cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.16410690
title: BiGran-NER

description: # 🔍 BiGran-NER: Semantic Alignment with Bi-Granularity for Noisy Clinical NER

## 📘 Overview

**BiGran-NER** is a deep learning framework that enhances named entity recognition (NER) performance in noisy clinical texts, such as those found in electronic health records (EHRs), medical reports, and user-generated health content. The model introduces a **Bi-Granularity Semantic Alignment** strategy that synergizes word-level and sentence-level representations to mitigate token fragmentation, out-of-vocabulary challenges, and contextual ambiguity.

> 🔬 Proposed in: *"Semantic Alignment with Bi-Granularity for Enhanced Named Entity Recognition in Noisy Clinical Texts" (BMC, 2025)*

---

## ✨ Key Features

- **Bi-Granularity Architecture**:  - Combines token-level and sentence-level embeddings  - Aligns semantic and syntactic spaces via contrastive and dynamic distillation

- **Dual Alignment Strategies**:  - *Semantic Contrastive Learning (SCL)* to align NER token spans across granularity levels  - *Dynamic Knowledge Distillation (DKD)* to transfer uncertainty-aware knowledge from sentence to token predictions

- **Noise-Robust Training**:  - Tailored for noisy, informal clinical corpora  - Efficient adaptation to short-form or fragmented expressions

---

## 🧠 Model Architecture
DOI: 10.5281/zenodo.16410691
title: BiGran-NER

description: # 🔍 BiGran-NER: Semantic Alignment with Bi-Granularity for Noisy Clinical NER

## 📘 Overview

**BiGran-NER** is a deep learning framework that enhances named entity recognition (NER) performance in noisy clinical texts, such as those found in electronic health records (EHRs), medical reports, and user-generated health content. The model introduces a **Bi-Granularity Semantic Alignment** strategy that synergizes word-level and sentence-level representations to mitigate token fragmentation, out-of-vocabulary challenges, and contextual ambiguity.

> 🔬 Proposed in: *"Semantic Alignment with Bi-Granularity for Enhanced Named Entity Recognition in Noisy Clinical Texts" (BMC, 2025)*

---

## ✨ Key Features

- **Bi-Granularity Architecture**:  - Combines token-level and sentence-level embeddings  - Aligns semantic and syntactic spaces via contrastive and dynamic distillation

- **Dual Alignment Strategies**:  - *Semantic Contrastive Learning (SCL)* to align NER token spans across granularity levels  - *Dynamic Knowledge Distillation (DKD)* to transfer uncertainty-aware knowledge from sentence to token predictions

- **Noise-Robust Training**:  - Tailored for noisy, informal clinical corpora  - Efficient adaptation to short-form or fragmented expressions

---

## 🧠 Model Architecture
DOI: 10.15468/dl.yz45kv
title: Occurrence Download

description: A dataset containing 2134 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Meise Botanic Garden Herbarium (BR)",
 "TaxonKey is Crassocephalum"
 ]
}

 The dataset includes 2134 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038743-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dbdcm6
title: Occurrence Download

description: A dataset containing 44 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acer negundo",
 "Country is Armenia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 44 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038745-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gq9phe
title: Occurrence Download

description: A dataset containing 392 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acer negundo",
 "Country is Argentina",
 "HasCoordinate is true"
 ]
}

 The dataset includes 392 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038744-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a37kss
title: Occurrence Download

description: A dataset containing 3253 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Apus pallidus",
 "MediaType is Image"
 ]
}

 The dataset includes 3253 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038747-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.khwcg2
title: Occurrence Download

description: A dataset containing 1703 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acer negundo",
 "Country is Austria",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1703 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038746-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ax8ufm
title: Occurrence Download

description: A dataset containing 521 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Meise Botanic Garden Herbarium (BR)",
 "TaxonKey is Solanecio"
 ]
}

 The dataset includes 521 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038749-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6skhdg
title: Occurrence Download

description: A dataset containing 24109 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((17.743452538339216 49.69139314934459, 17.75293504831395 49.56259829481756, 18.269334601464774 49.56942013069325, 18.224367569484986 49.725727053020655, 17.742917902429703 49.703409559963276, 17.743452538339216 49.69139314934459))"
 ]
}

 The dataset includes 24109 records from 62 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038748-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nwuarc
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Glebionis segetum",
 "Country is Slovakia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 7 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038751-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.krmuff
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Glebionis segetum",
 "Country is Russian Federation",
 "HasCoordinate is true"
 ]
}

 The dataset includes 23 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038750-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7ppn7k
title: Occurrence Download

description: A dataset containing 14428 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anthus spinoletta",
 "MediaType is Image"
 ]
}

 The dataset includes 14428 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038753-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15480892
title: Next-Gen Digital Advertising: Can AI Content Personalization Survive the Privacy Revolution?

description: (abstract)
DOI: 10.15468/dl.9h5622
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Pimelodella parnahybae)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 12 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038752-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15480891
title: Next-Gen Digital Advertising: Can AI Content Personalization Survive the Privacy Revolution?

description: (abstract)
DOI: 10.15468/dl.946fwq
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Elymus caninus"
 ]
}

 The dataset includes 14 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038755-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57745/mrz726
title: 2009-EGG-A-0202-Gottschalk.ogg

description: Interprétation en anglais, interprète/traducteur : Philippe Minns
DOI: 10.57745/i8gd53
title: 2009-EGG-A-0203-Gottschalk.ogg

description: Enregistrement audio en allemand avec interprétation en anglais, interprète/traducteur : Philippe Minns
DOI: 10.57745/rxtwxa
title: 2009-EGG-A-0201-Gottschalk.ogg

description: Enregistrement audio en version originale allemande
DOI: 10.57745/gfkjpu
title: Entretien avec Siegfried Gottschalk. Histoire de vie et expériences de déportation en URSS

description: Cet entretien a eu lieu le 6 février 2009 à Ludwigsburg, Allemagne, au domicile de l'interviewé. Il a été mené par Malte Griesse. L'entretien a été réalisé en allemand et traduit et interprété en anglais. Il a duré 2 heures et 21 minutes.
DOI: 10.15468/dl.x6prfh
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Glebionis segetum",
 "Country is South Africa",
 "HasCoordinate is true"
 ]
}

 The dataset includes 6 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038754-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qhkc27
title: Occurrence Download

description: A dataset containing 2742 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "License is one of (CC-BY 4.0, CC0 1.0)",
 "TaxonKey is Meles meles"
 ]
}

 The dataset includes 2742 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038756-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kdkpex
title: Occurrence Download

description: A dataset containing 1973 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aquila fasciata",
 "MediaType is Image"
 ]
}

 The dataset includes 1973 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038757-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kmmrjt
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Iva xanthiifolia",
 "Country is Russian Federation",
 "HasCoordinate is true"
 ]
}

 The dataset includes 6 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038758-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5tvhxe
title: Occurrence Download

description: A dataset containing 1213 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tripora divaricata"
 ]
}

 The dataset includes 1213 records from 99 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038759-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v2f7nq
title: Occurrence Download

description: A dataset containing 891 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acer negundo",
 "Country is Belarus",
 "HasCoordinate is true"
 ]
}

 The dataset includes 891 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038760-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57745/htqwyx
title: 2010-EGG-EST-0301-Eve-Isotamm.ogg

description: Enregistrement audio en version originale estonienne
DOI: 10.57745/gmpd5g
title: Entretien avec Eve Isotamm. Histoire de vie et expériences de déportation en URSS

description: Cet entretien a eu lieu le 16 mars 2010 à Tartu, Estonie. Il a été mené par Aigi Rahi-Tamm et Juliette Denis, avec la participation de Marc Fichet (technicien son, RFI) qui s'occupait de l'enregistrement. L'entretien a été réalisé en estonien. Il a duré 1 heure et 30 minutes.
DOI: 10.15468/dl.ajjb23
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acer negundo",
 "Country is Bosnia and Herzegovina",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038761-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bqpj5p
title: Occurrence Download

description: A dataset containing 76333 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anthus pratensis",
 "MediaType is Image"
 ]
}

 The dataset includes 76333 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038726-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16410727
title: data of research
DOI: 10.5281/zenodo.16410728
title: data of research
DOI: 10.15468/dl.fgcjsk
title: Occurrence Download

description: A dataset containing 806 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Fulica americana)",
 "Country is one of (Åland Islands, Albania, Andorra, Austria, Belarus, Belgium, Bosnia and Herzegovina, Bulgaria, Croatia, Czechia, Denmark, Estonia, Faroe Islands, Finland, France, Germany, Gibraltar, Greece, Guernsey, Holy See, Hungary, Iceland, Ireland, Isle of Man, Italy, Jersey, Latvia, Liechtenstein, Lithuania, Luxembourg, Malta, Moldova, Republic of, Monaco, Montenegro, Netherlands, North Macedonia, Norway, Poland, Portugal, Romania, Russian Federation, San Marino, Serbia, Slovakia, Slovenia, Spain, Svalbard and Jan Mayen, Sweden, Switzerland, Ukraine, United Kingdom of Great Britain and Northern Ireland)"
 ]
}

 The dataset includes 806 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038764-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/12564481
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.r7bmem
title: Occurrence Download

description: A dataset containing 28598 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Galeorhinus galeus",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900"
 ]
}

 The dataset includes 28598 records from 131 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038763-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57745/uhy67m
title: 2009-EGG-PL-1101-Jablonowski.ogg

description: Enregistrement audio en version originale polonaise
DOI: 10.57745/eolvrh
title: 2009-EGG-PL-1103-Jablonowski.ogg

description: Enregistrement audio en polonais avec interprétation en anglais, interprète/traducteur : Jan Krotki
DOI: 10.57745/o5bktd
title: 2009-EGG-PL-1102-Jablonowski.ogg

description: Interprétation en anglais, interprète/traducteur : Jan Krotki
DOI: 10.57745/owzx9m
title: Entretien avec Jozef Jablonowski. Histoire de vie et expériences de déportation en URSS

description: Cet entretien a eu lieu le 21 avril 2009 à Białystok, Pologne, dans la salle de réunion de l’hospice privé Opatrzności Bożej. Il a été mené par Agnieszka Niewiedzial, avec la participation de Marc Fichet (technicien son, RFI) qui s'occupait de l'enregistrement. L'entretien a été réalisé en polonais et traduit et interprété en anglais. Il a duré 1 heure et 51 minutes.
DOI: 10.15468/dl.ydm92x
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Palaemon macrodactylus",
 "Country is Romania",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038767-250717081556266/datasets/export for details.
DOI: 10.15468/dl.79qey9
title: Occurrence Download

description: A dataset containing 10993 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Glebionis segetum",
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "HasCoordinate is true"
 ]
}

 The dataset includes 10993 records from 79 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038766-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ra3yfk
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Typhleotris mararybe)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038768-250717081556266/datasets/export for details.
DOI: 10.15468/dl.7bxffu
title: Occurrence Download

description: A dataset containing 88 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Glebionis segetum",
 "Country is Switzerland",
 "HasCoordinate is true"
 ]
}

 The dataset includes 88 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038765-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57745/somrsh
title: 2011-EGG-LT-0401-Jakovonis.ogg

description: Enregistrement audio en version originale lituanienne
DOI: 10.57745/2skjq8
title: Entretien avec Zofia Jakavonienė. Histoire de vie et expériences de déportation en URSS

description: Cet entretien a eu lieu le 9 juin 2011 à Kasčiūnai, Lituanie, au domicile de l'interviewée. Il a été mené par Jurgita Mačiulytė, avec la participation de Alain Blum qui s'occupait de l'enregistrement. L'entretien a été réalisé en lituanien. Il a duré 1 heure et 5 minutes.
DOI: 10.15468/dl.yvycgv
title: Occurrence Download

description: A dataset containing 30666 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Apus apus",
 "MediaType is Image"
 ]
}

 The dataset includes 30666 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038769-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5xpa6h
title: Occurrence Download

description: A dataset containing 125374 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is DEMNA-DNE : Occurrences of Diatoms (Bacillariophyceae) in running waters of Wallonia, Belgium"
 ]
}

 The dataset includes 125374 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038762-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17866/rd.salford.29626583.v1
title: MAKERWORLD DOCUMENTARY

description: Makerworld is a 16 minute film I made working with families in Huddersfield in 2024. The film won The Children's International Film festival of Wales, it won best Social Impact Award for the Activists Without Borders Film festival and received an Honorable mention in the Big Syn Film Festival - the largest sustainable film festival in the world. It was also nominated in the Folkestone Film Festival and the Liverpool Indie Film Festival. The film had three screenings across Kirklees to members of Kirklees Council, the public, families, business leaders and Member of Parliamanet Harpreet Singh. <br><b><i>Makerworld </i></b>is a short documentary showing how artists are using an empty retail unit in Huddersfield to run free workshops for children, how this impacts the lives of the people who take part, and what this brings to the town.<b><i>Makerworld </i></b>offers a utopian glimpse of how town centres could thrive if they replaced consumerism with community.Told through the lens of the of the parents and children who attend the free weekly sessions; we hear about the benefits of free community art to young and old – from stress relief to confidence and from social mobility to inclusivity.The sessions are vibrant and multi-cultural, where families are united by the “foraging of sparkly bits of material or fluff”. A sharp contrast with the decline of the high street just a few metres away.Tactical urbanism is about reimagining and repurposing urban spaces to meet the evolving needs of communities. Town centres across the globe have been impacted by a massive reduction in footfall. People want to connect – they just need the space.<br>As town centres are rushing to reinvent themselves, <b><i>Makerworld</i></b> provides an alternative view of how free community art can change lives, bring families into our dying towns and help reimagine our town centres in the 21st century.
DOI: 10.15468/dl.byt6ry
title: Occurrence Download

description: A dataset containing 1095 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tangara cayana"
 ]
}

 The dataset includes 1095 records from 111 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038771-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.