DETAILED ACTION
Notice to Applicant
This action is in reply to the filed on 6/11/2026.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claims 1, 8. 12 and 16-19 have been amended.
Claims 2-4, 6, 14-15 and 20 have been cancelled.
Claim 1, 5, 7-13 and 16-19 currently pending and have been examined.
Response to Amendments
The Applicant’s amendments, and cancellation, of the claims as currently submitted have been noted by the Examiner. Said amendments, and cancellation(s), are not sufficient to overcome the rejection previously set forth under 35 U.S.C. §101. As such, said rejection is herein maintained for reasons set forth below.
Subject Matter Free of Prior Art
Jackson et al. (US 2013/0179091) and Morselli Gysi et al. (US 2022/0165352) teach a medical information processing apparatus. Jackson et al. and Morselli Gysi et al. do not teach “wherein the protein-protein interaction data comprises a protein-protein interaction (PPI) network...,” etc. Therefore, the Applicant has successfully overcome the Examiner’s 35 USC 103 rejection and Examiner withdraws his 35 USC 103 rejection.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Human Interactions Organized
Applicant discloses (Applicant’s Specification, [0002]-[0005]) that there is a need to explore polypharmacy in a way that considers the interactions among intermediate molecules. So a need exists to organize these human interactions by/through processing protein interaction data using the steps of “storing data, receiving data, performing random walks, filtering proteins, calculating scores, displaying graphs, determining influences, analyzing influences, displaying nodes,” etc. Applicant’s method/apparatus is therefore a certain method of organizing the human activities as described and disclosed by Applicant.
Rejection
Claim(s) 1, 5, 7-13 and 16-19 is/are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Claim(s) 1 is/are directed to the abstract idea of “processing protein interaction data,” etc. (Applicant’s Specification, Abstract, paragraph(s) [0001]), etc., as explained in detail below, and thus grouped as a certain method of organizing human interactions. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the additional computer elements, which are recited at a high level of generality, provide conventional computer functions that do not add meaningful limits to practicing the abstract idea. Accordingly, claims 1, 5, 7-13 and 16-19 recite an abstract idea.
Step 2A Prong 1 – The Judicial Exception
The claim(s) recite(s) in part, method/apparatus for performing the steps of “storing data, receiving data, performing random walks, filtering proteins, calculating scores, displaying graphs, determining influences, analyzing influences, displaying nodes,” etc., that is “processing protein interaction data,” etc. which is a method of managing personal behavior or relationships or interactions between people (social activities, teaching, following rules, instructions) and thus grouped as a certain method of organizing human interactions. Accordingly, claims 1, 5, 7-13 and 16-19 recite an abstract idea.
Step 2A Prong 2 – Integration of the Judicial Exception into a Practical Application
This judicial exception is not integrated into a practical application because the generically recited additional computer elements (i.e. processing circuitry, computing apparatus, memory, display screen, input device, graph circuitry, randomwalk circuitry, filger circuitry, interaction score circuitry, analysis circuitry, display circuitry (Applicant’s Specification [0019]-[0025]), etc.) to perform steps of “storing data, receiving data, performing random walks, filtering proteins, calculating scores, displaying graphs, determining influences, analyzing influences, displaying nodes,” etc. do not add a meaningful limitation to the abstract idea because they amount to simply implementing the abstract idea on a computer and this is nothing more than an attempt to generally link the product of nature to a particular technological environment. Accordingly, this additional element does not integrate the abstract idea into a practical application because it does not impose any meaningful limit on practicing the abstract idea. Accordingly, the claims are directed to an abstract idea.
Insignificant extra-solution activity
Claims 1, 5, 7-13 and 16-19 recites storing data steps, retrieving data steps, providing data steps, output steps (Bilski v. Kappos, 561 U.S. 593, 610-12 (2010), Bancorp Servs., L.L.C. v. Sun Life Assur. Co. of Can., 771 F.Supp.2d 1054, 1066 (E.D. Mo. 2011), aff’d, 687 F.3d at 1266), and/or transmitting data step (buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355 (Fed. Cir. 2014), Apple, Inc. v. Ameranth, Inc., 842 F.3d 1299, 1241-42 (Fed. Cir. 2016)) that is/are insignificant extra-solution activity. Extra-solution activity limitations are insufficient to transform judicially excepted subject matter into a patent-eligible application (MPEP §2106.05(g)).
Step 2B – Search for an Inventive Concept/Significantly More
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because as discussed above with respect to integration into a practical application, the additional elements (i.e. processing circuitry, computing apparatus, memory, display screen, input device, graph circuitry, randomwalk circuitry, filger circuitry, interaction score circuitry, analysis circuitry, display circuitry, etc.) are recited at a high level of generality, and the written description indicates that these elements are generic computer components. Using generic computer components to perform abstract ideas does not provide a necessary inventive concept (Alice, 573 U.S. at 223 (“mere recitation of a generic computer cannot transform a patent-ineligible abstract idea into a patent-eligible invention.”)). Accordingly, the claims are not patent eligible.
Individually and in Combination
The additional elements when considered both individually and as an ordered combination do not amount to significantly more than the abstract idea. The additional elements amount to no more than generic computer components that serve to merely link the abstract idea to a particular technological environment (i.e. processing circuitry, computing apparatus, memory, display screen, input device, graph circuitry, randomwalk circuitry, filger circuitry, interaction score circuitry, analysis circuitry, display circuitry, etc.). At paragraph(s) [0019]-[0025], Applicant’s specification describes generic computer hardware for implementing the above described functions including “processing circuitry, computing apparatus, memory, display screen, input device, graph circuitry, randomwalk circuitry, filger circuitry, interaction score circuitry, analysis circuitry, display circuitry,” etc. to perform the functions of “storing data, receiving data, performing random walks, filtering proteins, calculating scores, displaying graphs, determining influences, analyzing influences, displaying nodes,” etc. The recited “processing circuitry, computing apparatus, memory, display screen, input device, graph circuitry, randomwalk circuitry, filger circuitry, interaction score circuitry, analysis circuitry, display circuitry,” etc. does/do not add meaningful limitations to the idea of beyond generally linking the system to a particular technological environment, that is, implementation via computers. Thus, taken alone, the additional elements do not amount to significantly more than the above-identified judicial exception (the abstract idea). Looking at the limitations as an ordered combination adds nothing that is not already present when looking at the elements taken individually. There is no indication that the combination of elements improves the functioning of a computer, or improves any other technology, or improves a technical field, or provides a technical improvement to a technical problem. Their collective functions merely provide generic computer implementation. Therefore, claims 1, 5, 7-13 and 16-19 do not amount to significantly more than the underlying abstract idea of “an idea of itself” (Alice).
Dependent Claims
Dependent claim(s) 5, 7-13 and 16-19 include(s) all the limitations of the parent claims and are directed to the same abstract idea as discussed above and incorporated herein.
Although dependent claims 5, 7-13 and 16-19 add additional limitations, they only serve to further limit the abstract idea by reciting limitations on what the information is and how it is received and used. Dependent claims 5, 7-13 and 16-19 merely describe physical structures to implement the abstract idea. These information and physical characteristics do not change the fundamental analogy to the abstract idea grouping of certain method of organizing human interactions, and when viewed individually or as a whole, they do not add anything substantial beyond the abstract idea. Furthermore, the combination of elements does not indicate a significant improvement to the functioning of a computer or any other technology. Therefore, the claims when taken as a whole are ineligible for the same reasons as independent claim 1.
Response to Arguments
Applicant’s arguments filed 6/11/2026 with respect to claims 1, 5, 7-13 and 16-19 have been fully considered but they are not persuasive. Applicant’s arguments will be addressed herein below in the order in which they appear in the response filed 6/11/2026.
Applicant’s arguments filed on 6/11/2026 with respect to claims 1, 5, 7-13 and 16-19 have been fully considered but are moot in view of the new ground(s) of rejection.
Applicant argues that (A) the Applicant’s claimed invention is directed to statutory matter.
101 Responses
As per Applicant’s argument (A), Applicant’s remarks with regard to the statutory nature of Applicant’s claimed invention are addressed above in the Office Action.
Rehash
Applicant's remarks and arguments merely rehash issues addressed in the Office Action mailed 3/11/2026 and incorporated herein.
Applicant’s Amendments
Applicant amended claims recite “the filtering circuitry is further configured to normalize the count values based on a number of random walks for the first drug and the second drug, respectively, and filter the proteins based on the normalized count values using a first threshold that is determined according to a function of a degree of a starting node corresponding to a first protein associated with the first drug and a second threshold that is determined according to a function of a degree of a starting node corresponding to a second protein associated with the second drug, the interaction score circuitry is further configured to calculate an interaction score for each protein that remains in the filtered count values based on an average of the normalized count values obtained for the first drug and the second drug,” “based on the normalized count values,” “display a subgraph of the PPI network, the subgraph comprising the first set of proteins and the second set of proteins, visually indicate whether each of the nodes displayed belongs to the first set of proteins, the second set of proteins, or both the first set and the second set of proteins, and visually indicate the interaction scores by a color scale.” These are information processing steps that are part of Applicant’s abstract idea and do not move Applicant’s invention into eligible subject matter. Applicant’s argument is not persuasive.
Data Processing Step
Applicant’s amended steps of “display a subgraph of the PPI network, the subgraph comprising the first set of proteins and the second set of proteins, visually indicate whether each of the nodes displayed belongs to the first set of proteins, the second set of proteins, or both the first set and the second set of proteins, and visually indicate the interaction scores by a color scale,” are abstract compurational steps that are part of Applicant’s abstract idea. In Electric Power Group the collection, manipulation and display of data has been found to be an abstract process. When claims, such as Applicant’s claims, are “directed to an abstract idea” and “merely requir[e] generic computer implementation,” they “do[] not move into [§] 101 eligibility territory.” buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1354 (Fed. Cir. 2014). Further, analysis of information by steps people go through in their minds, or by mathematical algorithms, without more, is essentially a mental processes within the abstract-idea category (Electric Power Group, 830 F.3d at 1354). Further, Applicant appears to be claiming generic computer implementation of a certain method of organsing human interaction. Therefore, Applicant’s argument is not persuasive.
Applicant’s Graph Based on a Graph Data Structure
The Examiner is not alleging that Applicant’s “graph based on a graph data structure and the manipulation thereof, and the performance of random walks on the graph...” can practically be performed in the human mind.
Applicant’s Circuitry
Despite recitation of graph circuitry, randomwalk circuitry, filtering circuitry, interaction score circuitry, analysis circuitry, display circuitry, Applicant’s claims are, at bottom, directed to the collection, organization, grouping and storage of data. The graph circuitry, randomwalk circuitry, filtering circuitry, interaction score circuitry, analysis circuitry, display circuitry recited in Applicant’s claims are merely tools used for organizing human activity. Applicant’s claims elements either individually or as an ordered combination do not transform Applicant’s claims into a patent eligible application of the abstract idea. Applicant’s claims do not impose any meaningful limit on the method of collection, organization, grouping and storage of data. Rather the graph circuitry, randomwalk circuitry, filtering circuitry, interaction score circuitry, analysis circuitry, display circuitry elements recite generic technology for implementing the claimed abstract idea.
Integration into a Practical Application
Integration into a practical application requires additional elements or a combination of additional elements in the claims to apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception, such that it is more than a drafting effort designed to monopolize the exception (e.g. Enfish, McRO and Vanda) (2019 PEG).
Applicant’s “processing circuitry, computing apparatus, memory, display screen, input device, graph circuitry, randomwalk circuitry, filger circuitry, interaction score circuitry, analysis circuitry, display circuitry” is/are not an additional element(s) that reflects in the an improvement in the functioning of a computer, is/are not an additional element(s) that applies or uses the judicial exception to effect a particular treatment or prophylaxis, is/are not an additional element(s) that effects a transformation or reduction of a particular article to a different state or things, and is/are not an additional element(s) that applies or uses the judicial exception beyond generally linking the use of the judicial exception to a particular technological environment for the reasons explained in the 101 rejection above. Applicant’s “processing circuitry, computing apparatus, memory, display screen, input device, graph circuitry, randomwalk circuitry, filger circuitry, interaction score circuitry, analysis circuitry, display circuitry” is/are merely tools used by Applicant to implement data processing. Data processing is an abstract idea. Applicant’s argument is not persuasive.
Improvements – Advantageous over previous methods
The test for patent-eligible subject matter is not whether the claims are advantageous over previous methods (e.g. allowing for searches for a local neighborhood among the network structure, making it possible to compare the frequencies of distance between drugs, allowing the difference in network density to be taken into account, reducing the bias caused by a node of high or low degree, higher efficiency, improved filtering, computational savings, allowing a quantitative evaluation of proteins, effective visualization, improvement over a naive method of exploring graphs, improvement over existing biological network technology). Even if Applicant’s claims provide advantages over previous methos, Applicant’s claims no technological improvement beyond improvement beyond the use of generic computer components/a generic computer network. Applicant’s argument is not persuasive.
Improved – Technology
The Examiner respectfully disagrees. MPEP 2106.04(d)(1) states “the word ‘improvements’ in the context of this consideration is limited to improvements to the functioning of a computer or any other technology/technical field, whether in Step 2A Prong Two or in Step 2B.” Here, there is no improvement to the computer nor is there an improvement to another technology. Because neither type of improvement is present in the claims, an improvement to technology is not present and there is no practical application.
Applicant Admission
Applicant points to Applicant’s Specification at [0063] which argues that performing random walks on a PPI network “may offer improvement over a naive method” (e.g. increased the processing speed compared to the protein-protein interaction data received from another device, computer savings, increasing in the processing speed and a reduction of the processing load). This assertation is in the potential and is not a concrete fact. Therefore performing random walks on at PIT network may or may not offer improvement over a naïve method. Further, “performing random walks on a PPI network” without more is an abstract idea, and an (arguably) improved abstract idea is still an abstract idea. Applicant’s argument is not persuasive.
August 4, 2025 Memorandum
The Examiner thanks the Applicant remarks regarding the advisory August 4, 2025 Memorandum. The Examiner notes that the August 4, 2025 Memorandum contained advisory remarks but the remarks did not change the nature of examination of Applications under 35 USC 101. The Examiner asserts that the Examiner’s analysis and rejection of the Applicant’s claims under 35 USC 101 is compliant with the Office’s examination procedures under the MPEP. Applicant’s argument is not persuasive.
Ex Parte Desjardin
The Office has updated MPEP §2100 to incorporate the nonprecedential Desjardins decision and directed patent examiners to consider Enfish when evaluating claims directed to improvements to the functioning of a computer or other technology or technical field. The subject matter of the decision itself was directed to an innovation in Artificial Intelligence (AI), which is not the claimed subject matter of Applicant’s claimed invention. The Examiner maintains that the Examiner’s rejection of Applicant’s claims under 35 USC 101 is proper and consistent with Office patent examination procedures. Accordingly, Applicant’s argument is not persuasive.
Conclusion
Applicant’s amendment necessitated the new ground(s) for rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set for in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any extension free pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the date of this final action.
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/C. P. C./
Examiner, Art Unit 3683
/ROBERT W MORGAN/Supervisory Patent Examiner, Art Unit 3683
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