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 .
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
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.
Claim 1 is a method that recite(s) determining, by processing circuitry, a drug-forming property of the drug molecule based on a molecular property prediction network, the drug-forming property of the drug molecule being determined by the molecular property prediction network according to the three-dimensional structure information.
In the context of the claim the step of determining a drug-forming property, given its plain and ordinary meaning, encompasses the use of computational models to predict the properties of molecules. Thus, the limitations are accomplished using mathematical calculations, relationships, formulas or equations and so falls within the Mathematical Concepts grouping of abstract ideas. See MPEP 2106.04(a)(2)I. The claim recites an abstract idea.
This judicial exception is not integrated into a practical application. The claim recites the additional claim elements of processing circuitry, obtaining a text string of a drug molecule, the text string indicating a structural formula of the drug molecule; and obtaining three-dimensional structure information of the drug molecule, the three-dimensional structure information being generated according to the structural formula indicated by the text string. The processing circuitry is recited at a high level of generality and is merely used as a tool to perform the abstract idea. See MPEP 2106.05(f). The limitations of obtaining a text string of a drug molecule and obtaining three-dimensional structure information are recited at a high level of generality such that it merely amounts to necessary data gathering and outputting for performing the abstract idea. Thus, they amount to adding insignificant extra-solution activity. See MPEP 2106.05(g). The claim is directed to an abstract idea.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception. As disclosed above, the processing circuitry amounts to no more than merely using a generic computer as a tool to perform an abstract idea. As such, it cannot provide inventive concept. The steps of obtaining amount to no more than adding insignificant extra-solution activity. Additionally, the claim elements amount to receiving or transmitting data over a network and thus is no more than well-understood, routine, conventional activity. See MPEP 2106.05(d). As such, it cannot provide inventive concept. The claim is not patent eligible.
Claims 2-13 and 19 depend from claim 1 and recites the same abstract idea as claim 1. Claims 2-13 and 19 recite additional claim elements that amount to adding additional necessary data gathering and outputting steps for performing the abstract idea (claims 2-8 and 11) and/or adding additional limitations to the abstract idea (claims 7, 9 and 12-13) and/or a generic computer component merely used as a tool to perform the abstract idea (claim 19).
The additional limitations for obtaining are recited at a high level of generality such that it merely amounts to necessary data gathering and outputting for performing the abstract idea. Thus, they amount to adding insignificant extra-solution activity. See MPEP 2106.05(g). Additionally, the claim elements amount to receiving or transmitting data over a network and thus is no more than well-understood, routine, conventional activity. See MPEP 2106.05(d). As such, it cannot provide inventive concept. The limitations in claims 7, 9 and 12-13 of performing transformation, performing normalization, performing feature concatenation, determining a predicted property, determining M three-dimensional structures, performing energy minimization, determining a three-dimensional structure and removing a hydrogen atom encompasses the use of computations. Thus, the limitations are accomplished using mathematical calculations, relationships, formulas or equations and so falls within the Mathematical Concepts grouping of abstract ideas. See MPEP 2106.04(a)(2)I. The additional claim elements recite an abstract idea. As disclosed above, the non-transitory computer-readable storage medium and compter in claim 19 amounts to no more than merely using a generic computer as a tool to perform an abstract idea. As such, it cannot provide inventive concept. The claims neither recite limitations that integrate the abstract idea into a practical application nor amount to significantly more than the abstract idea. The claims are not patent eligible.
Claim 14 is a method that recite(s) performing feature concatenation on the three-dimensional structure coordinate matrix, the normalized adjacency matrix, the atomic feature, and the chemical bond feature of the sample molecule to obtain a second concatenated matrix; determining a predicted property value corresponding to the sample molecule according to the second concatenated matrix through an initial neural network; and iteratively updating, by processing circuitry, network parameters of the initial neural network in response to the loss value being greater than a second threshold until the loss value is not greater than the second threshold to obtain a molecular property prediction network.
In the context of the claim the steps of performing feature concatenation, determining a predicted property value and iteratively updating, given its plain and ordinary meaning, encompasses the use of computational models to predict the properties of molecules. Thus, the limitations are accomplished using mathematical calculations, relationships, formulas or equations and so falls within the Mathematical Concepts grouping of abstract ideas. See MPEP 2106.04(a)(2)I. The claim recites an abstract idea.
This judicial exception is not integrated into a practical application. The claim recites the additional claim elements of processing circuitry, obtaining a training data set, the training data set including a sample molecule and a property label associated with the sample molecule; obtaining a three-dimensional structure coordinate matrix, a normalized adjacency matrix, an atomic feature, and a chemical bond feature of the sample molecule; and obtaining a loss value between the predicted property value corresponding to the sample molecule and the property label of the sample molecule based on a target loss function. The processing circuitry is recited at a high level of generality and is merely used as a tool to perform the abstract idea. See MPEP 2106.05(f).
The limitations of obtaining a training data set, obtaining a three-dimensional structure coordinate matrix and obtaining a loss value are recited at a high level of generality such that it merely amounts to necessary data gathering and outputting for performing the abstract idea. Thus, they amount to adding insignificant extra-solution activity. See MPEP 2106.05(g). The claim is directed to an abstract idea.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception. As disclosed above, the processing circuitry amounts to no more than merely using a generic computer as a tool to perform an abstract idea. As such, it cannot provide inventive concept. The steps of obtaining amount to no more than adding insignificant extra-solution activity. Additionally, the claim elements amount to receiving or transmitting data over a network and thus is no more than well-understood, routine, conventional activity. See MPEP 2106.05(d). As such, it cannot provide inventive concept. The claim is not patent eligible.
Claims 15-17 and 20 depend from claim 14 and recites the same abstract idea as claim 14. Claims 15-17 and 20 recite additional claim elements that amount to adding additional necessary data gathering and outputting steps for performing the abstract idea (claim 17) and/or adding additional limitations to the abstract idea (claims 15-17) and/or a generic computer component merely used as a tool to perform the abstract idea (claim 20).
The additional limitations for obtaining are recited at a high level of generality such that it merely amounts to necessary data gathering and outputting for performing the abstract idea. Thus, they amount to adding insignificant extra-solution activity. See MPEP 2106.05(g). Additionally, the claim elements amount to receiving or transmitting data over a network and thus is no more than well-understood, routine, conventional activity. See MPEP 2106.05(d). As such, it cannot provide inventive concept.
As disclosed above, the non-transitory computer-readable storage medium and processor in claim 20 amounts to no more than merely using a generic computer as a tool to perform an abstract idea. As such, it cannot provide inventive concept. The limitations in claims 15-17 of performing, determining, inputting and encoding encompasses the use of computations. Thus, the limitations are accomplished using mathematical calculations, relationships, formulas or equations and so falls within the Mathematical Concepts grouping of abstract ideas. See MPEP 2106.04(a)(2)I. The additional claim elements recite an abstract idea. The claims neither recite limitations that integrate the abstract idea into a practical application nor amount to significantly more than the abstract idea. The claims are not patent eligible.
Claim 18 is an apparatus that recite(s) determine a drug-forming property of the drug molecule based on a molecular property prediction network, the drug-forming property of the drug molecule being determined by the molecular property prediction network according to the three-dimensional structure information.
In the context of the claim the step of determine a drug-forming property, given its plain and ordinary meaning, encompasses the use of computational models to predict the properties of molecules. Thus, the limitations are accomplished using mathematical calculations, relationships, formulas or equations and so falls within the Mathematical Concepts grouping of abstract ideas. See MPEP 2106.04(a)(2)I. The claim recites an abstract idea.
This judicial exception is not integrated into a practical application. The claim recites the additional claim elements of processing circuitry, obtain a text string of a drug molecule, the text string indicating a structural formula of the drug molecule; and obtain three-dimensional structure information of the drug molecule, the three-dimensional structure information being generated according to the structural formula indicated by the text string. The processing circuitry is recited at a high level of generality and is merely used as a tool to perform the abstract idea. See MPEP 2106.05(f). The limitations of obtain a text string of a drug molecule and obtain three-dimensional structure information are recited at a high level of generality such that it merely amounts to necessary data gathering and outputting for performing the abstract idea. Thus, they amount to adding insignificant extra-solution activity. See MPEP 2106.05(g). The claim is directed to an abstract idea.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception. As disclosed above, the processing circuitry amounts to no more than merely using a generic computer as a tool to perform an abstract idea. As such, it cannot provide inventive concept. The steps of obtain amount to no more than adding insignificant extra-solution activity. Additionally, the claim elements amount to receiving or transmitting data over a network and thus is no more than well-understood, routine, conventional activity. See MPEP 2106.05(d). As such, it cannot provide inventive concept. The claim is not patent eligible.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claim(s) 1 and 18-20 is/are rejected under 35 U.S.C. 103 as being unpatentable over Zhang in Foreign Patent CN 111243682A (see IDS 21 AUG 2022, see English translation), and further in view of Itai in U.S. Patent Publication 2004/0024772.
Regarding claim 1, Zhang teaches: obtaining a structural formula of the drug molecule (see “obtaining the drug molecule”, Abstract);
obtaining three-dimensional structure information of the drug molecule, the three-dimensional structure information being generated according to the structural formula indicated by the text string (see “detected description feature determining a first vector Q, K second vector and a third vector V. Specifically, the first vector Q, K second vector and a third vector V are the same as the described features”, p. 11 par 1); and
determining, by processing circuitry (see “computer storage medium and electronic device”, p. 2 par 3), a drug-forming property of the drug molecule based on a molecular property prediction network, the drug-forming property of the drug molecule being determined by the molecular property prediction network according to the three-dimensional structure information (see “Further classification layer, in step S240, the toxicity prediction model based on determining the splicing characteristic to be tested”, p11 par 6).
Zhang differs from the claimed invention is that it does not explicitly teach a text string of a drug molecule.
Itai teaches “A method of generating a molecule-function network” (Abstract) comprising a text string of a drug molecule (see “By searching through these texts based on the complete match or partial match of character strings, it is possible to screen biomolecules, biomolecule pairs, bio-events, pathological events, drug molecules, drug molecule-biomolecule pairs”, [0175]). Itai discloses relations between biomolecule/molecule network and biological responses/physiological actions ([0017]).
It would be obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have combined the teachings of Itai with Zhang to improve Zhang with a reasonable expectation that it would facilitate understanding of the drug molecule thereby improving the accuracy of predicting toxicity.
Regarding claim 18, Zhang teaches:
processing circuitry configured to (see “computer storage medium and electronic device”, p. 2 par 3):
obtain a structural formula of the drug molecule (see “obtaining the drug molecule”, Abstract);
obtain three-dimensional structure information of the drug molecule, the three-dimensional structure information being generated according to the structural formula indicated by the text string (see “detected description feature determining a first vector Q, K second vector and a third vector V. Specifically, the first vector Q, K second vector and a third vector V are the same as the described features”, p. 11 par 1); and
determine a drug-forming property of the drug molecule based on a molecular property prediction network, the drug-forming property of the drug molecule being determined by the molecular property prediction network according to the three-dimensional structure information (see “Further classification layer, in step S240, the toxicity prediction model based on determining the splicing characteristic to be tested”, p11 par 6).
Zhang differs from the claimed invention is that it does not explicitly teach a text string of a drug molecule.
Itai teaches “A method of generating a molecule-function network” (Abstract) comprising a text string of a drug molecule (see “By searching through these texts based on the complete match or partial match of character strings, it is possible to screen biomolecules, biomolecule pairs, bio-events, pathological events, drug molecules, drug molecule-biomolecule pairs”, [0175]). Itai discloses relations between biomolecule/molecule network and biological responses/physiological actions ([0017]).
It would be obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have combined the teachings of Itai with Zhang to improve Zhang with a reasonable expectation that it would facilitate understanding of the drug molecule thereby improving the accuracy of predicting toxicity.
Regarding claim 19, Zhang teaches A non-transitory computer-readable storage medium storing instructions which when executed by a computer cause the computer to perform the method according to claim 1 (see “computer storage medium and electronic device”, p. 2 par 3; see “with instructions”, p. 4 par 3).
Regarding claim 20, Zhang teaches A non-transitory computer-readable storage medium storing instructions which when executed by a processor cause the processor to perform the method according to claim 14 (see “computer storage medium and electronic device”, p. 2 par 3; see “with instructions”, p. 4 par 3).
Allowable Subject Matter
Claims 14-17 would be allowable if rewritten to overcome the rejection(s) under 35 U.S.C. 101, set forth in this Office action and to include all of the limitations of the base claim and any intervening claims.
The following is a statement of reasons for the indication of allowable subject matter:
Regarding claim 14, the prior art fails to anticipate or render obvious A method for training a model, the method comprising: obtaining a training data set, the training data set including a sample molecule and a property label associated with the sample molecule; obtaining a three-dimensional structure coordinate matrix, a normalized adjacency matrix, an atomic feature, and a chemical bond feature of the sample molecule; performing feature concatenation on the three-dimensional structure coordinate matrix, the normalized adjacency matrix, the atomic feature, and the chemical bond feature of the sample molecule to obtain a second concatenated matrix; determining a predicted property value corresponding to the sample molecule according to the second concatenated matrix through an initial neural network; obtaining a loss value between the predicted property value corresponding to the sample molecule and the property label of the sample molecule based on a target loss function; and iteratively updating, by processing circuitry, network parameters of the initial neural network in response to the loss value being greater than a second threshold until the loss value is not greater than the second threshold to obtain a molecular property prediction network, in combination with all other limitations as claimed by Applicant.
Claims 15-17 are indicated allowable by virtue of their dependence.
Claims 2-13 would be allowable if rewritten or amended to overcome the rejection(s) under 35 U.S.C. 101, set forth in this Office action.
Regarding claim 2, the prior art fails to anticipate or render obvious wherein the obtaining the three-dimensional structure information comprises: obtaining the three-dimensional structure information from cheminformatics software, the cheminformatics software being configured to generate the three-dimensional structure information according to the structural formula indicated by the text string, in combination with all other limitations as claimed by Applicant.
Regarding claim 3, the prior art fails to anticipate or render obvious obtaining two-dimensional structure information of the drug molecule, the two-dimensional structure information being generated according to the structural formula indicated by the text string, wherein the drug-forming property of the drug molecule is determined by the molecular property prediction network according to the three-dimensional structure information and the two- dimensional structure information, in combination with all other limitations as claimed by Applicant.
Regarding claim 4, the prior art fails to anticipate or render obvious obtaining an atomic feature and a chemical bond feature of the drug molecule according to the structural formula indicated by the text string, wherein the drug-forming property of the drug molecule is determined by the molecular property prediction network according to the three-dimensional structure information, the atomic feature, and the chemical bond feature of the drug molecule, in combination with all other limitations as claimed by Applicant.
Regarding claim 6, the prior art fails to anticipate or render obvious wherein the molecular property prediction network includes a transformer model, in combination with all other limitations as claimed by Applicant.
Regarding claim 7, the prior art fails to anticipate or render obvious performing transformation on the three-dimensional structure coordinates of the drug molecule when a shape of a three-dimensional structure of the drug molecule remains unchanged, to obtain a three-dimensional structure coordinate matrix as the three-dimensional structure information of the drug molecule, in combination with all other limitations as claimed by Applicant.
Claims 5 and 8-13 are indicated allowable by virtue of their dependence.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure:
Plumbley et al. in U.S. Patent Publication 2021/0117869 teaches “ a compound descriptor comprises a compound descriptor based on at least one or more of: International Chemical Identifier, InChI; InChIKey; MoIFile format; two dimensional Physical Chemical descriptors; three dimensional Physical Chemical descriptors; XYZ file format; Extended Connectivity Fingerprint, ECFP; Structure Data Format; structural formula or representation of the compound; Simplified Molecular Input Line Entry Specification, SMILES, strings or format; SMILES arbitrary target specification or format; Chemical Mark-up Language format; and any other chemical descriptor or chemical descriptor format for describing, representing and/or encoding molecular information and/or structure(s) of compounds” ([0017]).
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MISCHITA HENSON whose telephone number is (571)270-3944. The examiner can normally be reached Monday-Thursday 9am-6pm EST.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Arleen Vazquez can be reached at 571-272-2619. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/MI'SCHITA' HENSON/ Primary Examiner, Art Unit 2857