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Pointer network for multi spans#63

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ArneBinder wants to merge 66 commits intomainArneBinder/pie-modules:mainfrom pointer_network_for_multi_spansArneBinder/pie-modules:pointer_network_for_multi_spansCopy head branch name to clipboard

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Commits on Mar 21, 2024

• add use_multi_spans property

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• add todos

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• convert all AnnotationEncoderDecoder to GenerativeAnnotationEncoderDecoder, i.e. implement parse() for them

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• add LabeledMultiSpanEncoderDecoder (still without tests)

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• minor

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• handle none_id in BinaryRelationEncoderDecoder.parse()

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• fix LabeledMultiSpanEncoderDecoder.parse()

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• rename exception

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• raise error for nested / overlapping parsed spans

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• fix IncompleteEncodingException for SpanEncoderDecoderWithOffset.parse

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• better constrain the type for span_encoder_decoder in LabeledSpanEncoderDecoder and LabeledMultiSpanEncoderDecoder

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• disentangle raising DecodingSpanOverlapException and DecodingSpanNestedException

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• add EncodingException

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• add DecodingEmptySpanException, EncodingEmptySpanException, spans_have_overlap() and spans_are_nested()

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• add documentation

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• assert in SpanEncoderDecoder.encode() that span is not empty

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• fix SpanEncoderDecoder.parse() and add tests

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• add tests for SpanEncoderDecoderWithOffset.parse()

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• fix SpanEncoderDecoderWithOffset.parse()

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• add tests for LabeledSpanEncoderDecoder.parse()

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• improve thrown Exceptions and add tests for LabeledMultiSpanEncoderDecoder.encode() / .decode()

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• fix SpanEncoderDecoder.parse() for empty encoding

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• fix LabeledMultiSpanEncoderDecoder.parse() and add tests

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• add test_labeled_multi_span_encoder_decoder_parse_incomplete_with_previous_annotations()

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• add test_binary_relation_encoder_decoder_parse_incomplete() and test_binary_relation_encoder_decoder_parse_incomplete_with_previous_annotations()

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• tests for parsing loop dummy relations

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• allow to generate exact same spans again

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• adjust PointerNetworkTaskModuleForEnd2EndRE for LabeledMultiSpan (partly)

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• decoding exceptions contain remaining encoding when raised in parse()

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• use relation_encoder_decoder.parse() in decode_relations()

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• rename error identifier "index" to "negative_index"

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• outsource _parse_label and restrict labels if none was found

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• use relation_encoder_decoder.parse() in build_constraint(s)

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• implement GenerativeAnnotationEncoderDecoderWithParseWithErrors with parse_with_error_handling() and remove decode_relations()

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• minor fix

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• cleanup

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• ensure that parse_with_error_handling() does not get stuck in an infinite loop

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• fix forwarding DecodingExceptions in SpanEncoderDecoderWithOffset.parse()

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• cleanup sanity check in encode_annotations()

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• cleanup follow-up candidate / constraints creation

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• fix PrefixConstrainedLogitsProcessorWithMaximum

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• raise an exception if no follow-up candidates are found

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• enforce continuations when previously decoded spans are re-generated

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• harden _prefix_allowed_tokens_fn_with_maximum(): if the decoding failed, allow all tokens. Maybe the model can recover from this state

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• harden _prefix_allowed_tokens_fn_with_maximum(): If there is only one candidate, we add the eos token

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• _prefix_allowed_tokens_fn_with_maximum(): log a warning if get_follow_up_candidates() fails

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• LabeledSpanEncoderDecoder.parse(): check for same span with different label

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• LabeledMultiSpanEncoderDecoder.parse(): check for overlap with previous spans

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• harden decode_annotations(): catch any exception

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• increase test coverage

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• better error message

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• add test_decode_annotations_issue()

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• fix spans_have_overlap() and SpanEncoderDecoder.parse()

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• add test_decode_annotations_fuzzing()

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• fix variable name

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• speed up build_constraints()

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• add cache_decoded and to speed up get_follow_up_candidates() and use this again in build_constraints()

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• disable cache because it does not work as expected

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• add comment

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• fixes regarding #64

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• add disrespect_decoded_annotations parameter to parse_with_error_handling()

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• add constrain_with_previous_records parameter to PointerNetworkTaskModuleForEnd2EndRE

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• add test case

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• use are_nested and have_overlap from pie_modules.utils.span

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• disentangle and generalize naming

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• pre-commit

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