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First derivative #151

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@sjanssen2 sjanssen2 commented Oct 21, 2022 •
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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?

@sjanssen2 sjanssen2 changed the base branch from master to outside_looporder October 21, 2022 08:24
@sjanssen2
adding novel rtlib header file for derivative computation
8dd2887
@sjanssen2
codestyle
830d8d4
@sjanssen2
add a convenience function for debugging, which prints a list of stat…
7820102 
…ements
@sjanssen2
reorder declarations for better debugging
584f093
@sjanssen2
let the AST know that the user requested code generation for derivatives
fc73e8b
@sjanssen2
enable adding another argument to the front
19458b7
@sjanssen2
injecting first statements in inside code
5d388d2
@sjanssen2
adding first derivatives test
60c364c
@sjanssen2
add functions to generate getter and setter for derivatives
b35e257
@sjanssen2
report derivatives instead of outside results
50b95aa
@sjanssen2
pass calling-NT to alt code generation
eb7ed8b
@sjanssen2
moved additional functionallity from generated *.hh to here
4084123
@sjanssen2
make OUTSIDE_NT_PREFIX more visible in grammar.hh
6afe046
@sjanssen2
record user provided axiom, since it will be changes in outside gener…
087fabc 
…ation
@sjanssen2
pass ast to init_ret_stmts
60d2e7c
@sjanssen2
add "candidates" list in NT generation to record use of sub-solutions
44677b5
@sjanssen2
define functions for derivative reporting function generation
69cfed9
@sjanssen2
inject and init new traces Vector in Table Declartion; define DERIVAT…
ecef00b 
…IVES; generate method to print derivatives
@sjanssen2
pass calling-NT to alt code generation; for outside-NTs: retrieve pre…
58f7af2 
…-recorded trace weights as backward pass;
@sjanssen2
adding scoring algebra for derivative testing
402a382
@sjanssen2
use proper return variable name
8f600a0
@sjanssen2
move execution of statements to a) enable debugging and b) use same "…
40b4a23 
…code" for both getters
@sjanssen2
moving functionality into own function, since it need to be called in…
4da7e91 
… moving boundary and single split context
@sjanssen2
alts might be parameterized Terminals. Don't inject in these cases
ad1c566
@sjanssen2
activating two more tests: needleman wunsch derivatives
e01e058
@sjanssen2
adding Gotoh grammar for further testing
2f9cdc2
@sjanssen2
in order to add statements for tracing within the IF condition for pu…
4af9441 
…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
@sjanssen2
codestyle
edc2495
sjanssen2 and others added 29 commits December 9, 2022 13:28
@sjanssen2
Merge pull request #162 from jlab/todo_derivatives_create_candidate
efa94cf 
refactor: derivatives_create_candidate
@sjanssen2
also inject derivative recording code for simple blocks like weak = {…
26c6eca 
…stack | hairpin}
@sjanssen2
enable trace recording for nested Blocks
5159bcf
@sjanssen2
throw warning when using blocks - for now
e06053f
@sjanssen2
set recursion base to 1.0 for first derivative computation
23b388f
@sjanssen2
add Sonne-Regen test
c9cf750
@sjanssen2
add probabilistically proper Sonne Regen HMM
2de7319
@sjanssen2
log space requires re-transformation here
d9fcd54
@sjanssen2
replace h with sum
1ace193
@sjanssen2
add function to replace h with sum in outside rules for derivative ge…
6e59960 
…neration
@sjanssen2
fixing type optimization for derivative versions of choice functions
e7eb90f
@sjanssen2
remove tab
c6a3cd0
@sjanssen2
adding normalize_derivative functions
99962ec
@sjanssen2
pass the user prodived normalization function as another argument
30a1b90
@sjanssen2
lint & typo
0623602
@sjanssen2
new semantic check that tests for presense of normalization function …
77c0f39 
…for derivatives
@sjanssen2
make special normalization "static"
acbef3a
@sjanssen2
run check for derivative function
75f306f
@sjanssen2
use passed user function to normalize a trace VS partition function, …
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…i.e. all weights combined
@sjanssen2
when searching for answer type, skip choice functions
c7979c5
@sjanssen2
revert stupid error: type inference independent on actual check
76d87dd
@sjanssen2
definding alternative algebras with different probability normalizati…
634ed8e 
…ons, which should all compute identical first derivatives
@sjanssen2
fix error msg generation and print body of missing function
09383e1
@sjanssen2
add checks for normalize_derivative addition
8bd63fb
@sjanssen2
add choice function for summation over negative logarithms
5044024
@sjanssen2
Merge pull request #164 from jlab/hSUM
7a1656a 
H sum
@sjanssen2
Merge branch 'master' of github.com:jlab/gapc into hSUM
fa97cd9
@sjanssen2
Merge pull request #169 from jlab/hSUM
68ab4f0 
H sum
@sjanssen2
Merge branch 'outside_looporder' into first_derivative
ac5fa8f
@fymue fymue mentioned this pull request Jun 13, 2023
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