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Artificially Intelligent Therapy
Part 3: Review of prosecution history of AI or ML implemented therapeutic or diagnostic inventions at the Australian patent office

Published
14 August 2025
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Authors
Nicholas Lakatos

Nicholas Lakatos

Principal, Sydney | BEng (Telecom)(Hons), BCom, MIP Law
Julie Murison

Julie Murison

Associate, Melbourne | BS (Hons), PhD, MIP Law
Thomas Ware

Thomas Ware

Associate, Melbourne | BSc, MSc, PhD, MIP Law
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In part 1 of this article series, we provided recommendations that applicants may take to best position their applications to meet patentable subject matter requirements in Australia, particularly in respect of life-sciences inventions with a computer implemented aspect. Then in part 2, we discussed recent patent office decisions concerns computer implemented methods in the life sciences space to shed light on the approach currently taken by the Australian patent office.

Here in part 3, by reviewing publicly available prosecution histories we were able to confirm our theory that the Australia patent office is approaching these type of inventions with the sample principles they use for computer implemented inventions.

To investigate the approach of Australian patent examiners when examining applications in the AI/ML – therapy space we searched for patents and patent applications where the claims included the key words “artificial intelligence” or “machine learning” and the abstract included one of the keywords “therapy”, “therapeutic”, “diagnostic” or “diagnosis”.

While this is not an exhaustive search, 268 patents and applications were identified. The breakdown of application status is shown in the table below.

Status Number of patents/applications
Granted 38
Accepted 7
Converted 1 (not certified)
Filed 129
Lapsed 54
Ceased 38
Withdrawn 1

Application status of patents/applications identified through keyword searching

Lapsed applications

Of the 54 lapsed patent applications, we identified 13 applications that failed to gain acceptance where at least one response was filed to an examination report (suggestive that these cases were not abandoned). A brief summary of these applications is shown in the table below.

Application number Examination Division Type of outstanding objection
2012329088 Elec 4 Support and Enablement
2023204091 Elec 4 Patentable subject matter
2017229488 Chem 1 Patentable subject matter
2018219846 Elec 3 Novelty/IS
2018322189 Elec 4 Patentable subject matter
2018367925 Chem 1 Patentable subject matter
2020203660 Elec 3 Novelty/IS
2020244858 Mech 4 Novelty/IS
2019202082 Elec 4 Patentable subject matter
2011270731 Phys Novelty/IS
2017257785 Chem 1 Patentable subject matter
2017204178 Elec 4 Patentable subject matter
2016288666 Chem 1 Patentable subject matter

A further 8 applications were identified which had examination reports issuing patentable subject matter objections from either the Chem1, Elec3 or Elec4 examination divisions and no response to the examination report was filed.  In the subset of applications we looked at, both chemistry (Chem 1) and Electronics (Elec 3 and Elec 4) examining divisions raised patentable subject matter objections.

Overcoming Patentable Subject Matter objections

Next, we look at accepted applications or granted patents where patentable subject matter objections were raised during prosecution with respect to the AI/ML aspect of the claims which were ultimately overcome.

Spread of examination divisions

A summary of the 45 identified accepted applications and granted patents per examination division is shown in the table below.  Applications were fairly evenly distributed amongst Chem/Mech/Elec examination divisions.

Examining Division Accepted applications + Granted patents
Chem 1 8
Chem 4 2
Elec 2 2
Elec 3 8
Elec 4 8
Mech 4 16
Unknown (Innovation patent, certification not requested) 1
Total 45

In the set of identified applications, 5 patents/applications had patentable subject matter objections raised during examination on the basis that the claim referred to either a “mere scheme” or a “generic utilisation of well-known functions of a computer”.

These objections were addressed by:

  • In 1 case (2016273897), claims were amended to be methods of treating a patient, wherein the method involved a computer system and an additional step of administering a drug to the patient.
  • In 1 case (2017341084) dependent claims were amended to be method of treatment performed by a computer apparatus.
  • In 1 case the claims were amended to include further details about the AI implementation by limiting to a convolutional neural network (2021387426), adding further technical detail to the claim and requiring the method to produce a tangible result, ie a diagnosis.
  • In 1 case, the patent was converted to an innovation patent (certification was not requested) (2018102201)
  • In 1 case (2019253118), dependent claims relating computer systems for carrying out a method were deleted

While the data set is too small to draw conclusions on trends, the prosecution of these applications do illustrate potential for patentable subject matter objections in AI/ML assisted therapeutic and/or diagnostic applications and possible resolutions to the objections, noting that conversion to an innovation patent is only an option when the complete specification was filed before 25 August 2021.

For the claims that were amended, the originally filed claim, and the accepted amended claims are shown in the tables below.

Application number Original Claim Accepted Claim
2016273897

A method of determining a marker for treating a disease using a drug based on omics data of distinct diseased cell lines, comprising:

  • informationally coupling a pathway model database to a machine learning system,
  • wherein the pathway model database stores a plurality of distinct data sets derived from omics data of a plurality of distinct diseased cell lines, respectively and wherein each data set comprises a plurality of pathway element data;
  • receiving, by the machine learning system sensitivity data associated with the plurality of distinct diseased cell lines, wherein the sensitivity data indicates a sensitivity level of each of the plurality of distinct diseased cell lines reacting to the drug;
  • inferring by the machine learning system having a correlation with the sensitivity data with respect to the plurality of distinct diseased cell lines by traversing the plurality of pathway element data corresponding to the plurality of distinct diseased cell lines in the pathway model database;
  • and determining the machine meaning system, a threshold expression level exhibited by a patient for recommending the drug to treat the disease based on the correlation.

A computer-assisted method of treating a patient having a tumor comprising:

  • determining, from omics data of plurality of diseased cell lines, a plurality of expression magnitudes of a respective plurality of pathway elements, wherein each expression magnitude is a protein expression level of the pathway element and the omics data comprises genomics data and transcriptomics data, wherein each diseased cell line is associated with a quantitative responsiveness metric with respect to the action of the drug;
  • identifying one set of correlation data among a plurality sets of correlation data among a plurality sets of correlation data based on a quality of correlation, wherein each set of a correlation data corresponds to a plurality of correlations, each correlation between respective expression magnitude of one of the plurality of pathway elements and respective quantitative responsiveness metric of respective diseased cell line;
  • identifying a threshold expression magnitude of one of the plurality of pathway elements that qualitatively separates the plurality of correlations of the identified set of correlation data into a first set and a second set;
  • and treating the patient by administering the drug to the patient upon determining the expression magnitude is higher than the threshold magnitude.
2017341084

A computer apparatus configured to perform a method according to any one of claims 1 to 72.

A computer readable medium programmed to perform a method according to any one of claims 1 to 72.

The method according to any one of claims 1 to 6, wherein the method is performed by a computer apparatus.

The method according to any one of claims 1 to 6, wherein the method is stored as a computer readable medium programmed to perform said method.

2021387426

A method of providing information to diagnose cancer and predict a type of cancer based on artificial intelligence, the method comprising:

  • extracting nucleic acids from a biological sample to obtain sequence information;
  • aligning the sequence information (reads) with a reference genome database;
  • generating vectorized data using nucleic acid fragments based on the aligned sequence information (reads);
  • inputting the generated vectorized data to a trained artificial intelligence model, analysing the resulting output value, and comparing the resulting output value with a cut-off value to determine whether there is cancer; and
  • predicting the type of cancer through comparison of the output value.

A method of generating a cancer diagnosis and predicting a type of cancer based on artificial intelligence, the method comprising:

  • obtaining sequence information indicative of extracted nucleic acids from a biological sample;
  • the sequence information being aligned with a reference genome database, wherein the sequence information comprises at least 5,000 reads;
  • generating, by a computer system, vectorized data using nucleic acid fragments based on the aligned sequence information (reads), wherein the vectorized data is a Grand Canyon plot (GC plot) which is generated by calculating a distribution of aligned nucleic acid fragments in each chromosome bin based on the distance between the nucleic acid fragments;
  • inputting, by the computer system of the generated vectorized data to a trained artificial intelligence model, to generate a resulting output value; and
  • processing by the computer system of the resulting output value to generate a cancer diagnosis of whether there is cancer in the biological sample; and when the cancer diagnosis is that cancer is present in the biological sample, predicting from said resulting output value a type of cancer that is present in the biological sample, wherein the artificial intelligence model of step (d) is a convolutional neural network (CNN) and trained to distinguish between vectorized data of normal chromosomes and vectorized data of abnormal chromosomes.

“mere scheme”

In one case, application 2018102201, directed to a method of diagnosing cancer, the examiner took the view that neither the method of diagnosis or the computer implementation of the diagnosis could confer patentability. The examination report refers to the method of diagnosis as being a series of computer implemented procedural steps to evaluate the effectiveness of a therapy, and a lack of detail in the specification of how the method leads to an improvement in the elevated therapy.

Examining Division

The identified applications were allocated to several different examining divisions, Elec 2 (Electronics and Communications), Elec 3 (Computing) or Elec 4 (Data processing and measurements), Mech 4 (Medical Devices), Chem 1 (Biotechnology) or Chem 4 (Pharmaceuticals).

Depending on the nature of the invention, it can be advantageous to direct the application to the most appropriate examining division. In our experience examiners from a non-life science division sometimes fail to understand the nuances of biological systems, and may overly focus on the computer-implements aspects of the invention. On the other hand, examiners unfamiliar with computer implemented inventions may raise incorrect patentable subject matter objections.

Depending on the applicant’s commercially valuable embodiments of the invention, ordering independent claims to direct the application to the preferred examination division may be advantageous. For example, if the applicants preferred embodiments of the invention are the methods of treating patients, putting these claims first may increase the likelihood of the application being allocated to a life sciences examiner. Particularly when the inventiveness of the invention is best assessed by reference to biological information or a therapeutic outcome, it appears to be advantageous to direct examination to a life sciences examiner.

Summary

Our preliminary analysis does appear to confirm that Australian patent examiners will generally assess an invention involving an AI or ML element in the claims using the same principles as a computer implemented invention.

Based on our analysis, the strongest predictor of whether a case is likely to face a patentable subject matter objection despite relating to a method of therapy or diagnosis is if there are no examples in the specification, if the description is overly generic, and if the only new factor is the use of an AI or ML. 

It appears that applications which only have a “generic” description of AI or ML implementation will likely increase the chance of a patentable subject matter objection, whereas including a clear technical relationship between components of the AI/ML and the technical outcome achieved may put the applicant in the best position to overcome a patentable subject matter objection or better yet circumvent it altogether. 

There may also be some benefit in considering preliminary amendments, such as ordering of the claims, adjusting claim language for Australian practice and planning for post-filing data.

Please reach out to the team at FPA Patent Attorneys if you would like detailed advice regarding prosecution strategies for therapeutic or diagnostic methods involving an AI or ML component.

About the Authors

Nicholas Lakatos

Principal, Sydney | BEng (Telecom)(Hons), BCom, MIP Law

Nicholas’ focus: telecommunications, software, information and communications technology and electrical engineering-related inventions.

Learn more about Nicholas
About the Authors

Julie Murison

Associate, Melbourne | BS (Hons), PhD, MIP Law

Julie’s focus: agrochemistry, petrochemistry, materials chemistry and industrial chemistry.

Learn more about Julie
About the Authors

Thomas Ware

Associate, Melbourne | BSc, MSc, PhD, MIP Law

Thomas’ focus: gene therapy, molecular and cancer biology, cancer immunotherapy, gene silencing and RNA interference technology, infectious diseases, viral vectors, and blood serum diagnostics.

Learn more about Thomas
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