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Paper Citation Record · LEDGER

Deciphering genomic codes using advanced NLP techniques: a scoping review

As of 13 August 2026, this Paper Citation Record lists 57 of 57 outbound references and 0 inbound Pith citation observations for arXiv:2411.16084.

A citation records a reference. It does not transfer a finding from one paper to another.

pith.paper-citation-record.v1
2411.16084 v1

Coverage vector

measured 57 of 57 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-08-12T13:35:41.247616Z

measured 57 of 57 standing notices

One-hop event checks from named stored sources.

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measured 0 of 0 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links

measured 0 of 1 external citation measurements

A source-named dated measurement, never combined with another source.

Source: cited_works

Reference resolution

57 of 57 outbound references displayed

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  • verified fuzzy8
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External citation measurements

No source-named external measurement is stored.

Outbound references

Observation 86cd630e-eb49-40c1-b5c2-748597bf4b08 · outbound

This paper cites Representation learning applications in biological sequence analysis.

Deciphering genomic codes using advanced NLP techniques: a scoping review Representation learning applications in biological sequence analysis

Reference 1

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Observation 2ff0bd6c-fdb0-4302-91d1-576aa652d897 · outbound

This paper cites Large models for genomics.

Deciphering genomic codes using advanced NLP techniques: a scoping review Large models for genomics

Reference 2

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Observation 0a749b65-412a-4b3a-bf36-1d98e4279fef · outbound

This paper cites Human genome, 2024.

Deciphering genomic codes using advanced NLP techniques: a scoping review Human genome, 2024

Reference 3

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Observation 42dc4d07-66bd-4911-b7e6-51df447ef4b0 · outbound

This paper cites McPherson, and W.

Deciphering genomic codes using advanced NLP techniques: a scoping review McPherson, and W

Reference 4

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Observation 5e48ad9b-3ea9-4853-87d9-ea68c2630216 · outbound

This paper cites Effect of tokenization on transformers for biological sequences.

Deciphering genomic codes using advanced NLP techniques: a scoping review Effect of tokenization on transformers for biological sequences

Reference 5

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Observation 134e137d-0b9a-4d95-a996-135f09337a25 · outbound

This paper cites Enhancing machine learning prediction in computational chemistry by chemical language representa- tions.

Deciphering genomic codes using advanced NLP techniques: a scoping review Enhancing machine learning prediction in computational chemistry by chemical language representa- tions

Reference 6

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Observation 0a57294c-c2b2-4948-b1cc-0496eb6f3efd · outbound

This paper cites To Transformers and Beyond: Large Language Models for the Genome.

Deciphering genomic codes using advanced NLP techniques: a scoping review To Transformers and Beyond: Large Language Models for the Genome

Reference 7

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Observation 040f3e51-6f08-40bd-806b-58ecc03ca7a8 · outbound

This paper cites Transformer architecture and attention mechanisms in genome data analysis: A comprehensive review.

Deciphering genomic codes using advanced NLP techniques: a scoping review Transformer architecture and attention mechanisms in genome data analysis: A comprehensive review

Reference 8

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Observation 74ec0c31-c602-45e9-8fdc-bfeb959d5a93 · outbound

This paper cites melbourne, australia, 2024.

Deciphering genomic codes using advanced NLP techniques: a scoping review melbourne, australia, 2024

Reference 9

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Observation 086c21b8-c135-4b80-8a12-1c4ad111f1eb · outbound

This paper cites Novel transformer networks for improved sequence labeling in genomics.

Deciphering genomic codes using advanced NLP techniques: a scoping review Novel transformer networks for improved sequence labeling in genomics

Reference 10

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Observation df75abff-61f8-4271-88cf-6530d63f7269 · outbound

This paper cites Cpg island detection using transformer model with conditional random field.

Deciphering genomic codes using advanced NLP techniques: a scoping review Cpg island detection using transformer model with conditional random field

Reference 11

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Observation dbe764a4-5caf-4aec-91bb-46a46f188363 · outbound

This paper cites Davuluri.

Deciphering genomic codes using advanced NLP techniques: a scoping review Davuluri

Reference 12

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Observation 1739629d-9fd8-4982-bf7e-90bf67bc67e1 · outbound

This paper cites A trans- former architecture based on bert and 2d convolutional neural network to identify dna enhancers from sequence information.

Deciphering genomic codes using advanced NLP techniques: a scoping review A trans- former architecture based on bert and 2d convolutional neural network to identify dna enhancers from sequence information

Reference 13

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verified exact
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Observation 79bbb8c2-0edb-45f3-8aba-de43991d37fd · outbound

This paper cites Bert-promoter: An improved sequence-based predictor of dna promoter using bert pre-trained model and shap feature selection.

Deciphering genomic codes using advanced NLP techniques: a scoping review Bert-promoter: An improved sequence-based predictor of dna promoter using bert pre-trained model and shap feature selection

Reference 14

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verified exact
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Source-reported events for the cited work

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Observation 16c2663f-fc62-45df-a870-12c12ded22e7 · outbound

This paper cites Improving language model of human genome for dna–protein binding prediction based on task-specific pre-training.

Deciphering genomic codes using advanced NLP techniques: a scoping review Improving language model of human genome for dna–protein binding prediction based on task-specific pre-training

Reference 15

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Source-reported events for the cited work

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Observation cd60b858-4a5b-42af-819a-152a338bb900 · outbound

This paper cites Gene- mask: Fast pretraining of gene sequences to enable few-shot learning.

Deciphering genomic codes using advanced NLP techniques: a scoping review Gene- mask: Fast pretraining of gene sequences to enable few-shot learning

Reference 17

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Observation 0ce6a08a-f3ac-49a5-9d25-a6de375e4f87 · outbound

This paper cites Bert-5mc: an interpretable model for predicting 5-methylcytosine sites of dna based on bert.

Deciphering genomic codes using advanced NLP techniques: a scoping review Bert-5mc: an interpretable model for predicting 5-methylcytosine sites of dna based on bert

Reference 18

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Observation f8fc12f9-7cb7-4836-b504-7cb3e62f6133 · outbound

This paper cites Genome-wide identi- fication and characterization of dna enhancers with a stacked multivariate fusion framework.

Deciphering genomic codes using advanced NLP techniques: a scoping review Genome-wide identi- fication and characterization of dna enhancers with a stacked multivariate fusion framework

Reference 19

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Observation 033b0b35-da17-44db-8614-8c195ceb19d1 · outbound

This paper cites Predicting protein- dna binding sites by fine-tuning bert.

Deciphering genomic codes using advanced NLP techniques: a scoping review Predicting protein- dna binding sites by fine-tuning bert

Reference 20

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Observation a697653b-463b-4dcf-a266-9196d5f3ec86 · outbound

This paper cites Semanticcap: Chromatin accessibility prediction enhanced by features learning from a language model.

Deciphering genomic codes using advanced NLP techniques: a scoping review Semanticcap: Chromatin accessibility prediction enhanced by features learning from a language model

Reference 21

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Deciphering genomic codes using advanced NLP techniques: a scoping review Unresolved cited work

Reference 22

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Deciphering genomic codes using advanced NLP techniques: a scoping review Cpg island detection using modified transformer model with pre–trained embedding

Reference 23

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Deciphering genomic codes using advanced NLP techniques: a scoping review Unresolved cited work

Reference 24

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Deciphering genomic codes using advanced NLP techniques: a scoping review Unresolved cited work

Reference 25

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Deciphering genomic codes using advanced NLP techniques: a scoping review Predicting gene expression levels from dna sequences and post-transcriptional information with transformers

Reference 26

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Deciphering genomic codes using advanced NLP techniques: a scoping review Mt- tlm6a: A multi-task transfer learning approach for base-resolution mrna m6a site prediction based on an improved transformer

Reference 27

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Deciphering genomic codes using advanced NLP techniques: a scoping review Mscan: multi- scale self- and cross-attention network for rna methylation site prediction

Reference 28

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Deciphering genomic codes using advanced NLP techniques: a scoping review An efficient circrna-mirna interaction prediction model by combining biological text mining and wavelet diffusion-based sparse network structure embedding

Reference 29

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Deciphering genomic codes using advanced NLP techniques: a scoping review Bcmcmi: A fusion model for predicting circrna-mirna interactions combining semantic and meta-path

Reference 30

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Deciphering genomic codes using advanced NLP techniques: a scoping review Tmsc-m7g: A transformer architecture based on multi- sense-scaled embedding features and convolutional neural network to identify rna n7-methylguanosine 16 sites

Reference 31

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Deciphering genomic codes using advanced NLP techniques: a scoping review mitds: Uncovering mirna-mrna interactions with deep learning for functional target prediction

Reference 32

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This paper cites Transformer- based gene scoring model for extracting representative characteristic of central dogma process to pri- oritize pathogenic genes applying breast cancer multi-omics data.

Deciphering genomic codes using advanced NLP techniques: a scoping review Transformer- based gene scoring model for extracting representative characteristic of central dogma process to pri- oritize pathogenic genes applying breast cancer multi-omics data

Reference 33

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Observation 9aeca21a-ae16-45ee-9ce3-a4afdcff84e2 · outbound

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Deciphering genomic codes using advanced NLP techniques: a scoping review Transformer-based dna methylation detection on ionic signals from oxford nanopore sequencing data

Reference 34

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Deciphering genomic codes using advanced NLP techniques: a scoping review Alzheimer’s disease classification through imaging genetic data with ignet

Reference 35

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This paper cites Setquence & setomic: Deep set transformer-based representations of cancer multi-omics.

Deciphering genomic codes using advanced NLP techniques: a scoping review Setquence & setomic: Deep set transformer-based representations of cancer multi-omics

Reference 36

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verified exact
raw_fallback, observed 2026-08-12T13:35:41.604056Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

source=pdf_text observed=2026-08-12T13:35:41.180459Z digest=sha256:f7a461dba863e888ab63a1f31fc50ce353215e3a6a431921b11e5d7d5efd65b5

Observation c36fbe3e-3918-42c4-8859-a98425d0bfbd · outbound

This paper cites BERT: Pre-training of deep bidirectional transformers for language understanding.

Deciphering genomic codes using advanced NLP techniques: a scoping review BERT: Pre-training of deep bidirectional transformers for language understanding

Reference 37

Resolution
verified fuzzy
raw_fallback, observed 2026-08-12T13:35:42.221885Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

source=pdf_text observed=2026-08-12T13:35:41.189742Z digest=sha256:4477e748555785c0eb8ab6a46a3885cfe6fc3d39960c63ffcde035dd4c92cfdd

Observation 7c815e99-5618-489c-9107-0f4d74a8bd1e · outbound

This paper cites an unresolved cited work.

Deciphering genomic codes using advanced NLP techniques: a scoping review Unresolved cited work

Reference 38

Resolution
verified exact
doi, observed 2026-08-12T13:35:41.299064Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

source=pdf_text observed=2026-08-12T13:35:41.186834Z digest=sha256:978f60770fd104d7a2821a24565f9af36ef7eda792d62cf950e2913cb1d69bbb

Observation 8280d6f6-952c-4ddd-96a2-85afbc89096a · outbound

This paper cites Conditional random fields: probabilistic models for segmenting and labeling sequence data.

Deciphering genomic codes using advanced NLP techniques: a scoping review Conditional random fields: probabilistic models for segmenting and labeling sequence data

Reference 39

Resolution
verified fuzzy
raw_fallback, observed 2026-08-12T13:35:42.208071Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

source=pdf_text observed=2026-08-12T13:35:41.196661Z digest=sha256:e93b14f6545d8a5a631564bbad734643b5fa2f262ddaba81e00667cc722c5613

Observation a618857e-272e-4918-b4ac-fc8064c7f373 · outbound

This paper cites scGPT: toward building a foundation model for single-cell multi-omics using generative AI.

Deciphering genomic codes using advanced NLP techniques: a scoping review scGPT: toward building a foundation model for single-cell multi-omics using generative AI

Reference 40

Resolution
unresolved
no resolver link, observed 2026-08-12T13:35:41.199667Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-12T13:35:41.199667Z digest=sha256:6dd4eb2c92967a1b304ec74d142585990d6129d60e1c68d1ae0b767d5592fe4f

Observation ea7cc066-8c7e-4faa-afd6-9e73455079e9 · outbound

This paper cites Nlp course - chapter 6, section 5: Byte-pair encoding, 2024.

Deciphering genomic codes using advanced NLP techniques: a scoping review Nlp course - chapter 6, section 5: Byte-pair encoding, 2024

Reference 41

Resolution
verified fuzzy
raw_fallback, observed 2026-08-12T13:35:42.215310Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

source=pdf_text observed=2026-08-12T13:35:41.194523Z digest=sha256:ad3438714de1532b7f4b8a8b7ee24c48db96ddcf76be0c8cd9a1d13163c2a8e3

Observation 6a895ade-6caf-43ca-b692-c0bc6f88fd8e · outbound

This paper cites Schwartz, Katherine E.

Deciphering genomic codes using advanced NLP techniques: a scoping review Schwartz, Katherine E

Reference 42

Resolution
verified exact
doi, observed 2026-08-12T13:35:41.280331Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

source=pdf_text observed=2026-08-12T13:35:41.205734Z digest=sha256:c58db4d6550cd780ef974335f05275810b0e4d2b136ab826112f7c3b6d14d402

Observation 7628ae82-e24e-4f10-8a09-dd19ce2b4b18 · outbound

This paper cites Effect of tokenization on transformers for biological sequences.

Deciphering genomic codes using advanced NLP techniques: a scoping review Effect of tokenization on transformers for biological sequences

Reference 43

Resolution
verified fuzzy
raw_fallback, observed 2026-08-12T13:35:42.201110Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

source=pdf_text observed=2026-08-12T13:35:41.208298Z digest=sha256:ac462a1b4ff9babeb132042617bfb10de2f14d619689b1a61834a106d322479e

Observation 7d439bc6-117b-49c6-a98d-c37c99a3852c · outbound

This paper cites Genomic Language Models: Opportunities and Challenges.

Deciphering genomic codes using advanced NLP techniques: a scoping review Genomic Language Models: Opportunities and Challenges

Reference 44

Resolution
unresolved
no resolver link, observed 2026-08-12T13:35:41.201998Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-12T13:35:41.201998Z digest=sha256:bac37ff4228be3cbe98d047595ec75bfcffd4a6d1faf31cf106d0970a45f3633

Observation f015fd48-2dd9-4812-b284-4b6803c135b6 · outbound

This paper cites Gene co-expression network analysis reveals common system-level properties of prognostic genes across cancer types.

Deciphering genomic codes using advanced NLP techniques: a scoping review Gene co-expression network analysis reveals common system-level properties of prognostic genes across cancer types

Reference 47

Resolution
verified exact
doi, observed 2026-08-12T13:35:41.271618Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

source=pdf_text observed=2026-08-12T13:35:41.210424Z digest=sha256:508b7d85e3fc99749c37ec6a0965185298a316c58dba5f9b3fd6eaa624b96bb9

Observation 2d4c62d2-b1d6-4801-9dde-2a3f7e33d961 · outbound

This paper cites an unresolved cited work.

Deciphering genomic codes using advanced NLP techniques: a scoping review Unresolved cited work

Reference 48

Resolution
unresolved
raw_fallback, observed 2026-08-12T13:35:42.193900Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

source=pdf_text observed=2026-08-12T13:35:41.212841Z digest=sha256:86c8317eaaa420e5e24862134e549c4e46ccc03728500e532cd0c19b26eaa6e8

Observation dd3dd784-3886-4bcf-9268-be037a9c33af · outbound

This paper cites an unresolved cited work.

Deciphering genomic codes using advanced NLP techniques: a scoping review Unresolved cited work

Reference 50

Resolution
unresolved
raw_fallback, observed 2026-08-12T13:35:42.178192Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

source=pdf_text observed=2026-08-12T13:35:41.217830Z digest=sha256:2933fe228cbc5d339a70197e5a41163200ed35a7190792b691bb5db91540e1f8

Observation 7728301d-6716-4af7-a9be-5f6ac8088d71 · outbound

This paper cites an unresolved cited work.

Deciphering genomic codes using advanced NLP techniques: a scoping review Unresolved cited work

Reference 51

Resolution
unresolved
raw_fallback, observed 2026-08-12T13:35:42.170278Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

source=pdf_text observed=2026-08-12T13:35:41.220376Z digest=sha256:35e8e045785f1847509e485cdd261e8c6c01a933266f2928d4292f9b5c261852

Observation 908fee17-721e-4702-b6ba-09a07598906a · outbound

This paper cites an unresolved cited work.

Deciphering genomic codes using advanced NLP techniques: a scoping review Unresolved cited work

Reference 54

Resolution
unresolved
raw_fallback, observed 2026-08-12T13:35:42.147137Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

source=pdf_text observed=2026-08-12T13:35:41.230034Z digest=sha256:73e67058fd8a9e6a463d155c2869b4577644b6ffa70487b6abc9e42d7acea738

Observation ff4c958e-e2d5-47a0-b7c8-e090d8e384f6 · outbound

This paper cites an unresolved cited work.

Deciphering genomic codes using advanced NLP techniques: a scoping review Unresolved cited work

Reference 55

Resolution
unresolved
raw_fallback, observed 2026-08-12T13:35:42.140060Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

source=pdf_text observed=2026-08-12T13:35:41.232322Z digest=sha256:3baf8725870851eec0bc3c6ada370724d7c30ba7b0d8b2e384483769567968ed

Observation 4c09f513-a8d1-4ff7-a152-df95ef4af80d · outbound

This paper cites an unresolved cited work.

Deciphering genomic codes using advanced NLP techniques: a scoping review Unresolved cited work

Reference 56

Resolution
unresolved
raw_fallback, observed 2026-08-12T13:35:42.184994Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

source=pdf_text observed=2026-08-12T13:35:41.234657Z digest=sha256:3c16c9d3def35624cb1d2ef255806e37d44c00025f2a4bb03b338858ce5c8998

Observation 46a6afb1-870a-428d-8159-91a87c2fb5f3 · outbound

This paper cites an unresolved cited work.

Deciphering genomic codes using advanced NLP techniques: a scoping review Unresolved cited work

Reference 57

Resolution
unresolved
raw_fallback, observed 2026-08-12T13:35:42.133289Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

source=pdf_text observed=2026-08-12T13:35:41.236699Z digest=sha256:e86c09f07f9cecf4a216260e5bab8194e01d2c4b30c578bda22c7c24ce05dc41

Observation 71590727-a45c-4c0d-b2e8-90c0c4ebc45b · outbound

This paper cites an unresolved cited work.

Deciphering genomic codes using advanced NLP techniques: a scoping review Unresolved cited work

Reference 58

Resolution
unresolved
raw_fallback, observed 2026-08-12T13:35:42.125867Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

source=pdf_text observed=2026-08-12T13:35:41.239989Z digest=sha256:1bbf6662ac9dbf25b6716ecb11de48fe48d47cc581317c8807cf5012289d5e63

Observation ec503701-0c08-489a-8cb7-4854a5674a9c · outbound

This paper cites an unresolved cited work.

Deciphering genomic codes using advanced NLP techniques: a scoping review Unresolved cited work

Reference 59

Resolution
unresolved
raw_fallback, observed 2026-08-12T13:35:42.163398Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

source=pdf_text observed=2026-08-12T13:35:41.242342Z digest=sha256:adafa154adca9d8731b34020b64558b7346d61c28bc9a81212494e0234109cd6

Observation 38fb4d6c-d7b5-461b-b67f-93752f6f683a · outbound

This paper cites an unresolved cited work.

Deciphering genomic codes using advanced NLP techniques: a scoping review Unresolved cited work

Reference 60

Resolution
unresolved
raw_fallback, observed 2026-08-12T13:35:42.156330Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

source=pdf_text observed=2026-08-12T13:35:41.244969Z digest=sha256:47f2658a3cd9ee77dc6ab8db0cf3cfc6fbfbc1b078ec0571f6dc00146012b53d

Observation f67bf071-902a-4a64-80be-d122b56a8d7f · outbound

This paper cites an unresolved cited work.

Deciphering genomic codes using advanced NLP techniques: a scoping review Unresolved cited work

Reference 61

Resolution
unresolved
raw_fallback, observed 2026-08-12T13:35:42.118746Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

source=pdf_text observed=2026-08-12T13:35:41.247616Z digest=sha256:e2a666ed02b8dd5183975b577b937f89640ea3ed2b903c19fd540750d7d65440

Observation 2f479bfd-3b06-4dfd-8ee2-342b24d8ca5c · outbound

This paper cites doi: 10.18653/v1/N19-1423.

Deciphering genomic codes using advanced NLP techniques: a scoping review doi: 10.18653/v1/N19-1423

Reference 2019

Resolution
unresolved
no resolver link, observed 2026-08-12T13:35:41.192020Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-12T13:35:41.192020Z digest=sha256:7f6a23b793e970f44979284e8c67fabaa1ad2ab89b7b45ef2afd3e262120ce4f

Observation 4232d313-388d-4e59-bf09-5ec3a9c29b03 · outbound

This paper cites an unresolved cited work.

Deciphering genomic codes using advanced NLP techniques: a scoping review Unresolved cited work

Reference 2022

Resolution
unresolved
no resolver link, observed 2026-08-12T13:35:41.112658Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-12T13:35:41.112658Z digest=sha256:90f0b67bd7a0f18c96f4062077c76cc4913625d39bd74cb37889cb84f868146c

Pith citing papers

No inbound Pith citation observations are available.