Detailed Action
This Office Action is in response to the remarks entered on 03/11/2026. Claims 139-141, 144-145, 147-150, 153, 155-160, 171, 175-176, 179-183, 187, 196, 204-208 are pending.
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 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 139-141, 144-145, 147-150, 153, 155-160, 171, 175-176, 179-183, 187, 196, and 204-208 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Regarding claim 139,
2A Prong 1: A method of determining whether a first compound and a second compound are causal for a common biological state, the method comprising: (a mental process of opinion, as it merely recites determining a cause of a biological state, which can be done in human mind.)
C) determining a respective similarity between the first compound embedding and each respective transcriptional embedding in the plurality of transcriptional embeddings thereby determining a plurality of similarities, (a mental process of opinion, as it merely recites comparing two embeddings and determining the similarity between the embeddings, which can be done in human mind.)
the single structure encoder is trained to minimize a loss against the plurality of transcriptional embeddings; (mathematical concept – a loss function is used to calculate the similarity scores for the embeddings [0316] – [0318])
D) associating the first compound with a biological state that the second compound is known to be causal for when the comparing C) determines that the similarity between the first compound embedding and the respective transcriptional embedding of the second compound satisfies a similarity criterion. (a mental process of opinion, as it merely recites determining a cause of a biological state based on the determined similarity, which can be done in human mind.)
2A Prong 2: This judicial exception is not integrated into a practical application.
A) inputting a first input data structure into a structure encoder, (an insignificant extra-solution activity MPEP 2106.05(g) of transmitting data over a network.)
wherein the first input data structure comprises a combination of (i) a feature representation of a structure of the first compound and (ii) a baseline transcriptional representation, and (a field of use and technological environment MPEP 2106.05(h), as it merely limits the field of use of the encoder and the input data)
the feature representation comprises at least one hundred features of the structure of the first compound, (a field of use and technological environment MPEP 2106.05(h), as it merely limits the field of use of the encoder and the input data)
the single structure encoder comprises a first plurality of parameters, wherein the first plurality of parameters comprises 1000 parameters, and (mere instructions to apply an exception using a computer MPEP 2106.05(f), as it merely describes the structure of the neural network encoder.)
the single structure encoder is a convolutional neural network, a graph based neural network or a first multilayer perceptron having a first plurality of hidden layers, (mere instructions to apply an exception using a computer MPEP 2106.05(f))
thereby retrieving, by operation of the first plurality of parameters on the first input data structure in accordance with an architecture of the single structure encoder, as output from the single structure encoder, a first compound embedding having a first dimension; (mere instructions to apply an exception using a computer MPEP 2106.05(f), as it merely discloses utilizing a neural network encoder to generate output embeddings.)
B) generating a plurality of transcriptional embeddings, wherein each transcriptional embedding in the plurality of transcriptional embeddings has the first dimension, by inputting, for each respective transcriptional embedding in the plurality of transcriptional embeddings, a corresponding cellular constituent abundance data set representative of a first cell type exposed to a different perturban in a plurality of perturbans into a transcriptional encoder comprising a second plurality of parameters, wherein the corresponding cellular constituent data set comprises cellular constituent abundance values for a plurality of cellular constituents upon exposure to the different perturban, the plurality of transcriptional embeddings comprises at least 25 transcriptional embeddings, the second plurality of parameters comprises 1000 parameters; (mere instructions to apply an exception using a computer MPEP 2106.05(f), as it merely discloses utilizing a neural network encoder to generate output embeddings.)
the first compound is not in the plurality of perturbagens, (a field of use and technological environment MPEP 2106.05(h), as it merely limits the field of use of the first compound and the encoder)
the plurality of perturbans includes the second compound, (a field of use and technological environment MPEP 2106.05(h), as it merely limits the field of use of the second compound and the encoder)
The additional elements as disclosed above alone or in combination do not integrate the judicial exception into practical application as they are mere insignificant extra solution activity, combination of generic computer functions that are restricted to field of use implemented to perform the disclosed abstract idea above.
2B: The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception.
A) inputting a first input data structure into a single structure encoder, (was indicated as an insignificant extra-solution activity MPEP 2106.05(g) in 2A Prong 2, therefore re-evaluated in 2B as a well understood, routine, and conventional activity MPEP 2106.05(d) of transmitting data over a network)
wherein the first input data structure comprises a combination of (i) a feature representation of a structure of the first compound and (ii) a baseline transcriptional representation, (a field of use and technological environment MPEP 2106.05(h), as it merely limits the field of use of the input data and the encoder)
the feature representation comprises at least one hundred features of the structure of the first compound, (a field of use and technological environment MPEP 2106.05(h), as it merely limits the field of use of the encoder and the input data)
the single structure encoder comprises a first plurality of parameters, wherein the first plurality of parameters comprises 1000 parameters, (mere instructions to apply an exception using a computer MPEP 2106.05(f), as it merely describes the structure of the neural network encoder)
the single structure encoder is a convolutional neural network, a graph based neural network or a first multilayer perceptron having a first plurality of hidden layers, (mere instructions to apply an exception using a computer MPEP 2106.05(f))
thereby retrieving, by operation of the first plurality of parameters on the first input data structure in accordance with an architecture of the single structure encoder, as output from the single structure encoder, a first compound embedding having a first dimension; (mere instructions to apply an exception using a computer MPEP 2106.05(f), as it merely discloses utilizing a neural network encoder to generate output embeddings)
wherein each transcriptional embedding in the plurality of transcriptional embeddings has the first dimension, (a field of use and technological environment MPEP 2106.05(h))
B) generating a plurality of transcriptional embeddings, wherein each transcriptional embedding in the plurality of transcriptional embeddings has the first dimension, by inputting, for each respective transcriptional embedding in the plurality of transcriptional embeddings, a corresponding cellular constituent abundance data set representative of a first cell type exposed to a different perturban in a plurality of perturbans into a transcriptional encoder comprising a second plurality of parameters, wherein the corresponding cellular constituent data set comprises cellular constituent abundance values for a plurality of cellular constituents upon exposure to the different perturban, the plurality of transcriptional embeddings comprises at least 25 transcriptional embeddings, the second plurality of parameters comprises 1000 parameters; (mere instructions to apply an exception using a computer MPEP 2106.05(f), as it merely discloses utilizing a neural network encoder to generate output embeddings.)
the first compound is not in the plurality of perturbagens, (a field of use and technological environment MPEP 2106.05(h), as it merely limits the field of use of the first compound and the encoder)
the plurality of perturbans includes the second compound, (a field of use and technological environment MPEP 2106.05(h), as it merely limits the field of use of the second compound and the encoder)
The additional elements as disclosed above in combination of the abstract idea are not sufficient to amount to significantly more than the judicial exception as they are well, understood, routine and conventional activity as disclosed in combination of generic computer functions and usage of elements that are restricted to field of use that are implemented to perform the disclosed abstract idea above.
Regarding claim 140,
2A Prong 1: wherein the similarity criterion is satisfied when the similarity assigned to the respective transcriptional embedding by the determining B) is in a top Nth percentile of the plurality of similarities. (a mental process of evaluation, as it merely recites whether the similarity value satisfies the predetermined criteria which can be done in human mind.)
2A Prong 2: This judicial exception is not integrated into a practical application.
2B: The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception.
Regarding claim 141,
2A Prong 1: Incorporates the rejection of claim 140.
2A Prong 2: wherein the Nth percentile is between fifty percent and ninety-five percent. (a field of use and technological environment MPEP 2106.05(h).)
2B: wherein the Nth percentile is between fifty percent and ninety-five percent. (a field of use and technological environment MPEP 2106.05(h).)
Regarding claim 144,
2A Prong 1: wherein the similarity criterion is satisfied when the similarity assigned to the respective transcriptional embedding by the determining C) is in the top N similarities in the plurality of similarities. (a mental process of evaluation, as it merely recites whether the similarity value satisfies the predetermined criteria which can be done in human mind.)
2A Prong 2: This judicial exception is not integrated into a practical application.
2B: The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception.
Regarding claim 145,
2A Prong 1: Incorporates the rejection of claim 144.
2A Prong 2: wherein N is between 5 and 100 and the plurality of transcriptional embeddings comprises at least 1000 transcriptional embeddings. (a field of use and technological environment MPEP 2106.05(h).)
2B: wherein N is between 5 and 100 and the plurality of transcriptional embeddings comprises at least 1000 transcriptional embeddings. (a field of use and technological environment MPEP 2106.05(h).)
Regarding claim 147,
2A Prong 1: Incorporates the rejection of claim 139.
2A Prong 2: the method further comprising determining the feature representation of the structure of the first compound from a string representation of the structure of the first compound. (mere instructions to apply an exception using a computer MPEP 2106.05(f).)
2B: the method further comprising determining the feature representation of the structure of the first compound from a string representation of the structure of the first compound. (mere instructions to apply an exception using a computer MPEP 2106.05(f).)
Regarding claim 148,
2A Prong 1: Incorporates the rejection of claim 147.
2A Prong 2: wherein the string representation is in a SMARTS, DeepSMILES, or SELFIES format. (a field of use and technological environment MPEP 2106.05(h).)
2B: wherein the string representation is in a SMARTS, DeepSMILES, or SELFIES format. (a field of use and technological environment MPEP 2106.05(h).)
Regarding claim 149,
2A Prong 1: Incorporates the rejection of claim 147.
2A Prong 2: wherein the string representation is in a simplified molecular-input line-entry system (SMILES) format. (a field of use and technological environment MPEP 2106.05(h).)
2B: wherein the string representation is in a simplified molecular-input line-entry system (SMILES) format. (a field of use and technological environment MPEP 2106.05(h).)
Regarding claim 150,
2A Prong 1: Incorporates the rejection of claim 147.
2A Prong 2: wherein the determining the feature representation of the structure of the first compound from a string representation of a chemical structure of the first compound comprises inputting the string representation into each featurizer in a set of featurizers to obtain the feature representation. (mere instructions to apply an exception using a computer MPEP 2106.05(f).)
2B: wherein the determining the feature representation of the structure of the first compound from a string representation of a chemical structure of the first compound comprises inputting the string representation into each featurizer in a set of featurizers to obtain the feature representation. (mere instructions to apply an exception using a computer MPEP 2106.05(f).)
Regarding claim 153,
2A Prong 1: Incorporates the rejection of claim 139.
2A Prong 2: wherein the feature representation of the structure of the first compound consists of between 150 and 10,000 features. (a field of use and technological environment MPEP 2106.05(h).)
2B: wherein the feature representation of the structure of the first compound consists of between 150 and 10,000 features. (a field of use and technological environment MPEP 2106.05(h).)
Regarding claim 155,
2A Prong 1: Incorporates the rejection of claim 139.
2A Prong 2: wherein the baseline transcriptional representation is that of a first cell type. (a field of use and technological environment MPEP 2106.05(h).)
2B: wherein the baseline transcriptional representation is that of a first cell type. (a field of use and technological environment MPEP 2106.05(h).)
Regarding claim 156,
2A Prong 1: Incorporates the rejection of claim 155.
2A Prong 2: wherein the baseline transcriptional representation comprises pathway activation scores for a plurality of pathways derived from cellular constituent abundance data for a plurality of cellular constituents in a plurality of cells of the first type that are in a baseline state. (a field of use and technological environment MPEP 2106.05(h), as it merely what constitutes the baseline transcriptional representation.)
2B: wherein the baseline transcriptional representation comprises pathway activation scores for a plurality of pathways derived from cellular constituent abundance data for a plurality of cellular constituents in a plurality of cells of the first type that are in a baseline state. (a field of use and technological environment MPEP 2106.05(h), as it merely what constitutes the baseline transcriptional representation.)
Regarding claim 157,
2A Prong 1: Incorporates the rejection of claim 156.
2A Prong 2: wherein each cellular constituent in the plurality of cellular constituents uniquely maps to a different gene. (a field of use and technological environment MPEP 2106.05(h).)
2B: wherein each cellular constituent in the plurality of cellular constituents uniquely maps to a different gene. (a field of use and technological environment MPEP 2106.05(h).)
Regarding claim 158,
2A Prong 1: Incorporates the rejection of claim 156.
2A Prong 2: wherein each cellular constituent in the plurality of cellular constituents is a particular gene, a particular mRNA associated with a gene, a carbohydrate, a lipid, an epigenetic feature, an epitranscriptomic feature, a metabolite, an antibody, a peptide, a protein, or a post-translational modification of a protein. (a field of use and technological environment MPEP 2106.05(h).)
2B: wherein each cellular constituent in the plurality of cellular constituents is a particular gene, a particular mRNA associated with a gene, a carbohydrate, a lipid, an epigenetic feature, an epitranscriptomic feature, a metabolite, an antibody, a peptide, a protein, or a post-translational modification of a protein. (a field of use and technological environment MPEP 2106.05(h).)
Regarding claim 159,
2A Prong 1: Incorporates the rejection of claim 156.
2A Prong 2: wherein the plurality of cellular constituents comprises 50 or more cellular constituents (a field of use and technological environment MPEP 2106.05(h).)
2B: wherein the plurality of cellular constituents comprises 50 or more cellular constituents (a field of use and technological environment MPEP 2106.05(h).)
Regarding claim 160,
2A Prong 1: Incorporates the rejection of claim 156.
2A Prong 2: wherein the plurality of pathways comprises 10 or more pathways (a field of use and technological environment MPEP 2106.05(h).)
2B: wherein the plurality of pathways comprises 10 or more pathways (a field of use and technological environment MPEP 2106.05(h).)
Regarding claim 171,
2A Prong 1: Incorporates the rejection of claim 139.
2A Prong 2: wherein the first compound embedding having the first dimension consists of between 40 and 2000 dimensions. (a field of use and technological environment MPEP 2106.05(h), as it merely defines the number of dimensions of the input data.)
2B: wherein the first compound embedding having the first dimension consists of between 40 and 2000 dimensions. (a field of use and technological environment MPEP 2106.05(h), as it merely defines the number of dimensions of the input data.)
Regarding claim 175,
2A Prong 1: Incorporates the rejection of claim 139.
2A Prong 2: wherein the corresponding cellular constituent data set comprises single cell transcriptional data for a plurality of cells of a first type. (a field of use and technological environment MPEP 2106.05(h), as it merely defines what constitutes the cellular constituent data set.)
2B: wherein the corresponding cellular constituent data set comprises single cell transcriptional data for a plurality of cells of a first type. (a field of use and technological environment MPEP 2106.05(h), as it merely defines what constitutes the cellular constituent data set.)
Regarding claim 176,
2A Prong 1: Incorporates the rejection of claim 139.
2A Prong 2: wherein the corresponding cellular constituent data comprises bulk transcriptional data for a plurality of cells of the first type. (a field of use and technological environment MPEP 2106.05(h), as it merely defines what constitutes the cellular constituent data set.)
2B: wherein the corresponding cellular constituent data comprises bulk transcriptional data for a plurality of cells of the first type. (a field of use and technological environment MPEP 2106.05(h), as it merely defines what constitutes the cellular constituent data set.)
Regarding claim 179,
2A Prong 1: Incorporates the rejection of claim 139.
2A Prong 2: wherein each cellular constituent in the plurality of cellular constituents is a particular gene, a particular mRNA associated with a gene, a carbohydrate, a lipid, an epigenetic feature, an epitranscriptomic feature, a metabolite, an antibody, a peptide, a protein, or a post-translational modification of a protein. (a field of use and technological environment MPEP 2106.05(h), as it merely defines what constitutes the cellular constituent data set.)
2B: wherein each cellular constituent in the plurality of cellular constituents is a particular gene, a particular mRNA associated with a gene, a carbohydrate, a lipid, an epigenetic feature, an epitranscriptomic feature, a metabolite, an antibody, a peptide, a protein, or a post-translational modification of a protein. (a field of use and technological environment MPEP 2106.05(h), as it merely defines what constitutes the cellular constituent data set.)
Regarding claim 180,
2A Prong 1: Incorporates the rejection of claim 139.
2A Prong 2: wherein the plurality of cellular constituents comprises 50 or more cellular constituents (a field of use and technological environment MPEP 2106.05(h).)
2B: wherein the plurality of cellular constituents comprises 50 or more cellular constituents (a field of use and technological environment MPEP 2106.05(h).)
Regarding claim 181,
2A Prong 1: Incorporates the rejection of claim 139.
2A Prong 2: wherein the corresponding cellular constituent abundance data set comprises a corresponding differential expression signature for a plurality of cells of a first type. (a field of use and technological environment MPEP 2106.05(h).)
2B: wherein the corresponding cellular constituent abundance data set comprises a corresponding differential expression signature for a plurality of cells of a first type. (a field of use and technological environment MPEP 2106.05(h).)
Regarding claim 182,
2A Prong 1: the respective differential value represents a difference between (i) one or more abundance values measured for the respective cellular constituent in a first assay of a first plurality of cells of the first cell type that represent a first cell state and (ii) one or more abundance values measured for the respective cellular constituent in a second assay of a second plurality of cells of the first cell type that represent a second cell state. (a mathematical concept, as it merely recites calculating difference between the data values.)
2A Prong 2: the corresponding differential expression signature comprises a plurality of differential values, (a field of use and technological environment MPEP 2106.05(h).)
each respective differential value in the plurality of differential values corresponds to a respective cellular constituent in the plurality of cellular constituents, and (a field of use and technological environment MPEP 2106.05(h).)
2B: the corresponding differential expression signature comprises a plurality of differential values, (a field of use and technological environment MPEP 2106.05(h).)
each respective differential value in the plurality of differential values corresponds to a respective cellular constituent in the plurality of cellular constituents, and (a field of use and technological environment MPEP 2106.05(h).)
Regarding claim 183,
2A Prong 1: Incorporates the rejection of claim 182.
2A Prong 2: wherein the first cell state is exposure of the first plurality of cells to a respective perturban in the plurality of perturbans, and (a field of use and technological environment MPEP 2106.05(h).)
the second cell state is exposure of the second plurality of cells to a reference environment. (a field of use and technological environment MPEP 2106.05(h).)
2B: wherein the first cell state is exposure of the first plurality of cells to a respective perturban in the plurality of perturbans, and (a field of use and technological environment MPEP 2106.05(h).)
the second cell state is exposure of the second plurality of cells to a reference environment. (a field of use and technological environment MPEP 2106.05(h).)
Regarding claim 187,
2A Prong 1: Incorporates the rejection of claim 139.
2A Prong 2: wherein the plurality of transcriptional embeddings collectively represents over 500 different first cell states. (a field of use and technological environment MPEP 2106.05(h).)
2B: wherein the plurality of transcriptional embeddings collectively represents over 500 different first cell states. (a field of use and technological environment MPEP 2106.05(h).)
Regarding claim 196,
2A Prong 1: Incorporates the rejection of claim 139.
2A Prong 2: wherein the respective transcriptional embedding consists of between 40 and 2000 dimensions. (a field of use and technological environment MPEP 2106.05(h), as it merely defines the number of dimensions of the input data.)
2B: wherein the respective transcriptional embedding consists of between 40 and 2000 dimensions. (a field of use and technological environment MPEP 2106.05(h), as it merely defines the number of dimensions of the input data.)
Regarding claim 204,
2A Prong 1: Claim 204 is a system claim having similar limitation to the claim 139. Therefore, the claim is rejected under the same rationale as the claim 139 above.
2A Prong 2: A computer system, comprising one or more processors and memory, the memory storing instructions for performing a method of determining whether a first compound and a second compound are causal for a common biological state, the method comprising (mere instructions to apply an exception using a computer MPEP 2106.05(f).)
2B: A computer system, comprising one or more processors and memory, the memory storing instructions for performing a method of determining whether a first compound and a second compound are causal for a common biological state, the method comprising (mere instructions to apply an exception using a computer MPEP 2106.05(f).)
Regarding claim 205,
2A Prong 1: Claim 205 is a storage medium claim having similar limitation to the claim 139. Therefore, the claim is rejected under the same rationale as of claim 139 above.
2A Prong 2: A non-transitory computer-readable medium storing one or more computer programs, executable by a computer, for determining whether a first compound and a second compound are causal for a common biological state, the computer comprising one or more processors and a memory, the one or more computer programs collectively encoding computer executable instructions that performs a method comprising (mere instructions to apply an exception using a computer MPEP 2106.05(f).)
2B: A non-transitory computer-readable medium storing one or more computer programs, executable by a computer, for determining whether a first compound and a second compound are causal for a common biological state, the computer comprising one or more processors and a memory, the one or more computer programs collectively encoding computer executable instructions that performs a method comprising (mere instructions to apply an exception using a computer MPEP 2106.05(f).)
Regarding claim 206,
2A Prong 1: Incorporates the rejection of claim 139.
2A Prong 2: wherein the first plurality of parameters is one million parameters, and the second plurality of parameters is one million parameters. (mere instructions to apply an exception using a computer MPEP 2106.05(f) )
2B: wherein the first plurality of parameters is one million parameters, and the second plurality of parameters is one million parameters. (mere instructions to apply an exception using a computer MPEP 2106.05(f) )
Claim 207 is a non-transitory computer-readable medium having limitations similar to the claim 206 above. Therefore, claim 207 is rejected for the same reasons as claim 206.
Claim 208 is a non-transitory computer-readable medium having limitations similar to the claim 206 above. Therefore, claim 208 is rejected for the same reasons as claim 206.
Claim Rejections - 35 USC § 103
Amended claims were received on 03/11/2026. 35 U.S.C. 103 rejections have been withdrawn.
Response to Arguments
Response to Arguments under 35 U.S.C. 101
Arguments: Applicant asserts that (a) the claimed method requires specific machine-learning architectures and parameterized encoders that cannot be performed in the human mind [Remarks, page 13], (b) the claim must be evaluated as a whole and the pipeline for analyzing biological data is not a mental process [page 14], (c) the claim recites specific technological improvement in computational biological screening, and the Federal Circuit has repeatedly held that machine learning techniques applied to technological problems are patent-eligible [page 14-15], (d) the examiner incorrectly characterizes the neural network limitation as “generic computer functions” [page 15], and (e) the claim includes significantly more than an abstract idea [page 16].
Examiner’s Response: Examiner respectfully disagrees. Regarding (a), the applicant misunderstood the 35 U.S.C. 101 rejection in the Office Action. The Examiner agrees that a convolutional neural network operation cannot be performed in the human mind. However, claim 1 recites the convolutional neural network structure as mere instructions to apply an exception of generating embeddings and comparing the generated embeddings. The Broadest Reasonable Interpretation of ‘retrieving … a first compound embedding having a first dimension’ and ‘generating a plurality of transcriptional embeddings’ without technological details encompasses an expert extracting and selecting data from the compound data and the transcription data, which does not require a computer component. The cited decisions SRI Int’l v. Cisco Systems, McRO v. Bandai Namco Games, and Research Corp. Technologies v. Microsoft, are distinguishable from the instant application and the argument does not provide the reasons why the cited decisions are similar to the instant application. Additionally, one cannot assert that it is not practical for the human mind to perform 1000 parameter computations, because the court decision concluded that if a step was able to be performed mentally with a pen and paper, it qualified as a mental process. 654 F.3d at 1372-73, 99 USPQ2d at 1695. See also Flook, 437 U.S. at 586, 198 USPQ at 196 (claimed "computations can be made by pencil and paper calculations"); University of Florida Research Foundation, Inc. v. General Electric Co., 916 F.3d 1363, 1367, 129 USPQ2d 1409, 1411-12 (Fed. Cir. 2019) (relying on specification’s description of the claimed analysis and manipulation of data as being performed mentally "‘using pen and paper methodologies, such as flowsheets and patient charts’"); Symantec, 838 F.3d at 1318, 120 USPQ2d at 1360 (although claimed as computer-implemented, steps of screening messages can be "performed by a human, mentally or with pen and paper"). Generating embeddings, as discussed above, is a mental process because it can be performed with the aid of pen and paper, and the step of ‘computing nonlinear transformations across hidden layers’ is not claimed. Regarding (b), the Examiner performed the evaluation and concluded that the Claim as a Whole is directed to a mental process implemented using generic computer components.
Regarding (c), the cited decisions solve technical problems that are different than the instant specification, and the argument does not provide the reasons why the cited decisions are similar to the instant application. Regarding (d), the Examiner respectfully disagrees. The convolutional neural networks, graph neural networks, or multilayer perceptrons with hidden layers without technological detailed structure is mere instructions to apply an exception using generic computer components MPEP 2106.05(f). As discussed above, the cited decisions are not similar to the instant claims, and the applicant does not provide reasons why the cited references are similar to the instant application. Regarding (e), the Examiner respectfully reiterates the arguments regarding (d). Mere instructions to apply an exception using generic computer components does not provide meaningful limitation to the claims and the cited decisions are not similar to the instant application.
Additionally, MPEP 2106.05(a) shows that a claim whose entire scope can be performed mentally, cannot be said to improve computer technology. Synopsys, Inc. v. Mentor Graphics Corp., 839 F.3d 1138, 120 USPQ2d 1473 (Fed. Cir. 2016) (a method of translating a logic circuit into a hardware component description of a logic circuit was found to be ineligible because the method did not employ a computer and a skilled artisan could perform all the steps mentally). Since the entire scope of the claim, comparing the compounds and transcriptional embeddings and determine the similarity between them, and inferring a biological state which is related to the compound, can be performed mentally without a computer, the claim cannot be said to improve computer technology.
Accordingly, arguments to claim 139 is not persuasive and arguments to independent claims 204 and 205 are not persuasive. Therefore, arguments to dependent claims 140-141, 144-145, 147-150, 153, 155-160, 171, 175-176, 179-183, 187, 196, 206-208 which depend from independent claims 139, 204 and 205 are not persuasive.
Response to Arguments under 35 U.S.C. 103
Applicant’s arguments, see [Remarks, page 17-31], filed 03/11/2026, with respect to claims 139-141, 144-145, 147-150, 153, 155-160, 171, 175-176, 179-183, 187, 196, 204-208 have been fully considered and are persuasive. The 35 U.S.C. 103 rejections of claims 139-141, 144-145, 147-150, 153, 155-160, 171, 175-176, 179-183, 187, 196, 204-208 have been withdrawn.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Donner et al., "Drug Repurposing Using Deep Embeddings of Gene Expression Profiles" (This prior art is pertinent because it teaches calculating similarity score based on the perturbagen embeddings generated using a neural network)
THIS ACTION IS MADE FINAL. 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 nonprovisional extension fee (37 CFR 1.17(a)) 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 mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JUN KWON whose telephone number is (571)272-2072. The examiner can normally be reached Monday – Friday 7:30AM – 4:30PM ET.
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, Abdullah Kawsar can be reached at (571)270-3169. 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.
/JUN KWON/Examiner, Art Unit 2127
/ABDULLAH AL KAWSAR/Supervisory Patent Examiner, Art Unit 2127
Prosecution Insights