Text mining Montpellier

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Text mining Montpellier

  1. 1. Using language to detect potential change in ecosystem services in the light of ecological surprises ! Juan Carlos Rocha & Robin Wikström
  2. 2. Ecosystem services are the benefits humans receive from nature (MEA 2005) Foley et al. 2005. Science
  3. 3. 1980 1985 1990 1995 2000 2005 2010 2015 0500100015002000 Year ScientificPapers ISI Web of Knowledge Ecosystem services is a relatively recent field of studies. Yet, assessing which ecosystem services are likely to be affected by ecological surprises is one of the greatest challenges of current ecological research.
  4. 4. • Knowledge bias: we know a lot about easy to study stuff • There is the lack of high quality datasets and time series to assess ecosystem services change • It is difficult to experiment with ecosystems, especially when it comes to large scale phenomena, possible irreversible, with great potential to affect human well-being The problem
  5. 5. Latent Dirichlet Allocation (LDA) The main goal is to create algorithms for discovering main themes that pervades large and unstructured collection of documents The elemental idea is that documents consist of random mixtures of latent topics, topics that can be represented as a distribution of words The goal is to automatically discover these “hidden” topics, without having any prior knowledge about the text and its content
  6. 6. Model selection & number of topics • We test Variational Estimation Methods (VEM), correlated topic models (CTM) & Gibbs sampling. • We tested 5 models with different topic numbers (20:100) • VEM algorithm with 80 topics fit the best the MEA training dataset VEM1 VEM2 VEM3 VEM4 VEM5 0.010 0.012 0.014 0.016 alpha VEM1 VEM2 VEM3 VEM4 VEM5 -1280000 -1240000 -1200000 logLik VEM1 VEM2 VEM3 VEM4 VEM5 500 600 700 800 Perplexity VEM1 VEM2 VEM3 VEM4 VEM5 0.1 0.2 0.3 0.4 0.5 Entropy
  7. 7. Topics = 80 Millenium Ecosystem AssessmentTopics detection 38 58 5 14 73 41 22 70 45 80 72 55 18 19 15 44 52 56 57 78 9 1 47 28 12 39 29 30 40 75 6 27 4 35 68 71 42 48 11 51 59 2 66 63 25 34 67 3 65 60 46 32 10 21 54 7 37 17 23 69 20 49 26 8 13 16 64 77 76 33 50 53 24 61 62 31 74 79 43 36 Chapter 20 Inland Water Systems−2.pdf.txt Chapter 8 Food.pdf.txt Chapter 9 Timber Fuel and Fiber.pdf.txt Chapter 15 Waste Processing and Detoxi...cation.pdf.txt Chapter 17 Cultural and Amenity Services.pdf.txt Chapter 23 Island Systems.pdf.txt Chapter 5 Ecosystem Conditions and Human Well−being.pdf.txt Chapter 6 Vulnerable Peoples and Places.pdf.txt Fisher−2013−Strengthening_conceptual_foundations_Analysing_frameworks_for_e Stallman−2011−Ecosystem_services_in_agriculture_determining_suitability_for_pr Power−2010−Ecosystem_services_and_agriculture_tradeoffs_and_synergies.pdf.t Saad−2013−Land_use_impacts_on_freshwater_regulation_erosion_regulation_an Mitchell−2013−Linking_Landscape_Connectivity_and_Ecosystem_Service_Provisi Mann−2012−Ecosystem_Service_Value_and_Agricultural_Conversion_in_the_Am Maskell−2013−Exploring_the_ecological_constraints_to_multiple_ecosystem_serv Cardinale−2013−Biodiversity_simultaneously_enhances_the_production_and_stab Jax−2013−Ecosystem_services_and_ethics.pdf.txt Chapter 28 Synthesis Condition and Trends in Systems and Services Trade−offs fo Chen−2013−Changes_in_land_useland_cover_and_ecosystem_services_in_Cent Chapter 1 MA Conceptual Framework.pdf.txt Nelson−2005−Chapter 3 Drivers of ecosystem change summary chapter.pdf.txt Chapter 2 Analytical Approaches for Assessing Ecosystem Condition and Human W Chapter 14 Human Health Ecosystem Regulation of Infectious Diseases.pdf.txt Chapter 24 Mountain Systems.pdf.txt Zheng−−Benefits_costs_and_livelihood_implications_of_a_regional_payment_for_ Sircely−2012−Biodiversity_and_Ecosystem_Multi−Functionality_Observed_Relatio Langerwisch−2012−Potential_effects_of_climate_change_on_inundation_patterns_ Chapter 13 Climate and Air Quality.pdf.txt Qiu−−Spatial_interactions_among_ecosystem_services_in_an_urbanizing_agricult Chapter 22 Dryland Systems.pdf.txt Chapter 7 Fresh Water.pdf.txt Chapter 4 Biodiversity.pdf.txt Chapter 18 Marine Fisheries Systems.pdf.txt Chapter 12 Nutrient Cycling.pdf.txt Vidal−Abarca_Gutie..rrez−2013−Which_are_what_is_their_status_and_what_can_ Chapter 25 Polar Systems.pdf.txt Turner−2012−Consequences_of_spatial_heterogeneity_for_ecosystem_services_i Bai−2012−Grazing_alters_ecosystem_functioning_and_CNP_stoichiometry_of_gra Chapter 10 New Products and Industries from Biodiversity.pdf.txt Acreman−2013−How_Wetlands_Affect_Floods.pdf.txt Chapter 16 Regulation of Natural Hazards Floods and Fires.pdf.txt Chapter 11 Biodiversity Regulation of Ecosystem Services.pdf.txt Schmitt−2013−Capturing_Ecosystem_Services_Stakeholders'_Preferences_and_T Chapter 21 Forest and Woodland Systems.pdf.txt Chapter 27 Urban Systems.pdf.txt Chapter 26 Cultivated Systems.pdf.txt Chapter 19 Coastal Systems.pdf.txt 0.2 0.6 Value 02000 Color Key and Histogram Count
  8. 8. Topics matching Ecosystem Services Topics Words Ecosystem Processes Soil formation 12 species, fallows, soil, biomass, grazed, fallow Primary production 19 soil, carbon, species, freshwater, carbon Nutrient cycling 4 nutrient, organic, fertility, soil, ocean, cycling Water cycling 39 discharge, amazon, inundation, basing, slope Biodiversity 6 species, plant, richness, biodiversity, services Provisioning services Freshwater 75 freshwater, renewable, supply, freshwater, river Food crops 5 nutrition, countries, livestock, africa, health Livestock 11 grazing, steppe, soil, ground, biomass, pools Fisheries 27 marine, fisheries, fish, coastal, system, ocean Wild animals and plants products Timber 2 forest, countries, carbon, plantations, trees, fao Wood fuel 14 timeber, products, tao, forest, fuelwood, cotton Feed, fuel and fiber crops 14 timeber, products, tao, forest, fuelwood, cotton Hydropower Regulating services Air quality regulation 29 atmospheric, emissions, carbon, warming Climate regulation 29 atmospheric, emissions, carbon, warming Water purification 73 waste, chemicals, organic, health, exposure Regulation of soil erosion 72 cycle, soil, spatial, erosion, groundwater Pest and disease 1 disease, health, infectious,malaria, transmission Pollination 45 pollination, provision, benefits, farmers, landscape Natural hazards 67 fire, events, floods, drivers, wetlands, coastal Cultural services 41 landscapes, tourism, traditional, knowledge, heritage Recreation Aesthetic values Knowledge and educational values Spiritual and religious
  9. 9. Topics = 80 Corpus = 812 papersTopics detection Soilformation Primaryproduction Nutrientcycling Watercycling Biodiversity Freshwater Foodcrops Livestock Fisheries Timber Woodfuel Climateregulation Waterregulation Regulationofsoilerosion Pestanddiseaseregulation Pollination Naturalhazardregulation Cultural West Antarctic IceSheet Collapse Tundra to Forest Termohaline circulation Steppe to tundra Soil structure Soil salinization Sea grass collapse Salt marshes River channel change Peatlands Monsoon weakening Marine foodwebs Marine eutrophication Mangroves collapse Kelps transitions Hypoxia Greenland Forest to savannas Floating plants Fisheries collapse Eutrophication Encroachment Dry land degradation Coral transitions Bivalves collapse Arctic Sea Ice 0.1 0.4 Value 0250 Color Key and Histogram Count Soilformation Primaryproduction Nutrientcycling Watercycling Biodiversity Freshwater Foodcrops Livestock Fisheries Timber Woodfuel Climateregulation Waterregulation Regulationofsoilerosion Pestanddiseaseregulation Pollination Naturalhazardregulation Cultural West Antarctic IceSheet Collapse Tundra to Forest Termohaline circulation Steppe to tundra Soil structure Soil salinization Sea grass collapse Salt marshes River channel change Peatlands Monsoon weakening Marine foodwebs Marine eutrophication Mangroves collapse Kelps transitions Hypoxia Greenland Forest to savannas Floating plants Fisheries collapse Eutrophication Encroachment Dry land degradation Coral transitions Bivalves collapse Arctic Sea Ice 0 0.4 1 Value 180 Color Key and Histogram Count Human Readers Computer reading
  10. 10. Soilformation Primaryproduction Nutrientcycling Watercycling Biodiversity Freshwater Foodcrops Livestock Fisheries Timber Woodfuel Climateregulation Waterregulation Regulationofsoilerosion Pestanddiseaseregulation Pollination Naturalhazardregulation Cultural West Antarctic IceSheet Collapse Tundra to Forest Termohaline circulation Steppe to tundra Soil structure Soil salinization Sea grass collapse Salt marshes River channel change Peatlands Monsoon weakening Marine foodwebs Marine eutrophication Mangroves collapse Kelps transitions Hypoxia Greenland Forest to savannas Floating plants Fisheries collapse Eutrophication Encroachment Dry land degradation Coral transitions Bivalves collapse Arctic Sea Ice Topics = 80 Corpus = 812 papersTopics detection False positives Soilformation Primaryproduction Nutrientcycling Watercycling Biodiversity Freshwater Foodcrops Livestock Fisheries Timber Woodfuel Climateregulation Waterregulation Regulationofsoilerosion Pestanddiseaseregulation Pollination Naturalhazardregulation Cultural West Antarctic IceSheet Collapse Tundra to Forest Termohaline circulation Steppe to tundra Soil structure Soil salinization Sea grass collapse Salt marshes River channel change Peatlands Monsoon weakening Marine foodwebs Marine eutrophication Mangroves collapse Kelps transitions Hypoxia Greenland Forest to savannas Floating plants Fisheries collapse Eutrophication Encroachment Dry land degradation Coral transitions Bivalves collapse Arctic Sea Ice False negatives
  11. 11. Zooming problem Ecosystem services categories make sense for MEA authors but not necessarily for other scientist, readers or… computers.
  12. 12. Concluding remarks • It’s hard to make students do homework, but even harder to make your computer do it automatically for you…Errors • Broad categories such as supporting & cultural services are hard to identify, we did much better with regulating services. • Our results open the possibility of using text mining for monitoring trends on ecosystem services at larger scales and real time. Soilformation Primaryproduction Nutrientcycling Watercycling Biodiversity Freshwater Foodcrops Livestock Fisheries Timber Woodfuel Climateregulation Waterregulation Regulationofsoilerosion Pestanddiseaseregulation Pollination Naturalhazardregulation Cultural West Antarctica Ice Sheet collapse ( Tundra to forest (17) Thermohaline circulation (26) Steppe to tundra (10) Soil structure (2) Soil salinization (7) Sea grass collapse (6) Salt marshes (17) River channel change (22) Peatlands (21) Monsoon weakening (9) Marine foodwebs (50) Marine Eutrophication (8) Mangroves collapse (6) Kelps transitions (11) Hypoxia (7) Greenland (20) Forest to savannas (39) Floating plants (4) Fisheries collapse (75) Eutrophication (20) Encroachment (12) Dry land degradation (26) Coral transitions (33) Bivalves collapse (13) Arctic Sea Ice (19) 0 0.4 1 Value 215 Color Key and Histogram Count
  13. 13. Questions?? e-mail: juan.rocha@su.se twitter: @juanrocha slides: http://criticaltransitions.wordpress.com/ | data: www.regimeshifts.rog
  14. 14. Subscribe  to  our  newsletter   www.stockholmresilience.su.se/subscribe   Thank  you!

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