score row → family → input → chains → decoder. keep that trail intact or this becomes a spreadsheet séance... which is a terrible debugging strategy September 17 evidence cutoff: local repository e2b603d5 , as recorded in the milestone...
C = 36 from the one-SE rule, raw max was 144. ESS/iteration jump looks huge, ESS/hour much less dramatic... use the latter for compute planning. recorded calibration: fifteen proposal weights × three seeds = 45 points, each with 2,000...
keep chain-specific points next to pooled results. starts, decoder, version, model, budget all differ here, so don't squint at a scatterplot and blame everything on one thing. diagnostic panel: 24 families, two 30-minute chains per family. The...
flat alignment length trace can still hide completely different homology. ugh, need diagnostics that actually notice that. Save idea: animate samples w/ residue identities fixed, watch the pairings move instead. why scalar traces are...
runtime fit ends way before the longest family, big extrapolation gap. Need an actual packed-VM throughput test before trusting the cost math; 3 chains on one machine might just slow each other down. runtime model: nonnegative fit using sequence...
tiny smoke runs for execution → decode → burn-in → pooling. raw-OK can still leave zero usable samples... useful failure to catch before paying for the bigger run. simulation panel: six original conditions, twenty datasets each, 27 taxa,...
fixed two-bar case, actually enumerate the source + diagonal options. ties count with multiplicity; don't lose one just because the costs happen to match Worked window in Supplement S2: a=0.049 , b=0.105 , midpoint c=0.077 , half-width h=0.028 ....
seed isn't the whole reproduction recipe. draw order + versions + tolerances + finite-bar conventions too, otherwise same seed / different diagrams somehow Protocol distinction: the supplement's 300 cloud-pair stress study uses a common ruler of...
Interesting experiment- how well does AI critique? useful ones: what am i preserving, what gets discarded, why choose this over the simpler calculation? source provenance: the files are stored under Claude Review . Their referee-report style and...
sneaky normalization problem: cloud barely changes, its ruler does. suspicious now of comparisons where every object gets its own convenient ruler manuscript concept: a “ruler” is the positive scale dividing pairwise distances. If two clouds...
Unity → React/TS for the patient side, Electron console + Python signal engine. Keeping the folder map here; check the pending list before assuming a whole path is hooked up architecture revision in the engineering specification: replace the...
one pull for EEG + IMU, not two consumers fighting over the inlet! Check channel order/counters too. later: tiny timeline viewer for markers + sample gaps? code pointers: signal-engine/acquisition/ , MockUnicornOutlet , and...
artifact gates need the raw branch, before filtering/CAR can hide the thing being rejected. Also keep SOS state across chunks — check resets + chunk-size changes specified real-time chain: latched DC-offset subtraction → causal filter chain...
ERD formula + calibration timings here so I stop hunting around. near-zero baseline? check trial split BEFORE generating overlapping windows, sneaky leakage possibility Feature definitions recorded: ERD% = (Pbaseline - Ptask) / Pbaseline * 100 ;...
held score ≠ fresh score. Need artifact flag + null sub-scores, and don’t keep updating EMA/normalization while holding Specified score: IntentScore = w_eeg*EEG_Score + w_kin*Kinematic_Score - Penalty_Compensation , normalized to 0–100....
lost arm tracking ≠ arm stayed still, ugh this needs an explicit state. Check frame age all the way through WebRTC. Save for later: small camera-confidence indicator instead of making someone watch a skeleton overlay? target path: browser...
pairing codes: expiry, second browser, reconnect, sidecar dying. Need to try all the annoying paths, especially browser still connected while Python is gone lAN responsibilities: serve the React build over HTTPS, pair one browser to a live...
same packets through pure model + rendered game, compare behavior. Log the difficulty staircase too; higher score could just be easier targets game references: docs/gardengrow.md and docs/reachcollect.md ; patient-web/src/garden|reach/ for...
trace ONE window all the way from filter to hand command. primer and code should agree on the intermediate objects, especially covariance / tangent space / readout primer architecture: filter EEG, estimate sliding covariance, log-map it to...
7 populations, signed connections, PT readout. check the stability notation... spectral radius can't be negative, need the largest real part where i'm talking about continuous-time stability model in the anatomical draft: a two-dimensional...
tangents parking lot: Takens, PLLs, bifurcations, time scales... a loop still doesn't tell me speed or phase. keep coming back to that manifold question: does low-dimensional activity reflect a circuit constraint, a restricted task, or both?...
TDA on EEG can mean direct signal, connectivity, or delay clouds. need to check which object each paper is actually using before borrowing the method three analysis routes preserved in the review notes: filtration directly on a signal, topology...
can i build W and U around the feature geometry instead of hoping a random matrix behaves? keep the desired modes + input projection explicit, spectral radius alone isn't the full story february open problem: given Riemannian feature trajectories...
multiple primitives + rest + fast transitions, not just one nice stable cycle. wondering if faster switching makes the individual patterns harder to stabilize problem statement from the open-problems document: active movements are intended to...
EEG / reservoir / hand / maybe EMG + feedback... lots of possible pieces. keep the options here without making all of them prerequisites for the first version brainstorm structure: divide the prosthesis into mechanics, control, sensing and...
BAli-Phy wrote to baliphy-1, don't accidentally read the older folder. keep C1.run.json, numerical trace, trees + sampled alignments together; check the realized model there. SCOPt3 log: output is written under...
SIGSEGV followed by “trace parsed successfully”... seriously 🙃. process status and parser status need separate fields, partial output can still look completely readable. september 2–3 runtime log: SCOPt3 and SCOPt1 Historian processes...
start from cleaned families, keep filter counts alongside the params. Especially the class imbalance — don't let the tiny SCOP groups disappear into one pooled histogram. Source pipeline: Pfam v36 seed alignments and associated FastTree trees,...
sample within the birth–death regime, then invert the log / logit transforms carefully. Check rejection rates too, otherwise the nice fitted distribution isn't necessarily what comes out the other end. modelfit.py workflow: split parameter...
tree generation + annealing toward Colless / gamma targets. Need to see how far annealing moves things away from the original birth–death samples. Side rabbit hole: how many completely different trees share those same 2 stats? tree_gen_bd.py:...
raw trace → TSV / alignments / trees → scores. check what survives a failed run, plus leaf names and burn-in at each step. TreeStat errors belong here too, not buried somewhere in the terminal. artifact chain: raw Historian/BAli-Phy output...
equal iterations vs equal time, still need both views. “iteration” isn't necessarily the same amount of work across tools + concurrent processes can mess with timing. report design: Experiment 1 uses four representative SCOP parameter sets...
actual control file has different insertion + deletion rates... compare against the symmetric-settings description. Need to pair this file w/ the exact inference command, not assume the report settings match. recorded run: the INDELible log names...
gp120 trace: branch/node alignment moves, heights, rescale, prune/regraft. Count accepted / rejected / no-change separately, best likelihood alone misses most of what's happening. timestamped trace: Some log records MCMC starting July 15, 2025 at...
SATe reading — zero-event branches get contracted for PIMT. Interesting metric question: why penalize a branch distinction the sequence data never supported? keep the original tree too. paper notes: Liu et al., SATe, 2009 . The presentation...
Lambert W again... branch choices matter. keep the 1:1 response assumptions beside the inversion before using the quadratic shortcut elsewhere Theory reference: the theorem packet reduces a single-input response to f(x) = w*k*x*exp(-x/tau_m) and...
walk through attribution on a tiny graph. edge cost, combined path costs, averaged update—can actually do this by hand before scaling up later proposal: identify synapses in a layer with sufficiently similar timing errors, collect their...
coupled weight / plasticity system. negative plasticity-direction eigenvalue is only one piece; check the other slope + event updates too source evolution: the earlier packet labels the central result a theorem; the later preprint labels Section...
code map for finding things again. PDF filenames can run into the preceding text—check the repo when the boundary looks strange Repository reference: blizzard-labs/NMCtests . The March 2025 Code Base.pdf is an archived listing containing...
350 ms on, 150 ms settling—keep the rest of the schedule beside it. split / frozen weights / what “robustness” means all need to line up Later paper's stated protocol: static image presentation for 350 ms, followed by 150 ms to allow state...
these tables need run IDs. match split + settings + version before picking numbers from different drafts There are at least two result-table versions. The native MesoNet Data sheet reports MNIST accuracy 98.11% and CIFAR-10 56.6% for MesoNet....
demo list = trail back to scripts. heatmap, weight display, Turing map... find the config behind each, not only the slide what the organizers preserve: lists of intended live demonstrations—standard STDP learned weights, Lyapunov heatmap,...
what exactly gets checked before sourcing? changed dimensions should invalidate old instructions + quote, not leave three convincing versions floating around recorded workflow in the submission checklist: design selection/customization →...
DSP names changed between drafts. keep early distance/significance idea separate from later variable plasticity + triangulated attribution early formulation: the MIT THINK draft calls the mechanism Distributed Synaptic Plasticity (DSP). It...
DoG branch, different from bipolar TSC. flat image vs one sharp edge would be a useful tiny check—esp if thresholding leaves no latency events reference implementation: imgClassifierSDNN/src/dog_filter.py , explicitly attributed in the code to...
27.5% vs 10% markup — different draft bases, need to untangle. Shipping/review time/returns/payment fees all still count; don’t confuse markup w margin Keep the versions separate: the final write-up describes a 27.5% markup on supplier...
unsupervised features, then labels for readout assignment. keep assignment data away from the held-out evaluation set Readout functions: get_neuron_assignments(spike_counts, labels) assigns each neuron to the digit class with its largest mean...
connectivity experiments + SOM tangent. small-world / scale-free / recurrence, and how would a continuous SOM update turn into spike events? january 4 notebook content omitted from the first short collection: initial Brian2 neuron/synapse tests,...
STDP constants + handlers together. find where on_post is attached, not just where the string is defined Location: base_model/mnistV1.py , the stdp_eqs , stdp_eqs_pre and stdp_eqs_post strings. The prototype uses taupre = taupost = tau , with...
wrapper loop check: normalize, encode, run, count, clear, rest. reshape return + capture_period condition look worth slowing down for entry point: base_model/main.py → evalInstance.train(num_examples, target_weight, single_run_time, rest_time,...
