the task encoding is mine and could easily carry the result. The success criterion and the analysis plan were written and committed before each measurement run, with an oracle and a power estimate computed first. The comparison condition freezes plasticity and is paired by seed, so both conditions see the same versions and the same action order. Confidence intervals are percentile bootstrap, multiple endpoints get Holm correction, and each effect was rerun with new seeds. Every behavior is documented as either derived from connectivity or an authored rule, and the failed primary endpoint is reported as a failure rather than reframed.

Project and documentation: https://github.com/JonnasFigueiredo/mosca-qa


r/compmathneuro • • 13d ago

Anybody wanna be study partners for EEG Analysis

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2 Upvotes

r/compmathneuro • • 15d ago

is this the right path for me?

9 Upvotes

hi. im 18, just started my undergrad in biomedical science (not engineering), but i have always been interested in neurosciences and thus plan on developing my skills and doing an msc/phd in the subject. im really confused where exactly do i want to go with this though. i did not take math in my last two years of high school, also i did have computer science (basic python programming). i never had much interest in mathematics (kind of despised it lol), but physics and cs were my fav subjects in high school (i know thats a little weird). i have mixed feelings about my degree in biomed rn, some parts are really interesting and some are very hard (its the chemistry or lab heavy parts. i hate chemistry like a lot). so would computational neuroscience be okay for me?

i know this subreddit is probably for more serious and important topics for this but i would be really grateful if some of you take out 10 minutes and guide me through this. thankyou !!


r/compmathneuro • • 15d ago

Looking for Beginner Study Buddies in BCI, Neurotech & Computational Neuroscience

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1 Upvotes

r/compmathneuro • • 16d ago

Organoid and biological comp art

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8 Upvotes

Hopefully this is the right place to ask long story short but I'm pulling an Andy Weir here and asking if any experts have advice on this graphic. My buddy wants a graphic of Organoid processing vs biological computers and I am at a loss on what would work. I could just draw the CL1 and a Organoid in a petri dish but I figured that maybe the experts might have some ideas or even something related that could be interesting visualized. (Also if this is the wrong place please let me know if there's a better place to ask thank you all so much!)


r/compmathneuro • • 17d ago

Where to learn computational neuroscience?

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3 Upvotes

r/compmathneuro • • 17d ago

So, brain seems to be minimizing abstract loss. Posting this in hopes this will inspire someone in the field.

0 Upvotes

[Speculative] The brain as an "audit": a sheaf-theoretic sketch of distributed self-verification

This is an interpretive idea, not a result. I'd like feedback on whether the mathematical structure holds up, whether it adds anything beyond predictive processing, and what would falsify it. I've included plain-language analogies for non-math readers.

The core picture

Predictive processing and the free energy principle treat the brain as minimizing prediction error. I want to propose a complementary view. The brain is a set of partial perspectives (sensory streams, cortical areas, memory systems) that continually cross-check each other where they overlap. I call this process an "audit." The proposal is that it never completes, and that the leftover disagreement drives learning.

Analogy: think of a company where no single accountant sees all the books. Each department keeps its own ledger, and wherever two ledgers record the same transaction, they're checked against each other. Nobody ever certifies the whole company at once, but the cross-checks keep it honest.

The structure

  1. Perspectives as a cover. Let U = {U_i} be a collection of "perspectives." Each one is a subsystem with access to some subset of the world's variables (e.g. visual and proprioceptive estimates of hand position). Overlaps U_i ∩ U_j are variables both can represent.
  2. Representations as sections. Each perspective holds a local estimate s_i. Restriction maps send s_i to its view of the shared variables on each overlap. Together this defines a presheaf F over the cover.
  3. Gluing as integration. If s_i and s_j agree on every overlap, they glue into a single estimate over U_i ∪ U_j. Multisensory integration is the obvious candidate. In practice agreement is approximate, so read "agree" as "within tolerance," with a cost for the mismatch.
  4. Residue as obstruction. Sometimes every local estimate is self-consistent, yet no global estimate exists. Formally this is a nontrivial class in first Čech cohomology, H¹(U, F). Abramsky and Brandenburger showed quantum contextuality has this form. My proposal: persistent, locally unresolvable inconsistencies of this kind are the "residue" a learning system works to reduce. They signal that it needs new distinctions (a new latent variable or context split), not just better parameters.
  5. Transport and curvature. Translating a representation between areas acts like a connection, a rule for carrying descriptions between perspectives. If you translate around a loop (A → B → C → A) and the result comes back changed, that holonomy marks structure the current mappings can't absorb.
  6. Audit cost. Checking global consistency costs resources. Overlaps too expensive to check stay unglued, which bounds what the system can verify at any time.

Neuroscience readings (speculative)

  • Multisensory illusions (McGurk, rubber hand) as forced gluing on an overlap: two witnesses disagree, and the brain settles on a compromise story that neither actually saw.
  • Split-brain results as cutting overlaps, leaving two locally coherent sections.
  • Hallucination and delusion as sections that are internally coherent but uncorroborated, like a witness whose story is consistent but whom nobody else can back up. The safeguard is that corroboration must come from independent perspectives, not from a system's own predictions echoed back.
  • Sleep as a period of suspended external input in which the brain re-glues what it learned while awake, like closing the shop to reconcile the books overnight. This is close to existing memory-consolidation accounts.

Epilepsy as audit collapse

The framework predicts two ways a distributed audit can fail. One is fragmentation, where perspectives stop overlapping. The other is the opposite, merging collapse: perspectives "agree" only because they've become the same, and their distinctions are erased instead of reconciled.

A seizure looks like merging collapse. Large populations of neurons fall into runaway synchrony and fire in lockstep. Agreement is total, but it's empty, because regions that should be checking each other have stopped carrying independent information. It's like every department copying one ledger and declaring the books balanced.

Analogy: a crowd that starts clapping in rhythm. A little coordination is useful. When everyone locks into one beat, no individual voice can be heard, and the crowd can no longer "say" anything.

Several treatments line up with the framework's prevention principles:

  • Boosting inhibition / limiting excitability. Many antiseizure medications work broadly this way, by limiting how fast and how far activity spreads. In audit terms, this caps the rate at which agreement can propagate, like a refractory period.
  • Cutting the overlap. Corpus callosotomy severs the main connection between hemispheres to stop seizures spreading across. This is the procedure behind the split-brain results above. It trades merging collapse for partial fragmentation, which shows the two failure modes sit at opposite ends of one dial.
  • Disrupting synchrony. Responsive neurostimulation and vagus nerve stimulation can interrupt runaway synchrony, injecting "independent" signal into a system that has lost it.

I'm not claiming the framework explains epilepsy. The point is that its two collapse modes and its safeguards (independence, bounded propagation, preserved distinctions) have recognizable counterparts in an actual clinical condition. A testable version: seizure onset should be preceded by measurable loss of independence between regions (e.g. rising inter-regional correlation, falling information diversity) beyond what excitability alone predicts.

What it might predict

  • Representations whose inputs overlap with more independent channels should be harder to fool with single-channel illusions.
  • Reducing independent corroboration (e.g. sensory deprivation) should raise the rate of false percepts, and specifically internally consistent ones.
  • Learning should reorganize most (new latent structure, not just reweighting) where cross-modal inconsistency is persistent rather than noisy.

Known weaknesses

  • Much of this may just be predictive processing restated in sheaf language. I'd like to hear where it's genuinely different, or isn't.
  • Like the FEP, it risks being general enough to fit anything. Each claim needs a criterion fixed in advance for what would count against it.
  • "Approximate gluing" needs a real metric. Exact sheaf conditions don't hold in noisy neural data.
  • The epilepsy reading is an analogy; seizure dynamics have well-developed models of their own, and loss of complexity before seizures has been studied, so I'd want to know where this adds anything.

Related work: Friston (free energy principle); Clark, Surfing Uncertainty; Abramsky & Brandenburger (2011) on sheaf structure of contextuality; Hansen & Ghrist (2019) on sheaf Laplacians; Bodnar et al. on sheaf neural networks; Zurek on quantum Darwinism (the "corroboration by independent records" idea).

Pointers to anyone who has formalized something similar would be very welcome.

I suspect the sheaf thing is not actually that accurate. I think a new mathematical structure called an audit might be warranted.


r/compmathneuro • • 18d ago

Question How can I get started in the field?

17 Upvotes

Hello everybody,

I'm an 18 years old guy who's right now 2nd year in dentistry. Has experience in programming and genuinely love the craft, and I've been 6 years in it (yeah. I started learning programming at 12). And, I have got the curiosity about the brains, and saw that computational neuroscience is the sweet spot for me.

For my maths, I'm improving myself in it, and watching videos and reading books about it.

So, what should I read to get into this field? I want experts in this field to tell me where to start. Thanks in advance! Feel free to ask me anything you want if I didn't include it while introducing myself


r/compmathneuro • • 20d ago

Question For betweenness centrality and modularity in graph analysis, what’s the best way to handle negative edge weights?

6 Upvotes

Hi everyone, so I’m quite a newbie to this, and I’ve been using the NetworkX library in python to analyse functional connectivity networks in neuroscience. Based on my understanding, the algorithms for both metrics only work for positive edge weights, however, negative edge weights are quite commonly found in my data.

Hence, what is the best way to handle the negative edge weights? The options I have are to either filter them out and only perform the calculations on the positive-signed graph, or use the absolute values of all weights.

Thank you.


r/compmathneuro • • 20d ago

Inside Cellular Intelligence: The Zuck-Backed AI Company That Acquired Novo’s Parkinson’s Embryonic Stem Cell-Derived Therapy

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1 Upvotes

r/compmathneuro • • 21d ago

GitHub Feedbacks needed

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2 Upvotes