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,...
cloud budget = more than chains × CPU price. include parsing, retries, idle VM time, storage etc... all the tiny charges add up :/ retrospective summer 2026 direction: move the evaluation framework toward standard published protocols and cloud...
alignment accuracy, tree recovery, parameter recovery, mixing — separate axes. faster iterations are nice but ESS/time is the more useful number. Also come back to the fixed-tree vs fixed-alignment controls. code-reading pointers in the plan:...
need both biological + simulated cases. simulation gives known history; structural references are a different check, can't just call both “truth” and move on. saved reference: BAli-Phy biological-versus-simulation evaluation . The June 13...
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...
putting the summer pointers here before everything becomes a mystery folder. keep commands, seeds, versions, control files... a plot alone is not going to help me rerun anything. dated record: August 11 is the final summer meeting in the shared...
biological params → synthetic cases w/ known history → reconstruction tests. Keep the dependencies between params, random plausible values individually could still make a very weird family together. Benchmark problem: using an already...
confidence coloring could be useful, but first: confidence in WHAT exactly. Same width doesn't mean same homology, and missing confidence needs its own color / legend. uI idea: display confidence on alignment positions or tree nodes, rather than...
high likelihood but chain stuck in one spot... not really the win to reward. Need credit for exploration too; revisit ESS + clade summaries before deciding what the score should mean. working distinction: a high joint log-likelihood and good...
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...
saving the JBrowse demos, especially the synchronized views. how does a selected sequence / column / node keep its identity across panes? also maybe a back button for selections would be useful, not just more settings. july 7 references:...
alignment + tree + ancestral history = one state. no casually swapping bits between samples and creating a franken-tree; scoring inputs need to travel together meeting topic: June 30 covered EvolDeeds, indel models and pairHMMs. The later...
substitutions vs indels vs alignment paths—separate piles before this becomes model soup. pairHMM: which paths get summed over, which one gets picked? meeting topic: the June 23 log identifies substitution models of sequence evolution and...
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...
summer reading map, otherwise these repos are going to blend together in my head. Main thing to keep asking: what's fixed input vs what the sampler can actually change? dated record: June 9 begins the 2025 summer lab meeting series. The meeting...
PDB chain → TreeFam sequence → PyMOL, need the residue numbering to survive all 3. Missing residues / partial structures are the annoying bit here. Save for later: same highlight following a residue between sequence and 3D views? recorded...
