Promote fatty, and give every molecule a readable name - #271
Merged
Merged
Conversation
) Two data efforts, each of which ended somewhere other than where it started. #257 β THE FOOD SIDE OF THE BROAD HEADS. Calibration had already lifted sweet, ethereal and pungent over the 50% precision floor, but only by making them very reluctant to fire (thresholds 0.75 / 0.64 / 0.66) and they sat exactly on 0.50. Food-authorised character molecules were added to all three, plus fatty as a control. The results split cleanly: fatty n_pos 27 -> 41 AUROC 0.854 -> 0.917 precision 0.21 -> 0.51 PROMOTED sweet n_pos 208 -> 210 AUROC 0.718 -> 0.727 precision 0.50 -> 0.50 unmoved ethereal n_pos 98 -> 106 AUROC 0.924 -> 0.920 precision 0.50 -> 0.50 unmoved pungent n_pos 289 -> 295 AUROC 0.792 -> 0.802 precision 0.50 -> 0.50 unmoved "Broad" was never the discriminator β chemical COHERENCE is. fatty looks like an umbrella but is structurally crisp (mid-chain aldehydes, free fatty acids, lactones), so sixteen molecules more than doubled its precision. A sweet SMELL can be a lactone, a furanone, a vanillin, an ester or carbon tetrachloride; there is no shared substructure for a Morgan fingerprint to key on, so curation cannot touch it. That is a hard boundary on the method from #247/#256/#262, and it is pre-registered on #199 as a falsifiable prediction for the GNN. No industrial odorants were removed to achieve this β the additive approach from #257 held. #217 β NAMES. The premise was wrong, and finding that out was the work. A full PubChem crawl on Title AND IUPACName (the crawler previously asked for IUPACName only, which is why inorganic salts and glycosides kept coming back empty) resolved 41 of 784. An InChIKey lookup did WORSE than SMILES, 1/12 against 2/12, so the brittle-matching theory was wrong too. The remaining 743 are not lookup failures. They are the long tail that arrived with the broad food/safety universe: 159 multi-component salts, 197 very large structures, 100 peptide-like, 13 carbon-free. PubChem indexes salt components rather than the mixture, and most of these are not flavour-relevant at all. No crawl will ever name them. So instead of chasing names that do not exist, every molecule now falls back to its molecular formula, with multi-component structures labelled as mixtures rather than pretending to be a single substance (CaI2O6 (mixture: Ca+2 + IO3- + IO3-)). A raw SMILES in the grid looks broken; a formula is honest and tells a chemist something real. master_enrichment: 8,861 molecules, 8,861 named β down from 770 blank. Also reverted a failed chamomile rescue. Its additions were sesquiterpenes shared across many heads (bisabolol, farnesene, germacrene D), which made chamomile itself worse (0.691 -> 0.670) and cost the roster four confident heads. Same generic-molecule mistake blackberry taught us; the revert restored 108 capable. Roster: 166 aroma heads, 108 confident-capable, 58 indicative. Signed-off-by: Austin L. <86896075+rvnminers-A-and-N@users.noreply.github.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Closes #217. Follows on from #257 (closed with its finding recorded).
Two data efforts, each of which ended somewhere other than where it started.
#257 β the broad heads split cleanly
Calibration had already lifted
sweet/ethereal/pungentover the 50% floor, but only by making them very reluctant to fire (thresholds 0.75 / 0.64 / 0.66), sitting exactly on 0.50. Added food-authorised character molecules to all three, plusfattyas a control:fattysweetetherealpungent"Broad" was never the discriminator β chemical coherence is.
fattylooks like an umbrella but is structurally crisp (mid-chain aldehydes, free fatty acids, lactones), so sixteen molecules more than doubled its precision. A sweet smell can be a lactone, a furanone, a vanillin, an ester β or carbon tetrachloride. No shared substructure means no fingerprint can find it, and curation can't touch it.Hard boundary on the #247/#256/#262 method, pre-registered on #199 as a falsifiable GNN prediction. No industrial odorants were removed β the additive approach held.
#217 β the premise was wrong, and finding that out was the work
A full PubChem crawl on Title and IUPACName (the crawler had only ever asked for IUPACName, which is why inorganic salts and glycosides came back empty) resolved 41 of 784. I then theorised PubChem's SMILES matching was brittle and tested InChIKey lookup β it did worse, 1/12 against 2/12.
The remaining 743 aren't lookup failures. They're the long tail from the broad food/safety universe:
PubChem indexes salt components, not the mixture, and most of these aren't flavour-relevant. No crawl will name them.
So every molecule now falls back to its molecular formula, with mixtures labelled honestly rather than pretending to be one substance β
CaI2O6 (mixture: Ca+2 + IO3- + IO3-). A raw SMILES in the grid looks broken; a formula tells a chemist something real.master_enrichment: 8,861 molecules, 8,861 named β down from 770 blank.Also: a reverted failure
The
chamomilerescue backfired. Its additions were sesquiterpenes shared across many heads (bisabolol, farnesene, germacrene D) β chamomile got worse (0.691 β 0.670) and the roster lost four confident heads. Same generic-molecule mistakeblackberrytaught us earlier. Reverted; 108 capable restored.Verification
master_enrichment(8,861),profile_index(8,842 Γ 177),flavor_mapsudo systemctl restart flavormancerβ models and all three artifacts changed