Machine Learning a Probabilistic Network of Ecological ... - ART-Dijon

D.C. Weber and J.G. Lundgren. Assessing the trophic ecology of the coccinellidae: their roles as predators and as prey. Biological Control, 51(2):199–214, 2009.
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Machine Learning a Probabilistic Network of Ecological Interactions Alireza Tamaddoni-Nezhad

Department of Computing, Imperial College London [email protected]

David Bohan

INRA [email protected]

Alan Raybould

Syngenta Ltd [email protected]

Stephen Muggleton

Department of Computing, Imperial College London [email protected]

Overview

• Problem and data • Learning trophic links (i.e. food-webs) from FSE data • Functional food-webs • Pitfall vs Vortis food-webs • Automatic corroboration of learned trophic links • Discussion and further work

Ecosystems as networks of biomass flow Carabid larva

PREDATORS

Araneae

HERBIVORS

Can we apply machine learning on FSE data to construct food-webs from scratch?

Trechus quadristriatus

PLANTS

• Networks of trophic links (food webs) are important for explaining ecosystem structure and dynamics • It is difficult to establish trophic relationships between the many hundreds of species in an ecosystem • Project goal:

Auchenorhyncha

Isotomidae

Aphidoidea

Farm Scale Evaluation (FSE) of Genetically Modified herbicide-tolerant (GMHT) crops in the UK Samples from 257 sites, 4 different crops (spring beet, spring maize, spring oilseed rape and winter oilseed rape) across the UK between 2000 and 2004. Sites information: SITE_CODE SEASON CROP REGION B10 2000 B EASTERN B11 2000 B EASTERN B12 2000 B MIDLANDS&WESTER B13 2000 B MIDLANDS&WESTER B14 2000 B MIDLANDS&WESTER ... ... ... ...

SIZE 4.4 14.0 7.3 9.9 3.0 ...

INTENSITY 5 5 4 4 5 ...

BIODIVERSITY 1 1 0 1 0 ...

SOIL Medium Medium Medium Light Heavy ...

Species information: ARTHROPOD weight length 6453 4703 0 3.5 6455 59501 0 7 6453 3503 0.09 7 6453 3513 6.17E-02 8 ... ... ...

size class activity 1 1 3 1 3 1 4 0 ... ...

sap 0 0 0 0 ...

leaves 0 0 0 0 ...

seeds detritus spec pred gen pred 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 ... ... ... ...

Abundance of species in conventional and GMHT farms: ARTHROPOD 6400 111 6400 111 6400 111 6400 111 6400 111 ...

SITE_CODE CONVEN. B14 0 B15 0 B17 9 B18 1 B20 0 ... ...

GMHT 0 0 11 9 1 ...

ARTHROPOD 6400 111 6400 111 6400 111 6400 111 6400 111 ...

SITE_CODE abundance B18 up B21 down B34 down B66 down B67 up ... ...

Figure 1. Distribution of the 66 spring-sown beet (), 59 spring maize (), 67 spring oilseed rape () and 65 winter oilseed rape () fields sampled as part of the Farm Scale Evaluations (FSE) of Genetically Modified, herbicide-tolerant (GMHT) crops.

Abduction of trophic links Background knowledge

Observables

abundance(X, S, up):predator(X), abundance(Y, S, up), co_occurs(S, X, Y), bigger_than(X, Y), eats(X, Y).

X

Abduced hypotheses

eats(a1, a3). eats(a5, a6). eats(a5, a7). . .

Y

Z

Direction of effect

abundance(a1, s1, up). abundance(a2, s1, up). abundance(a3, s1, up). abundance(a1, s2, up). abundance(a2, s2, down). abundance(a3, s2, up). . . .

A probabilistic trophic network from Vortis data

D. Bohan, G. Caron-Lormier, S. Muggleton, A. Raybould and A. Tamaddoni-Nezhad, Automated Discovery of Food Webs from Ecological Data Using Logic-Based Machine Learning. PLoS ONE 6(12): e29028, 2011 A. Tamaddoni-Nezhad, D. Bohan, A. Raybould and S. Muggleton, Machine learning a probabilistic network of ecological interactions, In Proceedings of the 21st International Conference on Inductive Logic Programming, LNAI 7207, pages 332-346, 2012.

Corroboration of hypotheses in the literature and potential novel hypotheses (in red)

* Spearman's correlation between frequencies and number of references: 0.77 with p-value 0.009

Literature which support abduced trophic links 1. K.N.A. Alexander. The invertebrates of living and decaying timber in britain and ireland–a provisional annotated checklist. English Nature Research Reports, 467:1–142, 2002. 2. T. Bauer. Prey-capture in a ground-beetle larva. Animal Behaviour, 30(1):203–208, 1982. 3. J.R. Bell, R. Andrew King, D.A. Bohan, and W.O.C. Symondson. Spatial co-occurrence networks predict the feeding histories of polyphagous arthropod predators at field scales. Ecography, 33(1):64–72, 2010. 4. K. Berg. The role of detrital subsidies for biological control by generalist predators evaluated by molecular gut content Analysis. PhD thesis, Universit¨ats-und Landesbibliothek Darmstadt, 2007. 5. K. Desender and M. Pollet. Ecological data on clivina fossor(coleoptera, carabidae) from a pasture ecosystem. ii. reproduction, biometry, biomass, wing polymorphism and feeding ecology. Rev. Ecol. Biol. Sol., 22(2):233– 246, 1985. 6. A. Dinter. Intraguild predation between erigonid spiders, lacewing larvae and carabids. Journal of Applied Entomology, 122(1-5):163–167, 1998. 7. J.D. Lattin. Bionomics of the nabidae. Annual review of entomology, 34(1):383–400, 1989. 8. J. Lindsey. Ecology of Commanster, http://www.commanster.eu/commanster/insects/bugs/spbugs/ saldula.saltatoria.html. 9. X. Pons, B. Lumbierres, and R. Albajes. Heteropterans as aphid predators in inter-mountain alfalfa. European Journal of Entomology, 106(3):369–378, 2009. 10. C.W. Schaefer and A.R. Panizzi. Heteroptera of economic importance. CRC, 2000. 11. KD Sunderland. The diet of some predatory arthropods in cereal crops. Journal of Applied Ecology, 12(2):507–515, 1975. 12. K.D. Sunderland, G.L. Lovei, and J. Fenlon. Diets and reproductive phenologies of the introduced ground beetles harpalus-affinis and clivina-australasiae (coleoptera, carabidae) in new-zealand. Australian Journal of Zoology, 43(1):39–50, 1995. 13. S. Toft. The quality of aphids as food for generalist predators: implications for natural control of aphids. European Journal of Entomology, 102(3):371, 2005. 14. B.D. Turner. Predation pressure on the arboreal epiphytic herbivores of larch trees in southern england. Ecological Entomology, 9(1):91–100, 1984. 15. D.J. Warner, LJ Allen-Williams, S. Warrington, AW Ferguson, and IH Williams. Mapping, characterisation, and comparison of the spatio-temporal distributions of cabbage stem flea beetle (psylliodes chrysocephala), carabids, and collembola in a crop of winter oilseed rape (brassica napus). Entomologia experimentalis et applicata, 109(3):225–234, 2003. 16. D.C. Weber and J.G. Lundgren. Assessing the trophic ecology of the coccinellidae: their roles as predators and as prey. Biological Control, 51(2):199–214, 2009.

Functional Food-Webs: Can the FSE data be used to test the theory that ecosystems at the field-scale behave as networks that emerge from interactions between trophic functional types ?

A probabilistic trophic network for functional groups

A trophic network constructed by learning trophic interactions between functional groups.

Functional group

Name

Size

11 Large Predator

4

12 Aphid predator

3

10 Medium-large predator

3

23 Predatory heteroptera

3

13 L. pilicornis (1 species group)

3

9 Medium predator

2

22 Medium predator

2

14 Aphid predator (adult)

4

3 Leaf chewer 18 Sucking predator 1 Sap sucker

3 2 1

17 Sucking predator

1

25 Parasitoids

1

7 Detritivores

1

8 Small predators

1

2 Sap sucker

2

A probabilistic trophic network for functional groups

Each functional group is represented by a species which can be viewed as an archetype for the functional group.

Overall learning curves for functional vs individual food-webs (Vortis)

Pitfall vs Vortis sampling

Vortis suction sampler

ARTHROPOD 6400 111 6400 111 6400 111 6400 111 6400 111 ...

SITE_CODE CONVEN. B14 0 B15 0 B17 9 B18 1 B20 0 ... ...

GMHT 0 0 11 9 1 ...

Abundance of species

A pitfall trap

A (new) probabilistic trophic network from pitfall data

Overall learning curves for functional vs individual food-webs (pitfall)

Automatic corroboration of new food-webs (work-in-progress)

Manual corroboration of trophic links in the literature

Automatic corroboration of trophic links (text-mining)

?

Goal of automatic corroboration: Can we adapt existing text-mining techniques and tools (e.g. Pubgene, SciMiner, Lit.Search, ..) to generate Literature Network for the species involved in the learned food-webs ?

Examples of literature networks for genes

A literature network generated by LitSearch

A literature network generated by PubGene

Automatic corroboration of food-webs (using text-mining) Publication Databases

Interaction Lexicon Pair of Species

Food-web

Query

Text Mining

Literature Network

Publication Search Engines

WWW

Literature Network for Merged Vortis & pitfall data

Literature Network for merged Vortis & pitfall data Null hypothesis: The frequencies of merged trophic links (from HFE ) and the number of hits for these links from text-mining are not correlated. 12

Hypothesis Frequency (HFE)

10

8

6

4

2

0 0

500

1000

1500

2000

2500

3000

Total number of hits from text-mining

Results: Correlation between the hypothesis frequencies (HFE) for merged trophic links and the number of hits for these links. Spearman's correlation ρ value is 0.821 with p-value 0.01

Summary • Using FSE data to generate testable food-webs from scratch • Corroboration of many links in the literature • Potential novel hypotheses which could be tested • Functional food-webs are at least as accurate as individual species food-webs (importance of functional ecology) • Initial results on text-mining of trophic links are consistent with frequencies from HFE

Future work • Extending the model (e.g. plant data, temporal data, ..) • Cross-validation of text-mining and improving the accuracy • Learning functional groups as well as trophic links using predicate invention Acknowledgment: G. Afroozi Milani (Imperial College), G. CaronLormier (Rothamsted Research), S. Dunbar (Syngenta)