Pest Control – Subtopic Landscape

A synthetic biology perspective

The subset of SynBio – pest control related patents were further investigated to identify subtopics and assess trending areas. The topic model leverages a hybrid approach based on the optimised extractive summary for each publication. Using a combination of topic discovery via fine-tuned transformer based deep learning and ground truth cross referencing via keyword and classification codes. The process enables a patent to belong to more than one topic for accurate multi-classification trends, accounting for multiple invention embodiments. Please see the topic model page for further details regarding the topic model methodology to avoid duplication here.

Subtopic landscape

The synthetic biology – pest control topic model is visualised in figure 8.9, based on the dimensionality reduction of vector embeddings to map each patent to a contextually relevant x & y coordinate, the categorical clusters are colour coded to support review. The visual is based on patents assigned to one key subtopic for simplicity. However, trend analysis also enables a patent to belong to more than one subtopic which is consistent with the topic model methodology throughout this project.

Subtopic model – technology cluster totals

The hybrid topic model methodology identified 15 diverse topics which are ranked based on the total number of published applications in figure 8.10. A patent application can be counted more than once as it can belong to multiple topics.

In figure 8.10, the analysis enables multilabel classification for each patent application, to account for multiple invention embodiments. During the 20 year publication period 2004-2023, approx. 72% of documents were classified in the biocide subtopic. The genetic engineering of plants accounted for 54% of the classification of pest control patents identified, including methods such as introducing specific genes to confer resistance to pests e.g. transgenic pants. The nucleic acids subtopic such as iRNA, antisense, etc. accounted for the classification of 15.3% of pest control patents identified. Exemplified by GreenLight Biosciences, RNAi based crop protection has high potential and can reduce the need for chemical pesticides due to environmental concerns. Around 14% of documents were classified in the Bacillus subtopic where Bacillus Thuringiensis is the most commonly used biological pesticide worldwide. Recent studies have shown Bacillus Thuringiensis may also have potential as a biofertiliser. Approx.15.7% of the documents identified were classified as genetically modified microorganisms potentially driven by the engineering of Bacillus species. Insect resistance (20.4%) is a larger subtopic than herbicide resistance (14.2%), fungal resistance (13.7%) and biotic stress / pathogen / disease resistance (12%).

The pest control subtopic publication year trends are shown in figure 8.11. Publication trends discussed below are based on EP A1/A2 applications, identified patents can belong to more than one subtopic due to multiple invention embodiments.

In figure 8.11, there are a lack of fast growing subtopics when analysing the compound annual growth rates during 2014-23. Some topics have been consistent, whist others have declined since a peak period. The fastest growing subtopic is the antimicrobial peptides & compounds area at 7.8% CAGR, potentially driven by the move away from chemical pesticides. This is also supported by the growth of the fungal resistance subtopic (4.1%) and biocides which are bacteria related subtopic (3.1%). Genetically modified microorganisms grew at 2.9% CAGR.

Subtopic top 20 assignees distributions (2014-23)

The patent portfolios of the top 20 assignees within the SynBio – pest control dataset are analysed in figure 8.12. The portfolios are restricted to publications during 2014-23, mapped to the 15 subtopics identified, the counts represent total EPO publications.

The heatmap in figure 8.12 reveals the distribution of the top 20 pest control assignees during 2014-23, publications can be assigned to more than one subtopic, reflecting multiple invention embodiments. The top 3 assignees identified; MONSANTO TEHCNOLOGY, PIONEER HI BRED INTERNATIONAL & DOW AGROSCIENCES have quite diverse portfolios with leading positions across a variety of subtopics. MONSANTO has a leading position for herbicide resistance (68 publications). BAYER CROPSCIENCES has the largest distribution of Bacillus related pest control (38). KWS SAAT has a focus toward fungal resistance (24 publications). MONSANTO and DOW AGRISCIENCES have invested in nucleic acid based technology such as iRNA and antisense to a greater extent than PIONEER. The genetic engineering of plants is a focus for all three of the leading assignees identified.

The analysis does not account for earlier publications prior to 2014, which may have contributed to companies developing market share, etc. and potential licensing and acquisitions (subsidiaries). Data cleaning was carried out to clean names and consolidate. The analysis is an informative guide as some specific subtopics have strict content boundaries to enable differentiation, whilst others are broader to capture more generic areas.

Patent family territory analysis

The INAPDOC patent families comprising the identified pest control related EPO patents were analysed to identify the top 30 territories where patents are filed. Analysing the publication countries alone is insufficient as major countries such as France, the UK, Germany, etc. may not publish patents going through the European (EPO) route, especially when pending. To further supplement the available data, a bespoke analysis was conducted standardising the publication countries and including ‘protected countries’ to include patent rights which are pending or granted based on legal status. There are caveats which include:

  • The study methodology is focused on EPO patents and may not capture assignees/applicants that file only in home territories or don’t file in Europe via EPO filings.
  • The protected country data may not be fully up to date, due to INPADOC data availability and where EPO patents are recent filings.

The standardisation procedure ensures a territory is only counted once per family. The territory analysis is visualised in figure 8.13, EPO and WO (PCT) patents have been included for reference purposes. Despite the caveats, the analysis provides useful indicators regarding territories where applicants are filing patents within the pest control field, based on 2014-23 publications for a relatively recent perspective.

In figure 8.13, approx.92% of the patent families identified had at least one US (91.9%) national filing. Other key territories with at least one national filing include Canada (66.5%), China (64.9%) and Brazil (59.9%). Below the 50% threshold, key territories include Australia (49.8%), India (46.3%), Mexico (43%) and Japan (40.6%).

Investigating keyword trends provides a different perspective beyond the pest control subtopic model. The smart summaries used during the topic model stage were data mined for the most contextually important keywords leveraging transformer based embeddings. Identifying keywords and phrases most similar to the document plus manual auditing for relevance to the SynBio project, visualised in figure 8.14. The visualisation indicates how the cumulative publication counts have changed between the publication periods during 2014-18 & 2019-23. The methodology aims to identify contextually relevant and reliable keywords as a source of ground truth, signify important keywords within the corpus and audit the topic model subtrend analysis already carried out.

In figure 8.14, the following key findings are observed and also support the trending areas identified by the subtopic modelling: Genetic engineering is a consistent method for improving plant traits etc. exemplified by the growth of sequence from 403 to 423 publications, and encoding at 264 publications in 2019-23. Whilst transgenic has declined from 213 to 154 publications in 2019-23, resistance grew from 179 to 229 publications and insecticidal grew from 91 to 106 publications during 2019-23. Fungal and microbial keywords both increased at 93 and 81 publications during 2019-23, whilst Bacillus decreased from 93 to 70 publications but the specific Bacillus Thuringiensis species grew to 27 publications in 2019-23.

Subtopic keyword analysis

For a further perspective of contextually important keywords, a statistical procedure was applied selecting six subtopics from the corpus. The analysis contrasts how the usage or frequency of the keywords / phrases differs across the subtopics using a weighted log odds ratio. This aims to identify which differences are meaningful and weight the log odds ratio by a prior outlined in Monroe, Colaresi, and Quinn (2008). The statistical procedure requires the prior is estimated from the data itself rather than an uninformative prior, such as a Dirichlet prior. The procedure is an empirical Bayes approach with results identified in figure 8.15. A further motivation is to audit the subtopics for result relevance and transparency and provide insights into content. As a sidenote the transformer based keyword analysis provides powerful methods to review subtopics and extend the analytical power beyond procedures of evaluating a corpus such as TF-IDF (term frequency-inverse document frequency).

In figure 8.15, the keywords outlined are most characteristic of each subtopic based on the weighted log odds score which is labelled. Another implication of higher log odds scores is the ability to define the keyword identified as more likely to be used within the specific subtopic. This is interesting as some of the log odds scores are not very high, which is not surprising given the overlap encountered between the multiple subtopics identified within the specific topic landscape.

Some key findings observed are:

  • Within the Bacillus subtopic the Bacillus Amyloliquefaciens keyword was identified which is a promising bacteria for plant growth promotion without harmful side effects, an excellent biocontrol agent. The Bacillus species can be used for insecticidal and nematocidal purposes.
  • Methylobacterium was identified within the Biocide (bacteria related) subtopic, the species can promote plant growth, enhance disease resistance, and repel certain insects.
  • The nucleic acids subtopic highlighted the role of RNA interference, impacting gene expression and having an editing effect or influencing promoter activity.

It is difficult to distil and characterise the coverage of the subtopics via restricted keywords and phrases, this is also complicated by the weighting not always being frequency led but reflective of the terminology and context which is more characteristic of one subtopic in relation to others. It is fair to conclude that the subtopic model has successfully captured an extensive set of subtrends which are distinct, overlap exists but the trends are accurate once audited. The keywords are relevant to real word applications and suggest the insights identified are a useful tool to examine the specific topic landscape.