First derivative #151

sjanssen2 · 2022-10-21T08:22:28Z

open questions

will this work in window mode?
what about non tabulated NTs?
check in Symbol::NT::set_ret_decl_rhs if other cases also need a "track" call
can we have situations in which same q edge is used multiple times but with different weights? ntX = add(ntA, ntB, ntC) such that moving bundary between ntB and btC with same ntA is used?

…ements

…ation

…IVES; generate method to print derivatives

…-recorded trace weights as backward pass;

…code" for both getters

… moving boundary and single split context

…shing a valid candidate to the answer list, we create a new list::statement "derivative_statements" onto which these code lines get added, such that other functions can then directly add these lines at various situations

refactor: derivatives_create_candidate

…stack | hairpin}

…neration

…for derivatives

…i.e. all weights combined

…ons, which should all compute identical first derivatives

H sum

adding a new command line argument for derivatives

0b3cda2

sjanssen2 changed the base branch from master to outside_looporder October 21, 2022 08:24

sjanssen2 added 28 commits October 21, 2022 10:27

adding novel rtlib header file for derivative computation

8dd2887

codestyle

830d8d4

add a convenience function for debugging, which prints a list of stat…

7820102

…ements

reorder declarations for better debugging

584f093

let the AST know that the user requested code generation for derivatives

fc73e8b

enable adding another argument to the front

19458b7

injecting first statements in inside code

5d388d2

adding first derivatives test

60c364c

add functions to generate getter and setter for derivatives

b35e257

report derivatives instead of outside results

50b95aa

pass calling-NT to alt code generation

eb7ed8b

moved additional functionallity from generated *.hh to here

4084123

make OUTSIDE_NT_PREFIX more visible in grammar.hh

6afe046

record user provided axiom, since it will be changes in outside gener…

087fabc

…ation

pass ast to init_ret_stmts

60d2e7c

add "candidates" list in NT generation to record use of sub-solutions

44677b5

define functions for derivative reporting function generation

69cfed9

inject and init new traces Vector in Table Declartion; define DERIVAT…

ecef00b

…IVES; generate method to print derivatives

pass calling-NT to alt code generation; for outside-NTs: retrieve pre…

58f7af2

…-recorded trace weights as backward pass;

adding scoring algebra for derivative testing

402a382

use proper return variable name

8f600a0

move execution of statements to a) enable debugging and b) use same "…

40b4a23

…code" for both getters

moving functionality into own function, since it need to be called in…

4da7e91

… moving boundary and single split context

alts might be parameterized Terminals. Don't inject in these cases

ad1c566

activating two more tests: needleman wunsch derivatives

e01e058

adding Gotoh grammar for further testing

2f9cdc2

codestyle

edc2495

sjanssen2 and others added 29 commits December 9, 2022 13:28

Merge pull request #162 from jlab/todo_derivatives_create_candidate

efa94cf

refactor: derivatives_create_candidate

also inject derivative recording code for simple blocks like weak = {…

26c6eca

…stack | hairpin}

enable trace recording for nested Blocks

5159bcf

throw warning when using blocks - for now

e06053f

set recursion base to 1.0 for first derivative computation

23b388f

add Sonne-Regen test

c9cf750

add probabilistically proper Sonne Regen HMM

2de7319

log space requires re-transformation here

d9fcd54

replace h with sum

1ace193

add function to replace h with sum in outside rules for derivative ge…

6e59960

…neration

fixing type optimization for derivative versions of choice functions

e7eb90f

remove tab

c6a3cd0

adding normalize_derivative functions

99962ec

pass the user prodived normalization function as another argument

30a1b90

lint & typo

0623602

new semantic check that tests for presense of normalization function …

77c0f39

…for derivatives

make special normalization "static"

acbef3a

run check for derivative function

75f306f

use passed user function to normalize a trace VS partition function, …

2131890

…i.e. all weights combined

when searching for answer type, skip choice functions

c7979c5

revert stupid error: type inference independent on actual check

76d87dd

definding alternative algebras with different probability normalizati…

634ed8e

…ons, which should all compute identical first derivatives

fix error msg generation and print body of missing function

09383e1

add checks for normalize_derivative addition

8bd63fb

add choice function for summation over negative logarithms

5044024

Merge pull request #164 from jlab/hSUM

7a1656a

H sum

Merge branch 'master' of github.com:jlab/gapc into hSUM

fa97cd9

Merge pull request #169 from jlab/hSUM

68ab4f0

H sum

Merge branch 'outside_looporder' into first_derivative

ac5fa8f

fymue mentioned this pull request Jun 13, 2023

Outside #187

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First derivative #151

First derivative #151

sjanssen2 commented Oct 21, 2022 •

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First derivative #151

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