Table · dataset · 2026
<p>The parameters of the SINDy.</p>
Listed in UCL Research Data Repository and HKU DataHub and Swinburne Figshare and DaYta Ya Rona and SUNScholarData and figshare and Loughborough Research Repository and GRANTS Data and UP Research Data Repository — shown once because both records carry DOI 10.1371/journal.pone.0344409.t002
<div><p>The COVID-19 pandemic presented severe challenges in understanding and predicting the spread of infectious diseases, necessitating innovative approaches beyond traditional epidemiological models.
Description
This study introduces an advanced method for automated model discovery using the Sparse Identification of Nonlinear Dynamics (SINDy) algorithm, leveraging a dataset from the COVID-19 outbreak in Thuringia, Germany, encompassing more than 400,000 patient records and vaccination data.
We develop a flexible, data-driven model capturing pandemic dynamics, incorporating external factors and interventions into the mathematical framework. The fixed coefficient values globally determined by SINDy were not accurate for local modelling of the data, a limitation of prior SINDy-based epidemiological applications that our framework directly addresses. We therefore refined our technique based on the differential equations as found by SINDy, by investigating three modifications that account for recent local data, each offering different strengths for short-term prediction, scenario analysis, and capturing nonlinear effects, achieving an R² of 0.87 at a one-week horizon.
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In a first approach, we re-optimized the coefficient values using seven days of past data, without changing the globally determined differential equation. In a second approach, we allowed a temporal dependence of the coefficient values, fitted using all previous data, in combination with regularization. As a last method, we kept the coefficients fixed to the original values but augmented the differential equation with a small neural network, locally optimized to the data of the past week.
Our results link vaccination and public health measures to the pandemic's trajectory. The proposed model allows simulation of intervention scenarios, such as vaccination strategies and public health interventions. While the current study is based on retrospective data from a single region, the framework could serve as a basis for exploring responses to future outbreaks, subject to further validation.</p></div>
Links
Where it is published
- DOI doi.org/10.1371/journal.pone.0344409.t002 ↗
DOI / persistent id · from rdr ucl ac uk
Catalogue records · 1
- OAI-PMH record api.figshare.com/v2/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=oai%3Af… ↗
metadata API · from rdr ucl ac uk
Topics
- From keywords
- Astronomy & Astrophysics · Cancer · Cancer · Cancer · Cancer · Cancer · Cancer · Cancer · Cancer · Cancer · Chemistry · Chemistry · Computer Science & AI · Computer Science & AI · Earth & Environmental Science · Earth & Environmental Science · Earth & Environmental Science · Earth & Environmental Science · Earth & Environmental Science · Earth & Environmental Science · Earth & Environmental Science · Earth & Environmental Science · Earth & Environmental Science · Economics & Finance · Economics & Finance · Engineering · Engineering · Engineering · Engineering · Humanities · Humanities · Humanities · Humanities · Life Sciences · Life Sciences · Life Sciences · Life Sciences · Life Sciences · Life Sciences · Life Sciences · Life Sciences · Life Sciences · Materials Science · Mathematics & Statistics · Mathematics & Statistics · Mathematics & Statistics · Mathematics & Statistics · Mathematics & Statistics · Mathematics & Statistics · Mathematics & Statistics · Mathematics & Statistics · Mathematics & Statistics · Medicine & Health · Medicine & Health · Medicine & Health · Medicine & Health · Medicine & Health · Medicine & Health · Medicine & Health · Medicine & Health · Medicine & Health · Ocean & Atmospheric Science · Psychology & Behavioral Science · Research, science and technology policy · Research, science and technology policy · Research, science and technology policy · Research, science and technology policy · Research, science and technology policy · Research, science and technology policy · Research, science and technology policy · Research, science and technology policy · Research, science and technology policy · Social Science · Social Science · Social Science · Social Science
- Inferred from text
- Simulation 75%
Provenance · 9 source records, 82 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| UCL Research Data Repository | oai:figshare.com:article/34048853 | 12 d ago | JSON v1 |
| HKU DataHub | oai:figshare.com:article/34048853 | 12 d ago | JSON v1 |
| Swinburne Figshare | oai:figshare.com:article/34048853 | 12 d ago | JSON v1 |
| DaYta Ya Rona | oai:figshare.com:article/34048853 | 12 d ago | JSON v1 |
| SUNScholarData | oai:figshare.com:article/34048853 | 12 d ago | JSON v1 |
| figshare | oai:figshare.com:article/34048853 | 12 d ago | JSON v1 |
| Loughborough Research Repository | oai:figshare.com:article/34048853 | 11 d ago | JSON v1 |
| GRANTS Data | oai:figshare.com:article/34048853 | 11 d ago | JSON v1 |
| UP Research Data Repository | oai:figshare.com:article/34048853 | 11 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · rdr ucl ac uk | connector:rdr_ucl_ac_uk@1.0.0 | |
| concepts[disease].local:disease:cancer | mapping · figshare swinburne edu au | vocabulary-mapper@1.0.0 | keywords['Cancer'] |
| concepts[disease].local:disease:cancer | mapping · figshare com | vocabulary-mapper@1.0.0 | keywords['Cancer'] |
| concepts[disease].local:disease:cancer | mapping · datahub hku hk | vocabulary-mapper@1.0.0 | keywords['Cancer'] |
| concepts[disease].local:disease:cancer | mapping · researchdata up ac za | vocabulary-mapper@1.0.0 | keywords['Cancer'] |
| concepts[disease].local:disease:cancer | mapping · repository lboro ac uk | vocabulary-mapper@1.0.0 | keywords['Cancer'] |
| concepts[disease].local:disease:cancer | mapping · grantsdata jst go jp | vocabulary-mapper@1.0.0 | keywords['Cancer'] |
| concepts[disease].local:disease:cancer | mapping · scholardata sun ac za | vocabulary-mapper@1.0.0 | keywords['Cancer'] |
| concepts[disease].local:disease:cancer | mapping · dayta nwu ac za | vocabulary-mapper@1.0.0 | keywords['Cancer'] |
| concepts[disease].local:disease:cancer | mapping · rdr ucl ac uk | vocabulary-mapper@1.0.0 | keywords['Cancer'] |
| concepts[field].anzsrc:field:440710 | mapping · repository lboro ac uk | vocabulary-mapper@1.0.0 | keywords['Science Policy'] |
| concepts[field].anzsrc:field:440710 | mapping · scholardata sun ac za | vocabulary-mapper@1.0.0 | keywords['Science Policy'] |
| concepts[field].anzsrc:field:440710 | mapping · figshare com | vocabulary-mapper@1.0.0 | keywords['Science Policy'] |
| concepts[field].anzsrc:field:440710 | mapping · researchdata up ac za | vocabulary-mapper@1.0.0 | keywords['Science Policy'] |
| concepts[field].anzsrc:field:440710 | mapping · rdr ucl ac uk | vocabulary-mapper@1.0.0 | keywords['Science Policy'] |
| concepts[field].anzsrc:field:440710 | mapping · datahub hku hk | vocabulary-mapper@1.0.0 | keywords['Science Policy'] |
| concepts[field].anzsrc:field:440710 | mapping · grantsdata jst go jp | vocabulary-mapper@1.0.0 | keywords['Science Policy'] |
| concepts[field].anzsrc:field:440710 | mapping · figshare swinburne edu au | vocabulary-mapper@1.0.0 | keywords['Science Policy'] |
| concepts[field].anzsrc:field:440710 | mapping · dayta nwu ac za | vocabulary-mapper@1.0.0 | keywords['Science Policy'] |
| concepts[field].local:field:astronomy | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:chemistry | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:chemistry | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:computer-science-ai | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:computer-science-ai | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:earth-environmental | mapping · dayta nwu ac za | connector:dayta_nwu_ac_za@1.0.0 | |
| concepts[field].local:field:earth-environmental | mapping · grantsdata jst go jp | connector:grantsdata_jst_go_jp@1.0.0 | |
| concepts[field].local:field:earth-environmental | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:earth-environmental | mapping · datahub hku hk | connector:datahub_hku_hk@1.0.0 | |
| concepts[field].local:field:earth-environmental | mapping · scholardata sun ac za | connector:scholardata_sun_ac_za@1.0.0 | |
| concepts[field].local:field:earth-environmental | mapping · rdr ucl ac uk | connector:rdr_ucl_ac_uk@1.0.0 | |
| concepts[field].local:field:earth-environmental | mapping · researchdata up ac za | connector:researchdata_up_ac_za@1.0.0 | |
| concepts[field].local:field:earth-environmental | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:earth-environmental | mapping · figshare swinburne edu au | connector:figshare_swinburne_edu_au@1.0.0 | |
| concepts[field].local:field:economics-finance | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:economics-finance | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:engineering | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:engineering | mapping · researchdata up ac za | connector:researchdata_up_ac_za@1.0.0 | |
| concepts[field].local:field:engineering | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:engineering | mapping · dayta nwu ac za | connector:dayta_nwu_ac_za@1.0.0 | |
| concepts[field].local:field:humanities | mapping · researchdata up ac za | connector:researchdata_up_ac_za@1.0.0 | |
| concepts[field].local:field:humanities | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:humanities | mapping · dayta nwu ac za | connector:dayta_nwu_ac_za@1.0.0 | |
| concepts[field].local:field:humanities | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · figshare swinburne edu au | connector:figshare_swinburne_edu_au@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · datahub hku hk | connector:datahub_hku_hk@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · grantsdata jst go jp | connector:grantsdata_jst_go_jp@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · dayta nwu ac za | connector:dayta_nwu_ac_za@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · scholardata sun ac za | connector:scholardata_sun_ac_za@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · researchdata up ac za | connector:researchdata_up_ac_za@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · rdr ucl ac uk | connector:rdr_ucl_ac_uk@1.0.0 | |
| concepts[field].local:field:materials-science | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:mathematics-statistics | mapping · figshare swinburne edu au | connector:figshare_swinburne_edu_au@1.0.0 | |
| concepts[field].local:field:mathematics-statistics | mapping · rdr ucl ac uk | connector:rdr_ucl_ac_uk@1.0.0 | |
| concepts[field].local:field:mathematics-statistics | mapping · datahub hku hk | connector:datahub_hku_hk@1.0.0 | |
| concepts[field].local:field:mathematics-statistics | mapping · dayta nwu ac za | connector:dayta_nwu_ac_za@1.0.0 | |
| concepts[field].local:field:mathematics-statistics | mapping · scholardata sun ac za | connector:scholardata_sun_ac_za@1.0.0 | |
| concepts[field].local:field:mathematics-statistics | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:mathematics-statistics | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:mathematics-statistics | mapping · grantsdata jst go jp | connector:grantsdata_jst_go_jp@1.0.0 | |
| concepts[field].local:field:mathematics-statistics | mapping · researchdata up ac za | connector:researchdata_up_ac_za@1.0.0 | |
| concepts[field].local:field:medicine-health | mapping · figshare swinburne edu au | connector:figshare_swinburne_edu_au@1.0.0 | |
| concepts[field].local:field:medicine-health | mapping · datahub hku hk | connector:datahub_hku_hk@1.0.0 | |
| concepts[field].local:field:medicine-health | mapping · rdr ucl ac uk | connector:rdr_ucl_ac_uk@1.0.0 | |
| concepts[field].local:field:medicine-health | mapping · researchdata up ac za | connector:researchdata_up_ac_za@1.0.0 | |
| concepts[field].local:field:medicine-health | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:medicine-health | mapping · scholardata sun ac za | connector:scholardata_sun_ac_za@1.0.0 | |
| concepts[field].local:field:medicine-health | mapping · grantsdata jst go jp | connector:grantsdata_jst_go_jp@1.0.0 | |
| concepts[field].local:field:medicine-health | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:medicine-health | mapping · dayta nwu ac za | connector:dayta_nwu_ac_za@1.0.0 | |
| concepts[field].local:field:ocean-atmospheric | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:psychology-behavioral | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:social-science | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:social-science | mapping · dayta nwu ac za | connector:dayta_nwu_ac_za@1.0.0 | |
| concepts[field].local:field:social-science | mapping · researchdata up ac za | connector:researchdata_up_ac_za@1.0.0 | |
| concepts[field].local:field:social-science | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[method].local:method:simulation | enrichment · rdr ucl ac uk | keyword-concept-rules@1.0.0 | title+description (75%) |
| description | source · rdr ucl ac uk | connector:rdr_ucl_ac_uk@1.0.0 | /metadata/dc/description |
| license | source · rdr ucl ac uk | connector:rdr_ucl_ac_uk@1.0.0 | /metadata/dc/rights |
| publication_date | source · rdr ucl ac uk | connector:rdr_ucl_ac_uk@1.0.0 | |
| title | source · rdr ucl ac uk | connector:rdr_ucl_ac_uk@1.0.0 | /metadata/dc/title |