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Paper Citation Record · LEDGER

Deciphering genomic codes using advanced NLP techniques: a scoping review

As of 17 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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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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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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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

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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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Observation 419024f1-0800-4974-b9d9-835db70ccf5e · outbound

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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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Observation 47fa1374-640c-43e3-a984-f1af0c31e0ba · outbound

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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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Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

source=pdf_text observed=2026-08-12T13:35:41.180459Z digest=sha256:df54eff96059cb744c3de78adcf1dc611a99f036bf5fdf4e4c6f9f7082e14300

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 2026-08-17T06:30:58.91139+00:00.

source=pdf_text observed=2026-08-12T13:35:41.189742Z digest=sha256:005ebf5065558ffabfff63b12a1b51834a4d544c025b3b0449677b51f428afb8

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 2026-08-17T06:30:58.91139+00:00.

source=pdf_text observed=2026-08-12T13:35:41.186834Z digest=sha256:f8e79d8dfe9d6a8fad71c6a56151e5f9cde44b01e277b3f5d03af632cca41cfd

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 2026-08-17T06:30:58.91139+00:00.

source=pdf_text observed=2026-08-12T13:35:41.196661Z digest=sha256:06706e644706fb9b11d883717ff5f0d5436cd1febc84d746c1e94ea354d0d183

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:bfd31a1d2814f234670147a321e18312f01c81096ee0e44435aababac9cc9311

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 2026-08-17T06:30:58.91139+00:00.

source=pdf_text observed=2026-08-12T13:35:41.194523Z digest=sha256:9a126267fd9c1e81031639becc2c36853e7356ba56d3e79192ecd4a92a0be6da

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 2026-08-17T06:30:58.91139+00:00.

source=pdf_text observed=2026-08-12T13:35:41.205734Z digest=sha256:f93a1bd17826807a5b3c8715e49881269da74052999bae42790dfe6f1d31f2bc

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 2026-08-17T06:30:58.91139+00:00.

source=pdf_text observed=2026-08-12T13:35:41.208298Z digest=sha256:0c73d377d20ced69afda8084326d4ed4ce0d84c297f8d451735ae95ba2bfa8bf

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=sha256:12183f813dd65b81ba73dc8155da1f73efe9ac9c5fd6b5c139a5077b68a4d97f

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 2026-08-17T06:30:58.91139+00:00.

source=pdf_text observed=2026-08-12T13:35:41.210424Z digest=sha256:d1307f305877eaf1dac8d930f584249672d2d99e974d9182ef17ae5fc52047a6

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 2026-08-17T06:30:58.91139+00:00.

source=pdf_text observed=2026-08-12T13:35:41.212841Z digest=sha256:910adc74131b7205a72346d0cb387820965a545753339f0ecc5bf850d9bef1e4

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 2026-08-17T06:30:58.91139+00:00.

source=pdf_text observed=2026-08-12T13:35:41.217830Z digest=sha256:a9dac72736f8aee41e53f05f46892d06a59da1865bf9853b95a68cff34b90a21

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 2026-08-17T06:30:58.91139+00:00.

source=pdf_text observed=2026-08-12T13:35:41.220376Z digest=sha256:0569e9743970fc02a15538be3597a4a032f1da08ca1d9000043fd44e420ed6d6

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 2026-08-17T06:30:58.91139+00:00.

source=pdf_text observed=2026-08-12T13:35:41.230034Z digest=sha256:addc06348c9ec2ab8e18c4fda09d05245a293d0f81c9fd9470cadd8a486a2137

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 2026-08-17T06:30:58.91139+00:00.

source=pdf_text observed=2026-08-12T13:35:41.232322Z digest=sha256:5c46eab4844dbec4bda6ff7d1a7ac3aaf38a984d522b79f705ff48cd85e5036b

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 2026-08-17T06:30:58.91139+00:00.

source=pdf_text observed=2026-08-12T13:35:41.234657Z digest=sha256:4b27dcb43ca798af9cd16d18148391566ecebfe1ed62a8194b4fa1cca8858da5

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 2026-08-17T06:30:58.91139+00:00.

source=pdf_text observed=2026-08-12T13:35:41.236699Z digest=sha256:3101fc9abf37a67998dfd910d92acc07dde3571f1f1d918c3b34a983f38f2333

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 2026-08-17T06:30:58.91139+00:00.

source=pdf_text observed=2026-08-12T13:35:41.239989Z digest=sha256:28888d28239468bd610192672264c7fdb321597dd0d5753bb9c9bb4c03b9960d

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 2026-08-17T06:30:58.91139+00:00.

source=pdf_text observed=2026-08-12T13:35:41.242342Z digest=sha256:5a9964319b49ca07b325abb65d7042bb405c4938e6cba5f54e49aecfa7bf390f

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 2026-08-17T06:30:58.91139+00:00.

source=pdf_text observed=2026-08-12T13:35:41.244969Z digest=sha256:f6c458e1fe596f0e54e3acda5872676c4dd4f8788f376342d6119e68c95ce8b8

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 2026-08-17T06:30:58.91139+00:00.

source=pdf_text observed=2026-08-12T13:35:41.247616Z digest=sha256:9ec7051fd1f8b56ab8748f32bd3e35e673c868bf576c30ab529eed5b9dcf8c42

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:e7157006583d74bf9dd163c15e35932d439b1d57c5feaeb830cc2e0ee504190f

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=sha256:3063233df59036aab471e88c45b156399af53df411cf2248536ff9d236361c12

Pith citing papers

No inbound Pith citation observations are available.