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Should I file a patent before submitting a paper, or after?

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Manipal Academy of Higher Education · Posted
Chemistry Renewable Energy

Context

I am preparing to submit my first research paper to a Q1 journal (IEEE Transactions on Neural Networks). This will be my first submission and I am unsure about a few things.

Questions:

  1. Is it mandatory to submit the code and dataset along with the paper, or is that only required upon acceptance?
  2. My results show a 2.3% improvement over the SOTA baseline. Is that considered significant enough?
  3. How long does the review process typically take for IEEE Transactions journals?

I have read the author guidelines but they are somewhat ambiguous on point 1. Would appreciate guidance from anyone who has published in similar venues.

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73 Replies

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0
Lalitha Mohan Active 230 pts · Accepted answer

The IEEE TPAMI turnaround in my case was 7 months for the first review. Plan accordingly.

0
Jagdish Rawat · Accepted answer

Highly recommend checking out the PMRF portal for the actual numbers.they update the stipend structure annually.

0
Dinesh Kulkarni Distinguished 730 pts · Accepted answer

+1 to everything said above. My experience was identical.

0
Meghana Rao Growing 170 pts · Accepted answer

When you say 'multiple runs with confidence intervals', do you mean running the full training pipeline multiple times with different random seeds and reporting mean ± std? Or something more statistically rigorous?

0
Divya Krishnan Growing 85 pts · Accepted answer

For Zotero vs BibTeX management, I moved to Zotero + Better BibTeX 3 years ago and have not looked back.

My workflow:

  1. Zotero browser connector captures papers instantly from ArXiv, Google Scholar, ACM DL, IEEE Xplore
  2. Better BibTeX generates a clean .bib file that auto-updates whenever I add a paper
  3. Overleaf directly pulls from the .bib file via Dropbox sync

One tip: create a Zotero collection per paper/project. When you export the .bib, export only that collection to keep it clean.

0
Replying to Divya Krishnan
Divya Krishnan Growing 85 pts · Accepted answer

Really appreciate you taking the time to write this out in detail. This is going straight into my research notes.

0
Replying to Divya Krishnan
Chetan Jain Growing 100 pts · Accepted answer

I am in a very similar situation. Would you be willing to share the outline of your PMRF proposal? Not the content.just the section headings and approximate word allocation.

0
Replying to Divya Krishnan
Divya Krishnan Growing 85 pts · Accepted answer

Seconding the recommendation for Zotero. Game changer for managing references across multiple projects.

0
Xena D'Souza Starting 25 pts · Accepted answer

Seconding the recommendation for Zotero. Game changer for managing references across multiple projects.

0
Replying to Xena D'Souza
Ishaan Verma Growing 60 pts · Accepted answer

This is really helpful context. One more question: for the ethics committee approval, does the institution where the data is collected or the institution where the analysis is performed need to be the primary ethics approver?

0
Replying to Xena D'Souza
Ishaan Verma Growing 60 pts · Accepted answer

This is exactly what I needed to hear. One clarifying question: you mentioned FedProx handles non-IID data better.does that mean I should switch to FedProx by default, or only if I observe poor convergence with FedAvg first?

0
Rohan Desai Distinguished 950 pts · Accepted answer

The ethics review situation in Indian universities is actually more complex than most people realize.

There is no uniform national framework equivalent to the US Common Rule. Each institution has its own Institutional Ethics Committee (IEC) or Institutional Review Board (IRB).

For anonymous survey research with no identifiable data and no vulnerable populations: most Indian IECs would classify this as exempt, but 'exempt' still needs a formal determination from the IEC.it is not self-certifying.

My practical advice: go to your institution's research ethics office now, describe what you did, and request an exempt determination in writing. Better to have documentation than to discover the issue during thesis review.

0
Meghana Rao Growing 170 pts · Accepted answer

As a senior faculty member (25 years in the system), I want to offer a different perspective. Yes, the pressures are real. But I have also seen the other side: students who produce excellent work, publish honestly, and build reputations over time. The system is imperfect but not entirely broken.

What has actually helped my students: choosing venues carefully (a few strong papers rather than many weak ones), developing genuine collaborations rather than transactional coauthorships.

0
Replying to Meghana Rao
Geeta Rao · Accepted answer

Just to make sure I understand the Zotero workflow correctly.is the .bib file synced to Overleaf automatically every time you add a new paper, or do you need to trigger an export manually?

0
Replying to Meghana Rao
Rekha Shetty Starting 40 pts · Accepted answer

When you say 'multiple runs with confidence intervals', do you mean running the full training pipeline multiple times with different random seeds and reporting mean ± std? Or something more statistically rigorous?

0
Replying to Meghana Rao
Revathi Chandrasekaran Active 410 pts · Accepted answer

For longitudinal data with missing values, mixed-effects models handle this more gracefully than imputation in most cases.

0
Deepa Krishnamurthy Distinguished 810 pts · Accepted answer

For Zotero vs BibTeX management, I moved to Zotero + Better BibTeX 3 years ago and have not looked back.

My workflow:

  1. Zotero browser connector captures papers instantly from ArXiv, Google Scholar, ACM DL, IEEE Xplore
  2. Better BibTeX generates a clean .bib file that auto-updates whenever I add a paper
  3. Overleaf directly pulls from the .bib file via Dropbox sync

One tip: create a Zotero collection per paper/project. When you export the .bib, export only that collection to keep it clean.

0
Xena D'Souza Starting 25 pts · Accepted answer

Seconding the recommendation for Zotero. Game changer for managing references across multiple projects.

0
Amit Joshi Starting 15 pts · Accepted answer

This is a known issue with XLM-R on code-mixed data. The MuRIL preprint has a section specifically comparing these.

0
Wajid Khan Growing 110 pts · Accepted answer

I can answer your question about IEEE Transactions review timelines from my experience submitting to IEEE TNNLS.

For Q1 IEEE journals, expect:

  • Initial desk review: 2–4 weeks
  • Full peer review: 3–6 months
  • Major revision decision: another 2–3 months for re-review

As for code and data, most IEEE journals now request code upon acceptance, not submission. Regarding your 2.3% improvement.that is borderline. You will need very strong experimental rigor: multiple runs, confidence intervals, and significance tests.

0
Rekha Shetty Starting 40 pts · Accepted answer

Thank you for this detailed answer! A quick follow-up: when you mention cosine learning rate with warm-up, are you warming up the LoRA parameters specifically or the entire model including the frozen backbone?

0
Lakshmi Devi Growing 75 pts · Accepted answer

The ethics review situation in Indian universities is actually more complex than most people realize.

There is no uniform national framework equivalent to the US Common Rule. Each institution has its own Institutional Ethics Committee (IEC) or Institutional Review Board (IRB).

For anonymous survey research with no identifiable data and no vulnerable populations: most Indian IECs would classify this as exempt, but 'exempt' still needs a formal determination from the IEC.it is not self-certifying.

My practical advice: go to your institution's research ethics office now, describe what you did, and request an exempt determination in writing. Better to have documentation than to discover the issue during thesis review.

0
Chirag Mehta Starting 15 pts · Accepted answer

Flower (flwr) is the most actively maintained and research-friendly federated learning framework right now. My group has been using it for 18 months on a healthcare project with 4 hospital sites.

Strengths:

  • Clean simulation API that lets you test on a single machine before deploying
  • Good support for custom aggregation strategies (FedProx, FedNova)
  • Active Discord community with quick responses from the maintainers

For non-IID data specifically, look at the FedProx strategy.it handles heterogeneous data distributions much better than FedAvg.

0
Quamar Ahmed Growing 65 pts · Accepted answer

I'd push back slightly on the idea that industry collaboration is universally beneficial for academic research. The incentive misalignment is real.

Industry partners want deliverables on a schedule. Academic research is often exploratory and unpredictable. When the two clash, it is usually the researcher who has to compromise.either by rushing results, constraining publication, or steering away from results that are inconvenient for the sponsor.

This doesn't mean industry collaboration is bad. But the terms matter enormously. IP rights, publication rights, and the ability to pursue negative results should be negotiated upfront and protected in writing.

0
Replying to Quamar Ahmed
Geeta Rao · Accepted answer

Just to make sure I understand the Zotero workflow correctly.is the .bib file synced to Overleaf automatically every time you add a new paper, or do you need to trigger an export manually?

0
Meghana Rao Growing 170 pts · Accepted answer

Highly recommend checking out the PMRF portal for the actual numbers.they update the stipend structure annually.

0
Shiva Prasad Active 480 pts · Accepted answer

If you are not already using a reading group format with your students, I would strongly recommend it. Forces everyone to articulate what they read.

0
Sowmya Narayanan Active 310 pts · Accepted answer

If you are not already using a reading group format with your students, I would strongly recommend it. Forces everyone to articulate what they read.

0
Replying to Sowmya Narayanan
Revathi Chandrasekaran Active 410 pts · Accepted answer

The IEEE TPAMI turnaround in my case was 7 months for the first review. Plan accordingly.

0
Replying to Sowmya Narayanan
Lakshmi Devi Growing 75 pts · Accepted answer

Highly recommend checking out the PMRF portal for the actual numbers.they update the stipend structure annually.

0
Rekha Shetty Starting 40 pts · Accepted answer

I can answer your question about IEEE Transactions review timelines from my experience submitting to IEEE TNNLS.

For Q1 IEEE journals, expect:

  • Initial desk review: 2–4 weeks
  • Full peer review: 3–6 months
  • Major revision decision: another 2–3 months for re-review

As for code and data, most IEEE journals now request code upon acceptance, not submission. Regarding your 2.3% improvement.that is borderline. You will need very strong experimental rigor: multiple runs, confidence intervals, and significance tests.

0
Karthik Rajan Growing 180 pts · Accepted answer

The IEEE TPAMI turnaround in my case was 7 months for the first review. Plan accordingly.

0
Replying to Karthik Rajan
Rohan Desai Distinguished 950 pts · Accepted answer

Check whether your institution has a Springer/Elsevier waiver agreement.many NITs and IITs do.

0
Replying to Karthik Rajan
Dinesh Kulkarni Distinguished 730 pts · Accepted answer

This is exactly what I needed to hear. One clarifying question: you mentioned FedProx handles non-IID data better.does that mean I should switch to FedProx by default, or only if I observe poor convergence with FedAvg first?

0
Replying to Karthik Rajan
Indira Balan · Accepted answer

Open access is the right direction but the APCs are prohibitively expensive for many Indian researchers without institutional funding.

0
Yogesh Pandey Growing 70 pts · Accepted answer

Overleaf + GitHub integration is underrated. You get version control and collaboration in one place.

0
Eshan Patil Growing 70 pts · Accepted answer

FDR (Benjamini-Hochberg) is widely accepted and preferable to Bonferroni when you have many tests and limited power. The key is to be explicit about which correction you used and why.

On replication: No independent cohort is a genuine limitation but not a dealbreaker for rare disease research, where cohort availability is a known constraint. Many high-quality papers acknowledge this and still get published in good journals. Frame it as future work.

Power analysis: Yes, report it. Showing you are aware of the limitation is better than not mentioning it.

0
Replying to Eshan Patil
Ganesh Menon Growing 140 pts · Accepted answer

Open access is the right direction but the APCs are prohibitively expensive for many Indian researchers without institutional funding.

0
Replying to Eshan Patil
Amit Joshi Starting 15 pts · Accepted answer

If you are not already using a reading group format with your students, I would strongly recommend it. Forces everyone to articulate what they read.

0
Nandita Ghosh Distinguished 720 pts · Accepted answer

Strongly agree with the point about choosing venues carefully. One paper in NeurIPS > five papers in obscure workshops.

0
Rekha Shetty Starting 40 pts · Accepted answer

The short answer: it depends heavily on the journal and field, but here is a general framework.

If your null result is well-powered and the hypothesis was reasonable: Absolutely publish it. Null results in well-designed studies are as valuable as positive results. Journals like PLOS ONE explicitly welcome them.

If your study is underpowered: Be transparent about it. Report effect sizes and confidence intervals, not just p-values. A small, underpowered study with honest reporting is still a contribution.

What kills papers is when limitations are obvious but the authors have not addressed them.

0
Vikram Bhatia Active 420 pts · Accepted answer

Seconding the recommendation for Zotero. Game changer for managing references across multiple projects.

0
Replying to Vikram Bhatia
Pooja Nambiar Growing 115 pts · Accepted answer

For longitudinal data with missing values, mixed-effects models handle this more gracefully than imputation in most cases.

0
Replying to Vikram Bhatia
Sanjay Kumar Growing 145 pts · Accepted answer

Seconding the recommendation for Zotero. Game changer for managing references across multiple projects.

0
Neha Agarwal Growing 90 pts · Accepted answer

For longitudinal data with missing values, mixed-effects models handle this more gracefully than imputation in most cases.

0
Uday Bose Starting 5 pts · Accepted answer

As a senior faculty member (25 years in the system), I want to offer a different perspective. Yes, the pressures are real. But I have also seen the other side: students who produce excellent work, publish honestly, and build reputations over time. The system is imperfect but not entirely broken.

What has actually helped my students: choosing venues carefully (a few strong papers rather than many weak ones), developing genuine collaborations rather than transactional coauthorships.

0
Replying to Uday Bose
Xena D'Souza Starting 25 pts · Accepted answer

Thank you for this detailed answer! A quick follow-up: when you mention cosine learning rate with warm-up, are you warming up the LoRA parameters specifically or the entire model including the frozen backbone?

0
Ishaan Verma Growing 60 pts · Accepted answer

I think you are conflating two separate problems here. The publish-or-perish culture creates pressure, yes.but the solution is not to criticize researchers who are navigating an unfair system. The real problem is with evaluation committees who treat publication count as a proxy for research quality. Fix the evaluation, and the incentives change.

Also worth noting: open review has been implemented in some fields and has its own problems. It can disadvantage early-career researchers who fear retaliation from senior colleagues they have reviewed critically.

0
Preethi Anand Distinguished 690 pts · Accepted answer

I have successfully received PMRF (lateral entry, second year). Happy to share what worked in my proposal.

On the research proposal:

  • 60–70% technical approach, 30% context and impact
  • Preliminary results absolutely help. Coursework projects are fine if genuinely relevant
  • The societal impact section should be substantive.PMRF is a national initiative; reviewers want to see why this matters

On citations: Yes, cite your MTech thesis. Framing your PhD as an extension of prior work you did shows continuity of thought.

0
Replying to Preethi Anand
Rohan Desai Distinguished 950 pts · Accepted answer

Thank you for the honest take. This is the kind of answer I was looking for.not the sanitized version.

0
Preethi Anand Distinguished 690 pts · Accepted answer

I found that writing a paper abstract first (before the paper) and then reverse-engineering the paper from the abstract helped with clarity enormously.

0
Meena Sharma · Accepted answer

Could you clarify what you mean by results-blind review? I have heard of it but never understood how it works in practice. Wouldn't reviewers need to see results to evaluate whether the methodology is sound?

0
Om Prakash Growing 55 pts · Accepted answer

Thank you for this detailed answer! A quick follow-up: when you mention cosine learning rate with warm-up, are you warming up the LoRA parameters specifically or the entire model including the frozen backbone?

0
Replying to Om Prakash
Ishaan Verma Growing 60 pts · Accepted answer

CSIR-UGC NET preparation: past papers are the most important resource. Everything else is secondary.

0
Replying to Om Prakash
Admin NITK · Accepted answer

Thank you for the honest take. This is the kind of answer I was looking for.not the sanitized version.

0
Replying to Om Prakash
Xena D'Souza Starting 25 pts · Accepted answer

This question comes up a lot. The answer really depends on your specific field and what your committee values.

0
Ravi Patel Starting 25 pts · Accepted answer

This is exactly what I needed to hear. One clarifying question: you mentioned FedProx handles non-IID data better.does that mean I should switch to FedProx by default, or only if I observe poor convergence with FedAvg first?

0
Ishaan Verma Growing 60 pts · Accepted answer

Check whether your institution has a Springer/Elsevier waiver agreement.many NITs and IITs do.

0
Chetan Jain Growing 100 pts · Accepted answer

I'd push back slightly on the idea that industry collaboration is universally beneficial for academic research. The incentive misalignment is real.

Industry partners want deliverables on a schedule. Academic research is often exploratory and unpredictable. When the two clash, it is usually the researcher who has to compromise.either by rushing results, constraining publication, or steering away from results that are inconvenient for the sponsor.

This doesn't mean industry collaboration is bad. But the terms matter enormously. IP rights, publication rights, and the ability to pursue negative results should be negotiated upfront and protected in writing.

0
Wajid Khan Growing 110 pts · Accepted answer

This is a known issue with XLM-R on code-mixed data. The MuRIL preprint has a section specifically comparing these.

0
Priya Nair · Accepted answer

The IEEE TPAMI turnaround in my case was 7 months for the first review. Plan accordingly.

0
Replying to Priya Nair
Rekha Shetty Starting 40 pts · Accepted answer

Open access is the right direction but the APCs are prohibitively expensive for many Indian researchers without institutional funding.

0
Replying to Priya Nair
Nandita Ghosh Distinguished 720 pts · Accepted answer

Thank you! The reference to MuRIL is particularly useful.I had not considered it as an alternative to XLM-R for Indic languages.

0
Replying to Priya Nair
Zara Hussain Growing 55 pts · Accepted answer

Just to make sure I understand the Zotero workflow correctly.is the .bib file synced to Overleaf automatically every time you add a new paper, or do you need to trigger an export manually?

0
Deepa Krishnamurthy Distinguished 810 pts · Accepted answer

Strongly agree with the point about choosing venues carefully. One paper in NeurIPS > five papers in obscure workshops.

0
Sunil Bhattacharya Active 390 pts · Accepted answer

FDR (Benjamini-Hochberg) is widely accepted and preferable to Bonferroni when you have many tests and limited power. The key is to be explicit about which correction you used and why.

On replication: No independent cohort is a genuine limitation but not a dealbreaker for rare disease research, where cohort availability is a known constraint. Many high-quality papers acknowledge this and still get published in good journals. Frame it as future work.

Power analysis: Yes, report it. Showing you are aware of the limitation is better than not mentioning it.

0
Replying to Sunil Bhattacharya
Vikram Bhatia Active 420 pts · Accepted answer

This question comes up a lot. The answer really depends on your specific field and what your committee values.

0
Replying to Sunil Bhattacharya
Quamar Ahmed Growing 65 pts · Accepted answer

I found that writing a paper abstract first (before the paper) and then reverse-engineering the paper from the abstract helped with clarity enormously.

0
Replying to Sunil Bhattacharya
Admin NITK · Accepted answer

This is exactly what I needed to hear. One clarifying question: you mentioned FedProx handles non-IID data better.does that mean I should switch to FedProx by default, or only if I observe poor convergence with FedAvg first?

0
Tara Singh Starting 5 pts · Accepted answer

For longitudinal data with missing values, mixed-effects models handle this more gracefully than imputation in most cases.

0
Om Prakash Growing 55 pts · Accepted answer

The ethics review situation in Indian universities is actually more complex than most people realize.

There is no uniform national framework equivalent to the US Common Rule. Each institution has its own Institutional Ethics Committee (IEC) or Institutional Review Board (IRB).

For anonymous survey research with no identifiable data and no vulnerable populations: most Indian IECs would classify this as exempt, but 'exempt' still needs a formal determination from the IEC.it is not self-certifying.

My practical advice: go to your institution's research ethics office now, describe what you did, and request an exempt determination in writing. Better to have documentation than to discover the issue during thesis review.

0
Dinesh Kulkarni Distinguished 730 pts · Accepted answer

Respectfully, I think this framing misses the systemic dimension. Individual researchers cannot solve a collective action problem. If you submit to open-access journals and your colleague submits to Nature, your colleague gets the promotion. Until evaluation criteria change at the institutional level.which requires policy intervention.individual choices have minimal impact.

0
Jagdish Rawat · Accepted answer

When you say 'multiple runs with confidence intervals', do you mean running the full training pipeline multiple times with different random seeds and reporting mean ± std? Or something more statistically rigorous?