cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.13973760
title: Focused learning by antibody language models using preferential masking of non-templated regions

description: Motivation. While existing antibody language models (AbLMs) excel at predicting germline residues, they often struggle with mutated and non-templated residues, which concentrate in the complementarity-determining regions (CDRs) and are crucial for determining antigen-binding specificity. Many of these models are trained using a masked language modeling (MLM) objective with uniform masking probabilities; however, antibody recombination is modular in nature, creating relatively distinct regions of high and low complexity (non-templated and templated, respectively). We sought to determine whether and to what extent AbLMs can improve when trained using an alternative masking strategy based on this observation.

Results. We developed a variation on MLM called Preferential Masking, which alters masking probabilities to amplify training signals from the CDR3. We pre-trained two AbLMs using either uniform or preferential masking and observed that the latter improves pre-training efficiency and residue prediction accuracy in the highly variable CDR3. Preferential masking also improves antibody classification by native chain pairing and binding specificity, suggesting improved CDR3 understanding and indicating that non-random, learnable patterns help govern antibody chain pairing. We further show that specificity classification is largely informed by residues in the CDRs, demonstrating that AbLMs learn meaningful patterns that align with immunological understanding.

Files. The following files are included in this repository:



uniform_250k.tar.gz: Model weights for the Uniform-250k model.

uniform_350k.tar.gz: Model weights for the Uniform-350k model.

preferential_250k.tar.gz: Model weights for the Preferential-250k model.

train-eval-test_cdr-mask.tar.gz: Datasets used to train all three models above. Compressed folder containing three files: train.csv, eval.csv, and test.csv. Each row contains a natively paired sequence with its corresponding label-encoded CDR mask, designed to align with the tokenized amino acid sequence. Sequences were obtained from Jaffe et al. and Hurtado et al. These are referenced in the paper as Dataset A (train.csv, eval.csv), and Dataset B (test.csv).

pair_classification.tar.gz: Two classification datasets used to train the classifier models in Figure 4: C_native-0_shuffled-1.csv (Dataset C) and D_native-0_shuffled-1.csv (Dataset D). Dataset C sequences were obtained from Jaffe et al. and Hurtado et al (Dataset B), and Dataset D sequences were obtained from Phad et al and data generated as part of this study.

CoV_classification.tar.gz: Classification dataset used to train the classifier models in Figure 5: E_hd-0_cov-1.csv (Dataset E). CoV antibody sequences were obtained from CoV-AbDAb, and healthy donor sequences were obtained from Phad et al.


Code. All code used for model training, testing, and figure generation is available under the MIT license on GitHub.
DOI: 10.15468/dl.rfkwab
title: Occurrence Download

description: A dataset listing the 35 species recorded in GBIF matching the query:
{
 "TaxonKey" : [
 "is Vitis vinifera L."
 ]
}

 The dataset's 35 records were derived from 1021 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025745-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mhdzxs
title: Occurrence Download

description: A dataset containing 394 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Centaurea raphanina subsp. mixta (DC.) Runemark"
 ]
}

 The dataset includes 394 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025779-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xvvs65
title: Occurrence Download

description: A dataset containing 83 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Nephelomys moerex (Thomas, 1914)"
 ]
}

 The dataset includes 83 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025782-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v2wwmh
title: Occurrence Download

description: A dataset containing 3334 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mustela putorius Linnaeus, 1758",
 "HasCoordinate is true",
 "Year is greater than or equal to 2013",
 "Year is less than or equal to 2018",
 "CoordinateUncertaintyInMeters is less than or equal to 1000"
 ]
}

 The dataset includes 3334 records from 146 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025781-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15187732
title: Dataset Colina

description: Dataset associated with the paper "Dynamic Total Body PET Imaging Unfolds [11C]-choline kinetics and dosimetry in primary hyperparathyroidism".

This set of raw data cannot be made pubicly available as including sensitive information, but might be made be available to interested researcers upon reasonable requests. Please, rafward your request to: letizia.calderoni4@unibo.it
DOI: 10.5281/zenodo.15187733
title: Dataset Colina

description: Dataset associated with the paper "Dynamic Total Body PET Imaging Unfolds [11C]-choline kinetics and dosimetry in primary hyperparathyroidism".

This set of raw data cannot be made pubicly available as including sensitive information, but might be made be available to interested researcers upon reasonable requests. Please, rafward your request to: letizia.calderoni4@unibo.it
DOI: 10.15468/dl.ak4iao
title: Occurrence Download

description: A dataset containing 96 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Schefflera vieillardii Baill."
 ]
}

 The dataset includes 96 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008216-170826194755519/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jj94wx
title: Occurrence Download

description: A dataset containing 5191 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((66.44753 70.54838, 72 70.54838, 72 71.8559, 66.44753 71.8559, 66.44753 70.54838))"
 ]
}

 The dataset includes 5191 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041969-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ufp7gp
title: Occurrence Download

description: A dataset containing 35 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Jamesbrittenia barbata Hilliard"
 ]
}

 The dataset includes 35 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032462-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dssnah
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pinguicula parvifolia B.L.Rob."
 ]
}

 The dataset includes 49 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008217-151016162008034/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ebx3rw
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Justicia huambensis Hedrén"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032373-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dpjry8
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Nymphargus cristinae (Ruiz-Carranza & Lynch, 1995)"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041996-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.atwlev
title: Occurrence Download

description: A dataset containing 22 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Oligoplites saurus (Bloch & Schneider, 1801)",
 "Country is Colombia"
 ]
}

 The dataset includes 22 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008217-160118175350007/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.duyzef
title: Occurrence Download

description: A dataset containing 4190 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Isodon japonicus (Burm.f.) H.Hara"
 ]
}

 The dataset includes 4190 records from 140 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032376-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z9qzuj
title: Occurrence Download

description: A dataset containing 22653 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Prunus cerasus L.",
 "HasCoordinate is true"
 ]
}

 The dataset includes 22653 records from 460 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042263-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pxdry8
title: Occurrence Download

description: A dataset containing 154213 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Raphanus raphanistrum L.)"
 ]
}

 The dataset includes 154213 records from 1321 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042244-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yahhtm
title: Occurrence Download

description: A dataset containing 439 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.30_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Accipiter trivirgatus (Temminck, 1824)",
 "Year 2000-2020"
 ]
}

 The dataset includes 439 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008295-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gmjjts
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Porifera",
 "DatasetKey is NRW Regional Data: North Wales",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 7 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0207701-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z6s569
title: Occurrence Download

description: A dataset containing 474716 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "CoordinateUncertaintyInMeters 0.0-55.0",
 "Country is Mexico",
 "Geometry POLYGON((-113.93529 24.43529,-107.42305 21.32325,-104.08049 17.86542,-91.34417 14.23471,-92.38152 17.92305,-107.01964 30.717,-116.70155 31.81198,-113.93529 24.43529))",
 "HasGeospatialIssue is false",
 "MediaType is one of (Image, Audio)",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 474716 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0277029-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q89rkt
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cnidaria",
 "DatasetKey is NINA Artskart data",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0209174-230224095556074/datasets/export for details.
DOI: 10.15468/dl.qaxeah
title: Occurrence Download

description: A dataset containing 220 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-65.0",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Alouatta pigra Lawrence, 1933",
 "Year 2000-2023"
 ]
}

 The dataset includes 220 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0277043-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kgeuyn
title: Occurrence Download

description: A dataset containing 60 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eutrema cordifolium Turcz. ex Ledeb."
 ]
}

 The dataset includes 60 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0207711-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ywfw8p
title: Occurrence Download

description: A dataset containing 16967 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Charadrius falklandicus Latham, 1790)",
 "HasCoordinate is one of (true)"
 ]
}

 The dataset includes 16967 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0277049-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fcpwjd
title: Occurrence Download

description: A dataset containing 152 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eutrema fontanum (Maxim.) Al-Shehbaz & S.I.Warwick"
 ]
}

 The dataset includes 152 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0207723-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kxhuxv
title: Occurrence Download

description: A dataset containing 4616 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Arthropoda, Nematoda, Tardigrada, Rotifera, Annelida, Mollusca, Platyhelminthes)",
 "Geometry POLYGON ((-147.826667 65.287175, -147.818333 65.018024, -147.181723 65.020154, -147.183574 65.289331, -147.826667 65.287175))",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Year is greater than or equal to 1900",
 {
 "not" : {
 "CoordinateUncertaintyInMeters" : [
 "is one of (301, 3036, 999, 9999)"
 ]
 }
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 4616 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0236034-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j9bg28
title: Occurrence Download

description: A dataset containing 158 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bunodosoma californica Carlgren, 1951"
 ]
}

 The dataset includes 158 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0209256-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q5gh76
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Ecuador",
 "TaxonKey is Anolis vanzolinii (Williams, Orces, Matheus & Bleiweiss, 1996)"
 ]
}

 The dataset includes 10 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007157-240425142415019/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3a58rt
title: Occurrence Download

description: A dataset containing 7495 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Italy",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Coccinellidae"
 ]
}

 The dataset includes 7495 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0277067-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9x79gq
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is UTA Reptiles",
 "Geometry POLYGON((-115.92742 35.09528,-114.56597 35.09528,-114.56597 36.52636,-115.92742 36.52636,-115.92742 35.09528))"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0238704-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.abax3b
title: Occurrence Download

description: A dataset containing 5157 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Arthropoda, Nematoda, Tardigrada, Rotifera, Annelida, Mollusca, Platyhelminthes)",
 "Geometry POLYGON ((-149.755981 68.789881, -149.723102 68.52113, -148.989388 68.531424, -149.013425 68.800318, -149.755981 68.789881))",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Year is greater than or equal to 1900",
 {
 "not" : {
 "CoordinateUncertaintyInMeters" : [
 "is one of (301, 3036, 999, 9999)"
 ]
 }
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 5157 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0236036-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mnjkfp
title: Occurrence Download

description: A dataset listing the 2 species recorded in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Material sample, Material citation, Specimen, Occurrence evidence)",
 "Country is Greece",
 "OccurrenceStatus is Present",
 "TaxonKey is Alauda arvensis Linnaeus, 1758",
 "Year 1990-2022"
 ]
}

 The dataset's 2 records were derived from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0234941-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sqmvuk
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Nepeta schugnanica Lipsky"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047005-230530130749713/datasets/export for details.
DOI: 10.15468/dl.tarvfe
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sivameryx Lydekker, 1878"
 ]
}

 The dataset includes 29 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000142-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v75hgc
title: Occurrence Download

description: A dataset containing 5169392 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is INSDC Sequences"
 ]
}

 The dataset includes 5169392 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0247002-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ben58k
title: Occurrence Download

description: A dataset containing 814 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hydrolea zeylanica (L.) Vahl"
 ]
}

 The dataset includes 814 records from 56 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0249747-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4sy8qu
title: Occurrence Download

description: A dataset containing 25529 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cordyline Comm. ex R.Br."
 ]
}

 The dataset includes 25529 records from 388 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0238706-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.an59jn
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Porifera",
 "DatasetKey is Base BOMBINA du Parc Naturel régional Lorraine - Modernisation des ZNIEFF du PnrL",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0207721-230224095556074/datasets/export for details.