DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Status
Claims 1-20 are currently pending and under exam herein.
Priority
The instant Application claims no priority and therefore the Effective Filing Date of the instant application is the filing date of 24 August 2022.
Information Disclosure Statement
No Information Disclosure Statement has been filed.
Drawings
The Drawings filed 24 August 2022 are accepted.
Specification
Note: All references to the Specification herein pertain to the PG publication: US2024/0071578.
Objections to the Specification
The use of the terms Stardog, Amazon Neptune, Neo4j, SMILES, Mutulane, and OxyContin, for example, which are trade names or a marks used in commerce, has been noted in this application. The terms should be accompanied by the generic terminology; furthermore the terms should be capitalized wherever they appear or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the terms.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks. All instances of trade names or marks should be addressed herein.
The disclosure is objected to because of the following informalities: the Specification refers to simplified molecular-input line-entry as (SMILE). However, the appropriate designation is SMILES and “simplified molecular-input line-entry system”.
Appropriate correction is required.
Claim Objections
Claims 1-20 are objected to because of the following informalities: Claims 1-20 recite simplified molecular-input line-entry (SMILE). However, the appropriate designation is SMILES and “simplified molecular-input line-entry system”. Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)-Indefiniteness
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
Claims 1-20 recite, “determining, by the device, whether the new compound tensor matches the target compound tensor”, wherein it is not clear as to the step by which it is “determined’ that there is a “match” of the new compound tensor to the target compound tensor. The criteria necessary for establishing a match, such as compounds that share a common property or a distance similarity score or the like. Clarification through clearer claim language is requested.
Claims 1-20 recite, “returning, by the device, a policy based on the new compound tensor matching the target compound tensor” wherein it is unclear as to the “policy” intended in the claimed steps. The claim is indefinite with respect to what about the “new compound tensor match” informs a policy for the claimed operation, such as a strategy to inform further operation or particular function or probability or other result. As such, the recitation renders the metes and bounds of the claim unclear. Clarification is requested through clearer claim language.
As such, Claims 1-20 are rejected under 112(b) herein.
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.
Claims 1-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
The instant rejection reflects the framework as outlined in the MPEP at 2106.04:
Framework with which to Evaluate Subject Matter Eligibility:
(1) Are the claims directed to a process, machine, manufacture or composition of matter;
(2A) Prong One: Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea;
Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application (Prong Two); and
(2B) If the claims do not integrate the judicial exception, do the claims provide an inventive concept.
Framework Analysis as Pertains to the Instant Claims:
Step 1 Analysis: Are claims directed to process, machine, manufacture/composition of matter
With respect to step (1): yes, the claims are directed to a method, a device, and a non-transitory computer-readable medium.
Step 2A, Prong 1 Analysis: Do claims recite abstract idea
With respect to step (2A)(1), the claims recite abstract ideas. The MPEP at 2106.04(a)(2) further explains that abstract ideas are defined as:
mathematical concepts, (mathematical formulas or equations, mathematical relationships and mathematical calculations);
certain methods of organizing human activity (fundamental economic practices or principles, managing personal behavior or relationships or interactions between people); and/or
mental processes (procedures for observing, evaluating, analyzing/ judging and organizing information).
With respect to the instant claims, under the (2A)(1) evaluation, the claims are found herein to recite abstract ideas that fall into the grouping of mental processes (in particular procedures for observing, analyzing and organizing information) and in conjunction with mathematical concepts (in particular mathematical relationships and formulas).
The claim steps to abstract ideas are as follows:
Claims 1, 8, and 15:
projecting, by the device, the source compound SMILE data and the target compound SMILE data into the latent space to generate a source compound tensor and a target compound tensor, respectively; processing, by the device, the source compound tensor, with one or more pretrained models, to determine a reward for the source compound tensor; determining, by the device and based on the reward, a direction and a magnitude to move in the latent space from the source compound tensor; moving, by the device, the direction and the magnitude in the latent space to a new compound tensor; determining, by the device, whether the new compound tensor matches the target compound tensor; and returning, by the device, a policy based on the new compound tensor matching the target compound tensor, wherein said operations are directed to mathematical operations achieved by machine learning techniques. The machine learning herein is generic and operational on generic computing systems and provide the tool by which to perform the above abstract ideas. Projection into latent space may be achieved SMILES data into real numbers or numeric lists in n-dimensional space, for example (Specification at [0017]); processing using a pretrained model may be achieved using linear regression or classification techniques, for example (Specification at least at [0016]). Determination of magnitude and direction is a further mathematical operation whereby, for example, distance (d) between compound tensors may be divided by a value (k) to calculate movement (Specification at [0021]). Therefore, moving in sapid space is also a mathematical process. Determination o matching is a mental or mathematical process of determining the likeness of compounds in said space, whereby one could merely observe the data and make a determination or use mathematical processes by which to do so, such as assessment of compound properties, for example. Returning a policy is merely a step by which data are then provided which could be also be a list generation or other which is a mental activity. Save for the computer operations herein, there are no steps beyond the Broadest Reasonable Interpretation (BRI) above that would suggest otherwise and therefore the claims herein are directed to abstract ideas.
The dependent claims herein further explicitly recite numerous elements that, individually and in combination, constitute abstract ideas and further limit those as above. Said operations include “identification” (mental operations); “determination” (mental operations); calculating estimates and distances” (mathematical operations); “combining estimates” (mathematical operations); “determining magnitude and distance” (mathematical operations).
The abstract ideas recited in the claims are evaluated under the Broadest Reasonable Interpretation (BRI) and determined herein to each cover performance either in the mind (calculations by hand or pen and paper) and performance by mathematical operation (calculation for assessment of time points as per the recited specific equations in said claims). There are no specifics as to the methodology involved, as indicated above, and thus, under the BRI, one could simply, for example, perform said operation with pen and paper, or, alternatively with the aid of a generic computer as a tool to perform said calculations. These recitations are similar to the concepts of collecting information, analyzing it and providing certain results from the collection and analysis (Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), organizing and manipulating information through mathematical correlations (Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)) and comparing information regarding a sample or test to a control or target data in (Univ. of Utah Research Found. v. Ambry Genetics Corp. (774 F.3d 755, 113 U.S.P.Q.2d 1241 (Fed. Cir. 2014) and Association for Molecular Pathology v. USPTO (689 F.3d 1303, 103 U.S.P.Q.2d 1681 (Fed. Cir. 2012)) that the courts have identified as concepts that can be practically performed in the human mind with pen and paper, and can include mathematical concepts.
Further, see MPEP § 2106.04(a)(2), subsection III. The courts do not distinguish between mental processes that are performed entirely in the human mind and mental processes that require a human to use a physical aid (e.g., pen and paper or a slide rule) to perform the claim limitation (see, e.g., Benson, 409 U.S. at 67, 65, 175 USPQ at 674-75, 674: noting that the claimed "conversion of [binary-coded decimal] numerals to pure binary numerals can be done mentally," i.e., "as a person would do it by head and hand."); Synopsys, Inc. v. Mentor Graphics Corp., 839 F.3d 1138, 1139, 120 USPQ2d 1473, 1474 (Fed. Cir. 2016): holding that claims to a mental process of "translating a functional description of a logic circuit into a hardware component description of the logic circuit" are directed to an abstract idea, because the claims "read on an individual performing the claimed steps mentally or with pencil and paper"). Nor do the courts distinguish between claims that recite mental processes performed by humans and claims that recite mental processes performed on a computer. As the Federal Circuit has explained, "[c]ourts have examined claims that required the use of a computer and still found that the underlying, patent-ineligible invention could be performed via pen and paper or in a person’s mind" (see Versata Dev. Group v. SAP Am., Inc., 793 F.3d 1306, 1335, 115 USPQ2d 1681, 1702 (Fed. Cir. 2015); Mortgage Grader, Inc. v. First Choice Loan Servs. Inc., 811 F.3d 1314, 1324, 117 USPQ2d 1693, 1699 (Fed. Cir. 2016): holding that computer-implemented method for "anonymous loan shopping" was an abstract idea because it could be "performed by humans without a computer").
Step 2A, Prong 2 Analysis: Integration to a Practical Application
Because the claims do recite judicial exceptions, direction under (2A)(2) provides that the claims must be examined further to determine whether they integrate the abstract ideas into a practical application (MPEP 2106.04(d). A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. This is performed by analyzing the additional elements of the claim to determine if the abstract idea is integrated into a practical application (MPEP 2106.04(d).I.; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the abstract idea, the claim is said to fail to integrate the abstract idea into a practical application (MPEP 2106.04(d).III).
With respect to the instant recitations, the claims recite the following additional elements:
Claims 1, 8, and 15:
receiving, by a device, source compound simplified molecular-input line-entry (SMILE) data, target compound SMILE data, and a latent space representing compounds, wherein each of said limiting steps further serves to gather the data for computations in the abstract idea methods.
device, memory, processors, computer-readable media, wherein said components are generic computing elements herein.
Further with respect to the additional elements in the instant claims, those steps directed to data gathering perform functions of collecting the data needed to carry out the abstract idea. Data gathering does not impose any meaningful limitation on the abstract idea, or on how the abstract idea is performed. Data gathering steps are not sufficient to integrate an abstract idea into a practical application. (MPEP 2106.05(g).
Further, the device, processor, memory and instructions are part of a general purpose computer system and there are no details herein wherein of how the specific computer structures are used to implement the judicial exceptions beyond generic computing operations, i.e., the computer elements of the claims do not provide improvements to the functioning of the computer itself (see: DDR Holdings, LLC v. Hotels.com LP); they do not provide improvements to any other technology or technical field (see: Diamond v. Diehr); nor do they utilize a particular machine (see: Eibel Process Co. v. Minn. & Ont. Paper Co.). Hence, these are mere instructions to apply the judicial exception using a computer, and therefore the claim does not provide integration into a practical application of any judicial exception.
Step 2B Analysis: Do Claims Provide an Inventive Concept
The claims are lastly evaluated using the (2B) analysis, wherein it is determined that because the claims recite abstract ideas, and do not integrate that abstract ideas into a practical application, the claims also lack a specific inventive concept. Applicant is reminded that the judicial exception alone cannot provide the inventive concept or the practical application and that the identification of whether the additional elements amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they provide significantly more than the judicial exception. (MPEP 2106.05.A i-vi).
With respect to the instant claims, the additional elements of data gathering described above do not rise to the level of significantly more than the judicial exception. As directed in the Berkheimer memorandum of 19 April 2018 and set forth in the MPEP, determinations of whether or not additional elements (or a combination of additional elements) may provide significantly more and/or an inventive concept rests in whether or not the additional elements (or combination of elements) represents well-understood, routine, conventional activity. Said assessment is made by a factual determination stemming from a conclusion that an element (or combination of elements) is widely prevalent or in common use in the relevant industry, which is determined by either a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
With respect to the instant claims, steps directed to “receiving, by a device, source compound simplified molecular-input line-entry (SMILE) data, target compound SMILE data, and a latent space representing compounds” are those that as disclosed in the prior art to, Galushka et al. (Neural Computing and Applications (2021) 33:13345–13366), for example, encompass steps that are routine, well-understood and conventional in the art. Galushka et al. disclose predictions of chemical compounds using deep learning by which data are received to said system that include SMILES data and latent space representations (pp. 13353, 13355). As such, said “data” types are routine in the assessment of chemical prediction using machine learning. Further the prior art to Wigh et al. (WIREs Comput Mol Sci.2022;12:e1603:19 pages) discloses SMILES representations in latent space as disclosed at least at pp. 9-11.
With respect to the claims to the system and processor, memory and instruction, the computer-related elements or the general purpose computer do not rise to the level of significantly more than the judicial exception. The specification also discloses that computer processors and systems, as example, are generic computing systems [0047; 0063]. The additional elements are set forth at such a high level of generality that they can be met by a general purpose computer. Therefore, the computer components constitute no more than a general link to a technological environment, which is insufficient to constitute an inventive concept that would render the claims significantly more than an abstract idea (see MPEP 2106.05(b)I-III).
The dependent claims have been analyzed with respect to step 2B and none of these claims provide a specific inventive concept, as they all fail to rise to the level of significantly more than the identified judicial exception.
For these reasons, the claims, when the limitations are considered individually and as a whole, are rejected under 35 USC § 101 as being directed to non-statutory subject matter.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1-20 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Cai et al. (J. Med. Chem. (2020) Vol. 63(16): 8683–8694) and as evidenced by Zhavoronkov et al. (Nature Biotechnology (2019) Vol. 37, September 2019:1038–1040).
It is noted that the following limitations in claim 1 have been designed as (a)-(g) by the Examiner for ease of discussion. It is acknowledged that said lettering does not exist in the claims as filed.
Instant claim 1 is directed to:
A method, comprising:
(a) receiving, by a device, source compound simplified molecular-input line-entry (SMILE) data, target compound SMILE data, and a latent space representing compounds;
(b) projecting, by the device, the source compound SMILE data and the target compound SMILE data into the latent space to generate a source compound tensor and a target compound tensor, respectively;
(c) processing, by the device, the source compound tensor, with one or more pretrained models, to determine a reward for the source compound tensor;
(d) determining, by the device and based on the reward, a direction and a magnitude to move in the latent space from the source compound tensor;
(e) moving, by the device, the direction and the magnitude in the latent space to a new compound tensor;
(f) determining, by the device, whether the new compound tensor matches the target compound tensor; and
(g) returning, by the device, a policy based on the new compound tensor matching the target compound tensor.
Cai et al. disclose the application of transfer learning to drug discovery whereby in deep transfer learning, when given two problems (a source problem and a target problem), there are two domains (a source domain and a target domain) and two tasks (a source task and a target task). Further, the domain spaces and tasks can be different and include settings whereby there are three settings: inductive learning (transfer between different molecular properties, e.g.); transductive learning, transfer between different molecular data sets, e.g.,; and unsupervised learning (see Figure 1). With respect to the above claim 1, Cai et al. include the target and source data at Figure 1. Cai et al. further describe that in deep transfer learning applications, learned parameters (weights) associated with connections between neurons in deep neural networks contain useful information learned from the source data and the related target problem can be addressed by migrating those weights to the target model (with respect to steps (steps e-g). This includes using pretrained models as in (step c) [Cai-p.8685]. This includes applications in feature-based transfer learning that use deep learning neural networks as feature transformers to find common latent feature space where the source and the target can be in the same probability distribution (step b) [Cai-p.8686]. This means that the source data can be used as the target data’s training set in latent feature space to improve performance of the model for the target data [Cai-p.8686]. Cai et al. disclose combined RL with transfer learning that incorporates reward feedback (step c and d) [Cai-p.8688]. Cai et al. further disclose use of SMILES datasets in transfer learning approaches at Figure 5, for example (step a).
With respect to claims 8 and 15, said device and computer readable media are inherent in the machine operations as disclosed by Cai et al., disclosing each of the steps as operation thereon and thereby in the above discussed limitations. As such, Cai et al. anticipate claims 1, 8, and 15 herein.
With respect to claim 2, Cai et al. disclose SMILES data prior to projecting the source at Figure 5.
With respect to claim 3, Cai et al. disclose reward generation at p. 8688, col. 2 wherein reward data in an RL algorithm may be combined with fine-tuning in molecule generation techniques.
With respect to claim 4, Cai et al. disclose source and target as multi-dimensional tensors of real numbers [Figures 4 and 5].
With respect to claims 5, 6 and 16, Cai et al. disclose estimates of the source tensor, heuristics of the source tensor, distance between the source and target and reward determination based on such, as well as combinations [p. 8688, col. 2].
With respect to claims 7, 9, 17, and 18 Cai et al. and as evidenced by the reference to Zhavoronkov et al., discloses methods whereby mapping is utilized including distances and direction in multidimensional space (see Zhavoronkov et al. at p. 1042, col. 1). Zhavoronkov et al. further disclose a prioritization pipeline wherein thresholds are assessed and molecules may fail/be rejected [@p. 1042, col. 1].
With respect to claim 10, Cai et al. disclose deep reinforcement learning [p. 8688].
With respect to claim 11, Cai et al. disclose routes between source and target that define properties [p. 8687].
With respect to claims 12 and 19, Cai et al. disclose identification of new compounds [p. 8688].
With respect to claims 13 and 20, Cai et al. disclose new SMILES data at Figure 5.
With respect to claim 14, Cai et al. disclose training with a model that predicts SMILES data [Figure 5].
Conclusion
No claims are allowed.
E-mail Communications Authorization
Per updated USPTO Internet usage policies, Applicant and/or applicant’s representative is encouraged to authorize the USPTO examiner to discuss any subject matter concerning the above application via Internet e-mail communications. See MPEP 502.03. To approve such communications, Applicant must provide written authorization for e-mail communication by submitting following form via EFS-Web or Central Fax (571-273-8300): PTO/SB/439. Applicant is encouraged to do so as early in prosecution as possible, so as to facilitate communication during examination.
Written authorizations submitted to the Examiner via e-mail are NOT proper. Written authorizations must be submitted via EFS-Web or Central Fax (571-273-8300). A paper copy of e-mail correspondence will be placed in the patent application when appropriate. E-mails from the USPTO are for the sole use of the intended recipient, and may contain information subject to the confidentiality requirement set forth in 35 USC § 122. See also MPEP 502.03.
Inquiries
Papers related to this application may be submitted to Technical Center 1600 by facsimile transmission. Papers should be faxed to Technical Center 1600 via the PTO Fax Center. The faxing of such papers must conform to the notices published in the Official Gazette, 1096 OG 30 (November 15, 1988), 1156 OG 61 (November 16, 1993), and 1157 OG 94 (December 28, 1993) (See 37 CFR § 1.6(d)). The Central Fax Center Number is (571) 273-8300.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Lori A. Clow, whose telephone number is (571) 272-0715. The examiner can normally be reached on Monday-Thursday from 12:00PM to 10:00PM ET.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Karlheinz Skowronek can be reached on (571) 272-9047.
Any inquiry of a general nature or relating to the status of this application or proceeding should be directed to (571) 272-0547.
Patent applicants with problems or questions regarding electronic images that can be viewed in the Patent Application Information Retrieval system (PAIR) can now contact the USPTO’s Patent Electronic Business Center (Patent EBC) for assistance. Representatives are available to answer your questions daily from 6 am to midnight (EST). The toll free number is (866) 217-9197. When calling please have your application serial or patent number, the type of document you are having an image problem with, the number of pages and the specific nature of the problem. The Patent Electronic Business Center will notify applicants of the resolution of the problem within 5-7 business days. Applicants can also check PAIR to confirm that the problem has been corrected. The USPTO’s Patent Electronic Business Center is a complete service center supporting all patent business on the Internet. The USPTO’s PAIR system provides Internet-based access to patent application status and history information. It also enables applicants to view the scanned images of their own application file folder(s) as well as general patent information available to the public.
/Lori A. Clow/Primary Examiner, Art Unit 1687
Prosecution Insights