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Paired heavy-light modeling #92

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matsen
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@matsen matsen commented Dec 10, 2024

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@matsen matsen changed the title a sketch Paired heavy-light modeling Dec 10, 2024
@matsen matsen linked an issue Dec 10, 2024 that may be closed by this pull request
Do paired heavy-light modeling #57
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Will go along with https://github.com/matsengrp/dnsm-experiments-1/pull/66

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a sketch
dda468c 
WIP

WIP

next: fix nonzero subs prob for ^

WIP

WIP

remove joined_mode, make everything be joined_mode always

EOD commit: working on recovering OE plotting with changes

the final solution?

partial cleanup

some cleanup

more cleanup
matsen
matsen commented Dec 24, 2024
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Looking nice. Just a few suggested clarifications. I wonder if the way you are using "token" is more specialized than it appears.

netam/sequences.py Outdated Show resolved Hide resolved
netam/sequences.py Outdated
]
STOP_CODONS = ["TAA", "TAG", "TGA"]
# Each token in RESERVED_TOKENS will appear once in aa strings, and three times
# in nt strings.
TOKEN_TRANSLATIONS = {token * 3: token for token in RESERVED_TOKENS}
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So these are actually only reserved token translations?

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Prepended RESERVED_

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matsen commented Dec 28, 2024
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Seems like as elegant as one could ask for given the setting 👍

netam/dasm.py Show resolved Hide resolved
netam/dxsm.py Show resolved Hide resolved
netam/dxsm.py Outdated
# # The following can be used when one wants a better traceback.
# burrito = self.__class__(None, dataset, copy.deepcopy(self.model))
# return burrito.serial_find_optimal_branch_lengths(dataset, **optimization_kwargs)
# TODO
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Noting todo here

netam/framework.py Outdated
if chosen_v_families is not None:
chosen_v_families = set(chosen_v_families)
pcp_df = pcp_df[pcp_df["v_family"].isin(chosen_v_families)]
# TODO Does this seem like the right thing to do?
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I think we want AND here, not or. We want the H and L to be restricted to the specified set.

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matsen commented Dec 28, 2024

(BTW, because I initiated this PR, I can't approve it 😁 )

@willdumm willdumm marked this pull request as ready for review December 30, 2024 17:09
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matsen commented Dec 30, 2024

Great! @willdumm if you approve then you should be able to squash n merge.

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Do paired heavy-light modeling
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@matsen @willdumm