In re Stanford: Ruined by a Processor and a Memory

By William Morriss
April 6, 2021

“The Federal Circuit’s focus on an aspect of the Stanford application which no one could (or did) argue was a protectable innovation not only damaged Stanford, it also squandered an opportunity to bring clarity to an area of law that desperately needs it.”

In re Stanford - https://depositphotos.com/28557353/stock-photo-opportunity-missed-and-taken-green.htmlComputer boilerplate – such as including “a processor and a memory” in claims – is commonplace in patent applications. However, the recent case of In re Stanford shows that this can be a double-edged sword, having the potential to both undermine an application and to ruin an opinion that could otherwise have shed light on several of the thorniest open questions in patent eligibility jurisprudence. Skeptical that such a common practice could be so counterproductive? Read on.

Language with No Benefit

From the outset, the invention in Stanford is not one where computer components should have had any particular significance. The invention was not a new type of computer, or a new component, such as an innovative processor or memory. Instead, it was (at least according to Stanford) a significant advance in the field of genomics. Many types of analysis required for genome interpretation are dependent on haplotype phasing – i.e., determining whether a gene was inherited from a person’s father or mother. The Stanford invention used a particular type of model with particular states – a hidden Markov model with inheritance, compression fixed error, and MIE-rich fixed error states – to perform haplotype phasing. This significantly increased the resolution of haplotype phasing, moving from 80% in the prior art to 97.9% for phasing using the Stanford invention.

Despite the fact that the Stanford invention was not, and did not purport to be, an improved or a novel computer, both the claims and description of the Stanford application included computer components. The description explained that “the present invention relates to methods, techniques, and algorithms that are intended to be implemented in a digital computer system” (application 13/445,925, paragraph 56), before saying that “such a digital computer or embedded device is well-known in the art” (id.) and providing a description of a generic computer system that is repeated in a variety of other Stanford patents and applications (e.g., U.S. 8,966,413, U.S. 2013/0073329). The claims included similar generic computer language, with limitations requiring various steps of the innovative haplotype phasing method to be performed “on a computer system comprising a processor and a memory” or “using a computer system comprising a processor and a memory” being added to the claims in response to a rejection under 35 U.S.C. § 101.

From Ineffective to Detrimental

Stanford does not appear to have benefitted from the generic computer language in their application and, to the extent that language had any impact at all, the impact appears to have been negative. The addition of computer language to the claims did not convince the examiner to withdraw the 101 rejections. Instead, the examiner stated that “[t]here is no limitation in the claims that the claimed computer program or computer uses other than a generic computer,” maintained the rejection and made the successive office action final. (Office Action of 7-9-2015 on application 13/445,925). On appeal, the computer language appears to have gone from having no effect to being actively detrimental. The patent trial and appeal board explicitly referenced the application’s generic computer system description when explaining that “the claimed method does not teach a technical improvement in a computer processor, but rather use the computer as a tool to improve data analysis.” (Ex parte Dewey, Appeal No. 2018-005489, on application 13/445,925 (PTAB 2019) at 11). Similarly, the Federal Circuit specifically noted the claims’ recitation of a “processor” and a “memory” in support of its statement that “it is hard to imagine a patent than that recites hardware limitations in more generic terms than the terms employed in claim 1.” (In re Stanford, Case No. 20-1012 (Fed. Cir. 2021) at 11). Unsurprisingly, the attention paid to aspects of its application which were admittedly not innovative did not bode well for Stanford, and its appeals were unsuccessful at both the Patent Trial and Appeal Board (PTAB) and the Federal Circuit.

A Missed Opportunity for Clarity

The attention paid to the non-innovative aspects of Stanford’s technology also made the Federal Circuit’s opinion much less useful in terms of clarifying the proper application of section 101. Looking purely at the law, it would have been reasonable to expect the Federal Circuit to have found the Stanford claims eligible. In McRO, Inc. v. Bandai Namco Games America, Inc., the Federal Circuit had already dealt with the eligibility of a method which used an assertedly innovative computational tool to improve an inherently computerized process, and found that claims which recited the tool with sufficient specificity were not directed to an abstract idea. Additionally, McRO clearly undercut the reasoning used by the PTAB to find the Stanford claims ineligible – i.e., that they recited steps that could be performed in the mind or recited mathematical concepts – since the McRO claims had also recited mathematical concepts (i.e., determining morph weight sets based on phoneme subsequence timing) and improved a process that not only could be, but actually had been performed in the human mind (i.e., synchronizing character and lip models in computer animation). If the Federal Circuit was going to find Stanford’s claims ineligible, it had the opportunity to significantly clarify the rules of subject matter eligibility by clearly distinguishing McRO. It did not. Instead, its only mention of McRO was to note that the PTAB had distinguished that case because the McRO claims “improve ‘the computer animation process itself.’”  In re Stanford, at 6. It then stated that “we are not persuaded that claim 1 is not directed to an abstract mathematical calculation” and “we are not persuaded that the process is an improved technological process.” (id. at 10). No explanation whatsoever was provided for why an improved haplotype phasing process was not “an improved technological process” while an improved computer animation process was. Similarly, no explanation was provided for why Stanford was doomed for reciting mathematical calculations while McRO was not. Indeed, it appears that the most important factor for the Federal Circuit was that the claims recited “a processor and a memory” without purporting to improve them, since it saw fit to explicitly state that:

Notably, claim 1 neither requires nor results in, a specialized computer or a computer with a specialized memory or processor. Indeed, it is hard to imagine a patent claim that recites hardware limitations in more generic terms than the terms employed by claim 1.

Considerations Going Forward

The Federal Circuit’s focus on an aspect of the Stanford application which no one could (or did) argue was a protectable innovation not only damaged Stanford, it also squandered an opportunity to bring clarity to an area of law that desperately needs it. More ominously, it also raised the question of whether the nigh-ubiquitous practice of including form computer language may need to be rethought, since if the Federal Circuit puts so much weight on “a processor and a memory” in claims which recite those terms, maybe it would be better to omit them all together to avoid falling into the trap of having to assert an improvement to the processor and the memory, rather than being able to focus on the actual invention an application is intended to protect.

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The Author

William Morriss

William Morriss has spent the past fifteen years helping clients, from startups to Fortune 500 companies, navigate complex issues surrounding law and technology and obtain protection for their inventions. He is a passionate advocate for the value of patents in business, having seen the impact in the success of his clients and his own work as an entrepreneur. William is Senior Technology Advisor at IP Toolworks, a company which he founded with the goal of helping attorneys respond to rejections from the USPTO more effectively by leveraging a wealth of publicly available but previously inaccessible information.

For More information or to contact William, please visit his Firm Profile Page.

Warning & Disclaimer: The pages, articles and comments on IPWatchdog.com do not constitute legal advice, nor do they create any attorney-client relationship. The articles published express the personal opinion and views of the author as of the time of publication and should not be attributed to the author’s employer, clients or the sponsors of IPWatchdog.com. Read more.

Discuss this

There are currently 27 Comments comments.

  1. Anon April 6, 2021 4:41 pm

    The article, while no doubt written with good intentions, absolutely misses the mark with its focus of “and computing elements.”

  2. Easwaran April 6, 2021 6:33 pm

    This is actually a very thought-provoking article, thank you! Is the computer boilerplate doing us all a disservice? Is there a way to pare it back to avoid its pretextual use in 101 rejections while still retaining adequate support under 112? I’m going to think hard about it.

  3. Pro Say April 6, 2021 7:30 pm

    Well worth repeating:

    Say their names . . .

    Stanford: So now your inventors Nicholas Johnson, Wing H. Wong, Hua Tang, Euan Ashley, Carlos Daniel Bustamante, Frederick Dewey, Jake Byrnes, Atul Butte, and Rong Chen have all been denied the patents they clearly earned and deserved.

    Without patent eligibility for all areas of innovation, how many other deserving Stanford inventors will be so denied in the years and decades to come?

    How will you feel watching others steal with impunity the very innovations that your folks worked so hard to create and develop?

    How many 10’s and 100’s of millions of dollars a year will Stanford lose in the years and decades to come from such IP theft?

    Congress needs to hear from you.

    And all you other 100’s of Universities and Colleges . . . and all you innovators who work — and attend — there?

    Stanford is not alone.

    Unless you want what’s happening to Stanford to happen to you and your innovators as well, your Congressional representatives (Representatives and two Senators alike) needs to hear from you — and your innovators as well.

    ASAP.

  4. ipguy April 6, 2021 9:04 pm

    I appreciate the article. However, from a practical point of view, a patent prosecutor should be more concerned with how the PTAB has previously dealt with the Examiner handling your case. For example, take a look at what the PTAB said in the other cases where they reversed the rejections of the Examiner handling your case, and try to see how those arguments succeeded. The Examiner assigned to the Stanford matter had 101 rejections reversed by the PTAB in other cases. Analyze why the applicants in those cases succeeded whereas Stanford failed to convince the PTAB to reverse.

  5. Mark Hrozenchik April 7, 2021 7:38 am

    I think the article is a bit unfair to the patent in question – it should be noted that it was filed two years PRIOR to the Alice decision; at the time, the claims were in perfectly good form. And it took a while for us practitioners to figure out how to draft claims/specs that would avoid or lessen the Alice problems. In addition, the court mentioned that the Applicants raised a new issue on appeal not previously discussed; this could have made a difference. It certainly should be made part of the description in the specification.

  6. concerned April 7, 2021 8:32 am

    My application is following the same course. Yet the inventive concept has nothing to do with a generic computer.

    I was not trying to solve a computer problem. I was trying to solve a problem that existed years before computers existed and the examiner agreed I did.

    The PTAB used the mental process rejection on my application also. People had a brain before computers existed and did not solve the problem. However, now that computers exist, it is a good thing airplanes, cars, radio were previously invented as now those patents would have been rejected somehow because of a computer.

  7. Patent Investor April 7, 2021 9:42 am

    “since if the Federal Circuit puts so much weight on “a processor and a memory” in claims which recite those terms, maybe it would be better to omit them all together to avoid falling into the trap of having to assert an improvement to the processor and the memory”

    Which then leads us to…”Since the applicant failed to recite the methods by which the process was implemented…all claims unpatentable as indefinite.”

    Just one more CAFC ruling where patent holders/applicants are damned if they do and damned if they don’t. We’re getting to the point of confusion to where the CAFC can rule either way on any subject and recite their own case law to support their decision.

  8. Concerned April 7, 2021 10:41 am

    @7: Yes any ruling so desired and that would be a rejection ruling.

    There is a difference when a first ever solution is placed on a computer vs. when a well known solution is slapped on a computer. Obvious statement, but the USPTO and their PTAB do want to acknowledge the same.

    What is the purpose of patents if encouraging first ever solutions, with or without a computer, is not the aim?

  9. Stanton Braden April 7, 2021 9:41 pm

    I’ve never been much of a fan of “based on” language in a claim. Stanford’s recital, in claim 1, of “based on the identity between…variants…
    using a Hidden Markov Model…” doesn’t help turn the corner on providing something transformative, beyond conventional, or beyond that of patent ineligible subject matter (or whatever the case may be for the standard du jour) if only due to a lack of detail provided in the recited methodology. It’s difficult to criticize the CAFC on this one. As is often the case, perhaps a better opinion/discussion could have been drafted. However, that seems to beg the question, “How much discussion eloquence do less than well-drafted claims deserve?”

  10. Patent Investor April 7, 2021 11:36 pm

    @SB. Even if you don’t think that those who write poorly written claims deserve a proper explanation of their failures, would you agree that those that come after should expect (deserve) an appeals court to lay out their opinions cogently and articulately???

  11. Night Writer April 8, 2021 7:33 am

    Look, this is ridiculous. We need to remove the CAFC. The quote below captures the entire problem. Improving data analysis must be patentable. And there is a lot to unpack in all your statements but the big picture is that the CAFC is using 101 to just decide what they like and what they don’t like in terms of 102/103/112.

    McRO was held eligible because it used a different new method for the animation.

    Stanford was held ineligible because it was a “mere” combination of known elements. That is they applied the Markov chains which were known to a problem and the CAFC deems that obvious so they used 101 to hold it ineligible.

    Frankly, your post and the ones like it are brain dead. They are like starving beggars chasing a psychotic tyrant hoping they throw some bread for the beggars.

    The only solution is to remove the CAFC. The CAFC is stacked with poor quality people that are not interested in creating a jurisprudence for patents. Congress could act but given our current situation with the Ds in charge and the Ds in the pocket of big tech this seems unlikely.

    Would McRO have been held eligible if it had recited a processor? My bet is yes. The assumption was that it was performed by a computer or it would have been a mental process (another psychotic construct.)

    So, no I don’t agree with you. There is no easy solution as it is based on whatever the CAFC feels like doing that day.

    Just think that the CAFC makes their living by receiving data, processing the data, and outputting data. But somehow a computer that performs what a CAFC judge does is not patent eligible. Odd too that what we hold most dear to us our ability to process information is held ineligible by the CAFC.

    I don’t think we would have these problems had Obama selected real judges.

    “the claimed method does not teach a technical improvement in a computer processor, but rather use the computer as a tool to improve data analysis.” (Ex parte Dewey, Appeal No. 2018-005489, on application 13/445,925 (PTAB 2019) at 11).

  12. Night Writer April 8, 2021 7:38 am

    The other thing about this too is trying to pretend that an “abstract idea” or any of the 101 jurisprudence is anything but we will just do what we want jurisprudence is ridiculous.

    My feelings are that the 101 jurisprudence is bad enough to justify the dissolution of the CAFC and wiping their jurisprudence going back to 1995. Just wipe it all out.

  13. Night Writer April 8, 2021 9:15 am

    @9 Stanton Braden if only due to a lack of detail provided in the recited methodology.

    That isn’t the problem. The type of changes you are talking about making to the claim make NO difference in claim construction by a person of ordinary skill in the art.

    Please. Stop.

  14. Stanton Braden April 8, 2021 10:40 am

    @10 (Patent Investor) and @13(Night Writer) Perhaps a better explanation is deserved but then again, there are many ways (maybe save for in Latin) for the court to say, “No.” In my opinion, it’s not that the processor and memory recital killed the claims, it’s just that the processor and memory recital couldn’t save the claims.

  15. Anon April 8, 2021 2:32 pm

    I am wondering where Easwaran is going with, “Is there a way to pare it back to avoid its pretextual use in 101 rejections while still retaining adequate support under 112?

    I think it’s chasing fool’s gold, since the pretextual use is more than blatant for anyone active in these arts.

    The problem is simply deeper – and no amount of “scrivener’s tricks” (as viewed by the Supreme Court) is going to stop the Court from legislating from the bench.

    If the Supreme Court is not going to use their Kavanaugh Scissors to cut through the Gordian Knot of their own creation (sadly, even with the Amici Briefs in the last round all but begging them to do so, it appears unlikely), then the only real and lasting option is going to have to be Congress abrogating the Supreme Court mess, resetting eligibility law, AND exercising their own Constitutional authority to employ jurisdiction stripping of the non-original jurisdiction of hearing patent cases from the Supreme Court (along with resetting the CAFC so as to have a non-bullied Article III court of review).

    Anything short of these two options simply will not work.

    And certainly not anything dreamed up of directly from practitioners (or as the Court references: scriveners).

  16. Joachim Martillo April 8, 2021 6:03 pm

    Back when I was on the faculty at MIT, I used to spend a lecture in explaining the physical nature of an executable program or the physical nature of a data structure.

    A few years ago I developed a new claim type that uses my course material.

    I call this claim type the Logic Gate State (LGS) claim. The claim type is an extension of the product by process type of claim. See MPEP 2113 Product-by-Process Claims [R-08.2017]. I have never tried this sort of claiming, but I wonder whether claiming thus might be able to avoid patent-eligibility issues.

    To claim a data structure the preamble should specify

    an unordered set of logic gate states,

    that are produced during operation of a digital logic device, which is at least one of:

    a program-executing device and
    a programmable device, and

    that are specified from a program that {enter details}, said program as appropriate having in order to run on the digital logic device undergone at least one of:

    interpretation,
    assembly,
    compilation, and
    synthesis,

    said unordered set of logic gate states {transitional phrase} {body}.

    To claim a subroutine the preamble should specify

    an ordered sequence of logic gate states,

    that are produced during operation of a digital logic device, which is at least one of:

    a program-executing device and
    a programmable device, and

    that are specified from a program that {enter details}, said program as appropriate having in order to run on the digital logic device undergone at least one of:

    interpretation,
    assembly,
    compilation, and
    synthesis,

    said ordered sequence of logic gate states {transitional phrase} {body}.

    I submitted the containing essay to the Senate Judiciary Committee’s Intellectual Property Panel. Senator Tillis considered it to be helpful. The essay can be read at the following URL.

    https://drive.google.com/file/d/1V3NOg4nyYq9j0WDSZpyuPUrZpGh8id9d/view?usp=sharing

    Does the LGS claim work and avoid eligibility doctrine?

  17. Anon April 8, 2021 7:41 pm

    Does the LGS claim work and avoid eligibility doctrine?

    Short answer: No.

    Again, the issue is not ANY type of logic or plain claiming. TO think so is to ignore the elephant that pretext is happening.

    The answer – the ONLY answer – is to punch the pretext ‘bully’ in the nose.

    It happened in 1952.
    It needs to happen again – this time with more force.

  18. Pro Say April 8, 2021 8:52 pm

    Thanks Joachim — interesting claiming approach.

    Sadly for America, unless what Anon says (currently @ 15) comes to pass, the CAFC will reach into any specifications which has such claims and proclaim (in their best Aflac! Aflac! voice) “abstract! abstract!” (while silently thinking to themselves: “you can’t fool us . . . you, you . . . scrivener, you!”).

    China silently cheers with every baloney 101 rejection the CAFC makes.

  19. Joachim Martillo April 9, 2021 1:17 am

    A few years ago I ran the LGS claim by a CAFC judge, whom I can’t name because of the confidentiality rules of the meeting I was attending.

    The Judge told me that is seemed like a claim to physical structure and that it might overcome abstract idea doctrine, but he would not know until he saw an actual LGS claim. He was sure that if I ever used such a claim, it would be rejected and then eventually be appealed to the CAFC.

    However a panel ruled, he could foresee an en banc hearing, which would then be followed by a petition for writ of certiorari and then by a grant of certiorari because the new claim type was likely to pique SCOTUS’ interest.

    We agreed that SCOTUS’ likes to provide generalizing guidance and that it would be intrigued by the use of a product-by-process claim across multiple technological arts. The product-by-process claim type has been around since the 1880s but has only been used for complex molecule claiming.

    (A) If SCOTUS’ grants cert after reviewing my current petition for writ of certiorari and then rules in my favor and (B) if I manage to quiet title to the ‘161 Application in Massachusetts state court, I will revive the ‘161 Application for a 2nd time. I will then add some LGS claims and navigate them to SCOTUS to try to obtain some guidance from SCOTUS.

    It would be hard to reject a packet switch (in this case a bridge-router) by means of § 101 subject matter eligibility doctrine.

    You can find a continuation of the 1991 ‘161 Application at the following URL.

    https://patents.google.com/patent/US20120257634A1/en

  20. Anon April 9, 2021 6:38 am

    It would be hard to reject a packet switch (in this case a bridge-router) by means of § 101 subject matter eligibility doctrine.

    Same short answer: No.

    Are you forgetting that there were claims in Alice that were averred — by both parties — to be actual hardware claims?

    All claims still held to be “Abstract.”

    You are chasing fool’s gold.

  21. Joachim Martillo April 9, 2021 9:55 am

    The settlement scheme of Alice Corp. is something that could have been carried out by means of the 19th century financial district pneumatic tube mail system of either NY City or of Philadelphia and a room full of accountants and clerks, who were performing pencil-and-paper calculations.

    SCOTUS is unwilling to consider computerization of such a system an eligible invention even if the original pencil-and-paper-based system never existed or only existed in the form of a gedanken experiment (a reverse prophetic reduction to practice).

    It will be interesting to learn whether SCOTUS will dare to hold that switching digital packets (creating digital data in computer memory from received signals on one interface and then converting selfsame digital data into transmitted signals on another interface) can be envisioned in terms of a (hypothetically) previously existent pencil-and-paper calculation.

  22. Night Writer April 9, 2021 10:08 am

    @16 Joachim Martillo

    Interesting. I think the problem would be a Markmen hearing and trying to get a judge and jurors to understand this claim construction. I’ve been saying for many, many years that information processing is a physical process. People like J. Stevens believed that human thought was processed in the spirit world.

    But the core of why 101 is so wrong is that information processing is a physical process that takes time, energy, and space.

  23. TFCFM April 9, 2021 10:57 am

    The relevant difference between the (held-ineligible) claims in Stanford and the (held-eligible) claims in McRO seems pretty clear to me:

    In McRO, the claims recited an abstract calculations performed as a part of a specific, adequately disclosed process which depended critically upon how the calculations are performed, while in Stanford, claim 1 merely recited performing the abstract calculation and dependent claims merely recited using the calculated value in generic processes which are not in any way affected by how the value is calculated.

  24. Joachim Martillo April 9, 2021 12:06 pm

    @22 Night Writer

    I managed to explain to my 9-year-old physical computer structure and logical gate state structure associated with a computer program by means of the Turing Tumble toy.

    It might be somewhat strange, but the toy could probably be used by an expert in the same way in a Markman hearing to assist in explaining an LGS claim to a judge and then later to explain issues of fact to the jurors.

  25. Anon April 9, 2021 12:23 pm

    Joachim,

    You rather badly missed the point.

    No matter how “elegant” (in fact, such will likely be a detriment, as the Justices will surely look on it as merely being a scrivener’s truck), the point of the matter is that pretext is happening.

    You are not addressing the critical point that the Court is willfully engaging in pretext.

  26. Joachim Martillo April 9, 2021 3:14 pm

    As the unnamed CAFC judge told me, we won’t know how SCOTUS will view an LGS claim until the issue is fully litigated.

    It will shortly be seven years since SCOTUS ruled on Alice Corporation Pty. Ltd. v. CLS Bank International. I invented a hardware device. If the LGS claim is rejected, it’s not likely to be rejected on § 101 subject matter eligibility grounds.

    The ‘161 Application discloses physical and virtual ports and interfaces The claims refer to I/O ports, network interfaces, and well-defined data structures as well as a processor and memory. The precedent of In re Lowry, 32 F.3d 1579 (Fed Cir 1994), should apply.

    If the case is properly argued, upholding a rejection of an LGS claim, should call into question the precedent of In re Breslow, 616 F.2d 516, 521, 205 USPQ 221, 226 (CCPA 1980).

    2021 SCOTUS differs greatly from 2014 SCOTUS. Of course, at this point I do not even know whether SCOTUS will enable the quieting of title to the ‘161 Application. If title can be quieted, the ‘161 Application will have to be revived once again and reprosecuted. It will be several years before the ‘161 Application reaches the CAFC. By that time SCOTUS will probably be even more different with the replacement of perhaps two or more justices. If possible, it’s worth a shot to try to introduce the LGS claim type.

  27. Anon April 9, 2021 4:28 pm

    Joachim – you appear to be engaging in flights of fancy and even down right willful disregard of reality.

    Not know how SCOTUS will rule? This is dealing with computing – do you really not have any guess whatsoever?

    Seven years since Alice – and how many opportunities and cert denials do you need to get a clue as to how even this changed Bench approaches the critical area of innovation?

    It is absolutely quaint that you offer that In re Lowry should apply – you are correct, but that also should have applied to the objectively physical claims in Alice that were ALSO deemed to be “Abstract” (without defining that term).

    If the case is properly argued” – sorry, but you entirely miss the point now with that.

    At least have the decency to recognize that you are chasing F00l’s gold. Is it “worth a shot?” Sure. It is always worth a shot, and you never hit a home run on pitches that you do not swing at.