DETAILED ACTION
This application is being examined under AIA first-to-file provisions.
SUPERSEDING OFFICE ACTION
This final Office action supersedes the 6/1/2026 Office action, which previous action was ambiguous as to whether it was a final Office action.
On 5/29/2026, a voicemail was left for Applicant's representative, Adam K. Richards at (801) 532-1500, indicating that this is a superseding Office action. Applicant may call with any questions.
Status of claims
Canceled:
none
Pending:
1-20
Withdrawn:
16-20
Examined:
1-15
Independent:
1 and 9
Allowable:
none
Rejections applied
Abbreviations
112/b Indefiniteness
PHOSITA
"a Person Having Ordinary Skill In The Art before the effective filing date of the claimed invention"
112/b "Means for"
BRI
Broadest Reasonable Interpretation
112/a Enablement,
Written description
CRM
"Computer-Readable Media" and equivalent language
112 Other
IDS
Information Disclosure Statement
102, 103
JE
Judicial Exception
x
101 JE(s)
112/a
35 USC 112(a) and similarly for 112/b, etc.
101 Other
N:N
page:line
Double Patenting
XXDATE
date format
Priority
As detailed on the 3/31/2021 filing receipt, this application claims priority to as early as 12/7/2020. At this point in examination, all claims have been interpreted as being accorded this priority date.
Withdrawal / revision of objections and/or rejections
In view of the amendment and remarks:
The 112/b and 112/a rejections are withdrawn.
The 102 and 103 rejections are withdrawn at least because close art, for example Kim and Capela as cited in the now withdrawn 102 and 103 rejections, as well as Deursen (as cited on the 6/1/2026 "Notice of References Cited" form 892), as well as other art found in the search histories and on the IDSs, while addressing graph neural networks of molecules and message passing, does not teach the instant and particularly-recited embedded features based on a message and an edge weight, the edge weight based on a relationship of features of nodes. It is not clear that any combinable art of record would have rendered the claims obvious. In this regard, Applicant's 2/25/2026 remarks at pp. 11-13 support withdrawal of the rejection.
Rejections and/or objections not maintained from previous office actions are withdrawn. The following rejections and/or objections are either maintained or newly applied. They constitute the complete set applied to the instant application.
Claim rejections - 101
35 USC 101 reads:
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.
For each rejection below, dependent claims are rejected similarly as not remedying the rejection, unless otherwise noted.
Response to arguments regarding Claim Rejections - 35 USC 101 -- Abstract idea
Applicant states (original emphasis removed, bold emphasis added, applicant remarks: p. 9 and 10):
The subject matter of claims 1 and 9 recite an improved way of identifying portions of molecules that play a more important role during inference than other portions of the molecule. See Specification ⁋⁋[0046], [0061], [0063], [0094], [0100], [0105]. ... As stated in the Specification, "[u]sing... edge weights that are based on features of a sending node and features of a receiving node may improve accuracy of the embedding model when used in connection with performing downstream tasks." Specification ⁋[0046]. The Specification adds that "[t]hese weights may also make the node embedding model 310 more transparent and explainable because the weights may make it possible to see which part of a molecule structure played a more important role during the inference." Id. ⁋[0094].
...
The limitations of currently amended claims 1 and 9, when performed in combination, solve an issue in identifying molecules with similar properties using an "edge weight" that "is based on a relationship of the first features and the second features."
Regarding 101 JE analysis as organized in MPEP 2106, Applicant's argument pertains to a Step 2A, 2nd prong, 1st consideration explanation of improvement over the previous state of the technology field (MPEP 2106.04(d) and (d)(1)). However, the explanation is not yet sufficiently clear to be persuasive at least with regard to what is the particular improvement, what is the relationship of the improvement to a practical application (the purpose of the improvement consideration and explanation being demonstration of practical application), how is the improvement gauged and whether the claim must deliver the asserted improvement for all embodiments within the scope of the claim. It is not clear that PHOSITA would have understood the above issues so as to persuasively support practical application and patent eligibility.
For example, the above remarks assert "improved way of identifying portions of molecules that play a more important role during inference than other portions of the molecule" and "improve accuracy of the embedding model," but it is not clear particularly how the "way" is improved, e.g. regarding accuracy of what aspect or property of the embedding model? And, how is this accuracy gauged? It may not be necessary to provide data, but it should be clear in detail how PHOSITA would assess the asserted improvement, including as examples accuracy of what parameter and how that accuracy could be measured at least in terms of defining what it is particularly.
Also, the remarks and specification use conditional language, e.g. "may improve," and it is not clear that the claims must deliver the improvement for all embodiments within their scope.
Also, the remarks assert "solve an issue." This probably relates more to the above Step 2A, 2nd prong, explanation of improvement than Step 2B in which it is presented. Second, it is insufficiently clear what are the asserted "issue" and solution.
The following additional examiner suggestions are provided regarding explanations of improvement.
Step 2A, 2nd prong, 1st consideration: explanation of improvement over the previous state of the technology field (MPEP 2106.04(d) and (d)(1)) -- An explanation of a technical improvement may help to overcome a 101 rejection, as discussed at Step 2A/2nd Prong, 1st consideration of the 101 analysis in MPEP 2106.04(d) and (d)(1). Such an improvement requires detailed explanation applicable to all embodiments reasonably within the claim scope.
In particular, such an explanation of improvement over the previous state of the technology field may include:
identification of the technology field,
the particular improvement, as particular as possible identification of any asserted improvement(s),
explanation of a clear difference from the technology field (since there can be no improvement without a difference),
explanation that reasonably all embodiments within the claim scope will result in the asserted improvement, and
finally, extension of the explanation as far as possible to include the result of an identified practical application in order to persuasively demonstrate integration of the identified judicial exception(s) (JEs), i.e. nexus between improvement associated with a JE and a practical application.
As further examples, argument may clearly and adequately explain cause and effect leading to improvement or, for example when such cause and effect explanation is not possible, then may include evidence (e.g. experimental data) comparing a claimed result to conventional results.
Also, arguments and evidence may be extrinsic to the original disclosure, including references available after the priority date, as long as it is clear that an argument applies to all embodiments of a properly supported claim.
Applicant is welcome to request an interview to discuss overcoming the 101 rejections.
Applicant states (original emphasis removed, bold emphasis added, applicant remarks: p. 10):
Applicant respectfully submits that the claims, when considered as a whole, recite "significantly more" than any alleged abstract idea under step two of the Alice/Mayo test because they include "specific limitation[s] other than what is well-understood, routine and conventional in the field." MPEP § 2106.05(d).
Arguments as to non-conventionality apply only to additional elements, not to the identified judicial exception(s), and the only additional element identified is "receiving," which is understood to be conventional as discussed in the rejection.
Judicial exceptions (JE) to 101 patentability
Claims 1-15 are rejected under 35 USC 101 because the claimed inventions are not directed to patent eligible subject matter. After consideration of relevant factors with respect to each claim as a whole, each claim is directed to one or more JEs (i.e. an abstract idea, a natural phenomenon, a law of nature and/or a product of nature), as identified below. Any elements or combination of elements beyond the JE(s) (i.e. "additional elements") are conventional and do not constitute significantly more than the JE(s). Thus, no claim includes additional elements amounting to significantly more than the JE(s), as explained below.
In Alice, citing Mayo and Bilski, two Mayo/Alice questions determine eligibility under 101: First, is a claim directed to a JE? And second, if so, does the claim recite significantly more than the JE?
MPEP 2106 organizes JE analysis into Steps 1, 2A (1st & 2nd prongs) and 2B as follows below.
MPEP 2106 and the following USPTO website provide further explanation and case law citations: www.uspto.gov/patent/laws-and-regulations/examination-policy/examination-guidance-and-training-materials.
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter? -- MPEP 2106.I and 2106.03
[Step 1: claims 1-15: YES]
Step 2A, 1st prong: Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea? -- abstract idea -- MPEP 2106.I and 2106.04
Preliminarily, in a 1st prong of Step 2A, elements of independent claim 1 are interpreted as directed to the abstract idea of calculating embedded features including the JE elements of "determining... embedded features...," each of which, including all recitation within each listed element, in at least some embodiments within a BRI, involves only manipulation of data. While manipulation of data is not per se directed to an abstract idea, in this instance the above-identified elements are directed to the abstract ideas identified below.
Preliminarily, in a 1st prong of Step 2A, elements of independent claim 9 are interpreted as directed to the abstract idea of calculating graph features including the JE elements of "determining... embedded features..." and "determining graph features...," each of which, including all recitation within each listed element, in at least some embodiments within a BRI, involves only manipulation of data. While manipulation of data is not per se directed to an abstract idea, in this instance the above-identified elements are directed to the abstract ideas identified below.
BRIs of the claims are analogous to an abstract idea in the form of at least a mental process, at least equivalent to a computer-implemented process, including obtaining and comparing intangible data (e.g. Cybersource, Synopsys and Electric Power Group). In a BRI, it is not clear that the claim embodiments are limited so as to require complexity precluding analogy to a mental process.
BRIs of the claims also are analogous to an abstract idea in the form of a mathematical concept, including mathematical relationships and calculations, as found in the following case law, as cited and discussed above: collecting information, analyzing it, and displaying certain results of the collection and analysis (Electric Power Group) and/or obtaining and comparing intangible data (e.g. Cybersource, Ambry and Myriad CAFC) and/or execution of an algorithm to implement mathematical relationships and/or formulas, including image processing (e.g. TLI, Digitech, Benson, Flook, Diehr, FuzzySharp, In re Grams and In re Abele all as cited in MPEP 2106).
Instant examples of math concepts include the recited embedded features as a function of a message and an edge weight, as well as the recited graph features as a function of embedded features, as well as relationships inherent in recitations as the only supported embodiments.
The preceding case law examples are cited for the basic form of their identified abstract ideas, and analogy to these example abstract ideas need not be within the same technology field, 101 analysis generally being assumed to be neutral with respect to technology field.
Regarding inherency of abstract ideas, MPEP 2106.04.II.A.1 includes: "the claims in Alice Corp. v. CLS Bank, 'described' the concept of intermediated settlement without ever explicitly using the words 'intermediated' or 'settlement'" (emphasis added, p. 1). Similarly, inherency can effectively be recitation, as in, for example, "By claiming simply 'crystalline paroxetine hydrochloride hemihydrate' with no reference to how it was produced, SKB effectively claimed 'crystalline paroxetine hydrochloride hemihydrate whether non-naturally occurring or arising through natural conversion.' Claim 1, as issued, therefore combines patentable and unpatentable subject matter, and is invalid under Section 101." (capitalization added, SmithKline Beecham Corp. v. Apotex Corp., 365 F.3d 1306, 1321-33, Fed. Cir. 2004).
In the instant type of data processing claims, the specification is not merely adding background explanation as to how a claimed process works, e.g. a physical process based on, involving or further explained by abstract ideas and natural laws. Rather, the specification is detailing the only disclosed way that a programmer may proceed from the recited inputs to the recited outputs, e.g. through actual performance of the disclosed judicial exceptions (JEs).
Regarding the "Meaning of 'Recites,'" MPEP 2106.04.II.A.1 states:
In Prong One examiners evaluate whether the claim recites a judicial exception, i.e. whether a law of nature, natural phenomenon, or abstract idea is set forth or described in the claim. While the terms "set forth" and "described" are thus both equated with "recite", their different language is intended to indicate that there are two ways in which an exception can be recited in a claim. For instance, the claims in Diehr, 450 U.S. at 178 n. 2, 179 n.5, 191-92, 209 USPQ at 4-5 (1981), clearly stated a mathematical equation in the repetitively calculating step, and the claims in Mayo, 566 U.S. 66, 75-77, 101 USPQ2d 1961, 1967-68 (2012), clearly stated laws of nature in the wherein clause, such that the claims "set forth" an identifiable judicial exception. Alternatively, the claims in Alice Corp., 573 U.S. at 218, 110 USPQ2d at 1982, described the concept of intermediated settlement without ever explicitly using the words "intermediated" or "settlement."
While the "set forth" language approximates explicit recitation, it also is fundamental that all recitation must be interpreted and that to be patent eligible a claim must satisfy 101 according to its properly interpreted scope, e.g. for all embodiments on which the claim reads, e.g. according to any inherency pertinent to a given claim and disclosure accompanying that claim, i.e. consistent with the "described" meaning of "recites" as in the MPEP. Thus, within a BRI, the identified abstract idea elements read on one or more embodiments which only involve manipulation of data. It is not clear than any improvement argument clearly on the record causes a claim not to be directed to a JE for all embodiments within the scope of the claim.
As in Alice (at 306, as cited in the MPEP above) and Bilski (as cited in Alice, id), an abstract idea may comprise multiple abstract elements or steps (i.e. from Alice: "a series of steps" at 306) and need not be a single equation, relationship or principle.
It is not clear that the identified elements must represent other than an abstract idea according to any relevant analysis or case law.
[Step 2A, 1st prong, abstract idea: claims 1 and 9: YES]
Step 2A, 2nd prong: If the claims recite a judicial exception under the 1st prong, then is the judicial exception integrated into a practical application? -- MPEP 2106.I and 2106.04(d)
MPEP 2106.04(d).I lists the following example considerations for evaluating whether a judicial exception is integrated into a practical application:
An improvement in the functioning of a computer or an improvement to other technology or another technical field, as discussed in MPEP §§ 2106.04(d)(1) and 2106.05(a);
Applying or using a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition, as discussed in MPEP § 2106.04(d)(2);
Implementing a judicial exception with, or using a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim, as discussed in MPEP § 2106.05(b);
Effecting a transformation or reduction of a particular article to a different state or thing, as discussed in MPEP § 2106.05(c); and
Applying or using the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception, as discussed in MPEP § 2106.05(e).
In Step 2A, 1st prong above, claim steps and/or elements were identified as part of one or more judicial exceptions (JEs).
In Step 2B below, any remaining steps and/or elements are therefore in addition to the identified JE(s). Any such additional steps and additional elements are further discussed in Step 2B.
Here in Step 2A, 2nd prong, no additional step or element clearly demonstrates integration of the JE(s) into a practical application.
At this point in examination it is not yet the case that any of the Step 2A, 2nd prong considerations enumerated above clearly demonstrates integration of the identified JE(s) into a practical application. Referring to the considerations above, none of 1. an improvement, 2. treatment, 3. a particular machine or 4. a transformation is clear in the record.
For example, regarding the first consideration at MPEP 2106.04(d)(1), the record, including for example the specification, does not yet clearly disclose an explanation of improvement over the previous state of the technology field. The claims do not yet clearly result in such an improvement (e.g. specification: [2]).
[Step 2A, 2nd prong: claims 1 and 9: NO]
Step 2B: Do the claims recite a non-conventional arrangement of additional elements in addition to the identified JEs? -- MPEP 2106.I and 2106.05
Addressing the second Mayo/Alice question, all elements of claims 1 and 9 are part of one or more identified JEs (as described above), except for elements identified here as conventional elements in addition to the above judicial exceptions:
The recited "receiving..." are conventional elements of a laboratory and/or computing environment and/or conventional data gathering, as exemplified in MPEP 2106.05(d).II and 2106.05(f-g).
Data gathering does not impose any meaningful limitation on the judicial exceptions or on how the judicial exceptions are performed. Data gathering are not sufficient to integrate judicial exceptions into a practical application (MPEP 2106.05(g)).
It is emphasized that, outside of an improvement argument, analysis of what is conventional generally pertains to the above-identified additional elements and not to elements identified as part of a JE.
[Step 2B: claims 1 and 9: NO]
Summary and conclusion regarding claims 1 and 9
Summing up the above analysis of claims 1 and 9, each viewed as a whole and considering all elements individually and in combination, no claim recites limitations that transform the claim, finally interpreted as directed to the identified JE(s), into patent eligible subject matter, and it is not clear that any claim is sufficiently analogous to controlling case law identifying an example of an eligible claim.
Remaining claims
Claims 2-8 and 10-15 add elements which also are part of the identified JEs for the same reasons described above regarding the independent claims and therefore do not provide the something significantly more necessary to satisfy 101.
None of the dependent claim elements provides the something significantly more than the identified JE(s) necessary to satisfy 101.
Citations to art
In the above citations to documents in the art, rejections refer to the portions of each document cited as example portions as well as to the entirety of each document, unless otherwise noted in the situation of lengthy, multi-subject documents. Other passages not specifically cited within a document may apply as well.
Conclusion
No claim is allowed.
Applicant's amendments necessitated the new grounds for rejection in this action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth 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 fee 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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The examiner for this Office action, G. Steven Vanni, may be contacted at:
(571) 272-3855 Tu-F 8-7 (ET).
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Larry D. Riggs, II, may be reached at (571) 270-3062.
/G. STEVEN VANNI/Primary patents examiner, Art Unit 1686
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