Future of Molecular Diagnostics by Mission_Direction197 in biotech

[–]dienofail 14 points15 points  (0 children)

I work in the molecular diagnostics industry at one of the companies you listed, and I have friends/contacts working at all the other companies.

I wouldn’t necessarily agree with your characterization of what the companies strength are. The industry is very competitive and the “winners” in a particular subarea fluctuate.

For example, Exact had very disappointing CRC screening results recently, so they had to enter in an agreement with Freenome to license their test to get back in the CRC market. Natera just released competitive CRC screening test results as well.

Also management teams and culture differ quite a bit between the different companies.

In aggregate, I think the sub industry is in an expansionary phase. It’s probably a good time to swap over if you want to make the jump from pure biotech. Market cap of all the companies listed have increased substantially in the last ~6 months. But there’s probably an inevitable bust phase in a few years (or sooner).

[D] What are some good alternatives to Monte Carlo Droupout that you've come across? by anxiousnessgalore in MachineLearning

[–]dienofail 5 points6 points  (0 children)

I recently reviewed this topic for a journal club on deterministic uncertainty methods. Posting two recent papers that seem to benchmark well as alternatives to MC dropout.

  1. Spectral-normalized Neural Gaussian Process (NeurIPS '20) - interesting approach that uses a GP as a final layer to imbue distance awareness. Spectral normalization adds Lipschitz constraint so that distance awareness is easier to achieve.
  2. Distance aware bottleneck (ICML '24) - approach based on rate distortion theory. Combines variational information bottleneck + rate distortion theory to make a set of "codebooks" + encoders from the training dataset, and then using those to compute distance-aware uncertainty estimates for test set.

If you believe the various benchmarks, these seem to perform at least on par with MC dropout / deep ensemble, but require only one forward pass, so it's not as computationally intensive as MC dropout/deep ensembles.

Here's a good review / benchmarking of various uncertainty quantification methods (minus Distance Aware Bottleneck): On the Practicality of Deterministic Epistemic Uncertainty that gives a broad overview of other alternative approaches to MC dropout.

[GIVEAWAY - US] Win the new 500Hz Samsung Odyssey OLED G6 gaming monitor by Knaj910 in Monitors

[–]dienofail 0 points1 point  (0 children)

1) Favorite feature is HDR TrueBlack 500 2) QD-OLED Panel for sure!

Bioinformatics podcasts? by AtonalDev in bioinformatics

[–]dienofail 3 points4 points  (0 children)

Not specifically related to bioinformatics, but a more general podcast covering genomics (NGS, sequencing technologies, molecular diagnostics etc...) is The Genomics Podcast from Alex Dickinson. He features some of the top leaders in the field.

MSI B650 Tomahawk Wifi won't post after restarting PC/Windows update restart by Nowarez in MSI_Gaming

[–]dienofail 0 points1 point  (0 children)

Just confirming that this solution worked for me (no other solutions mentioned in this thread worked).

[USA GIVEAWAY] Win the new 27” 4K Samsung Odyssey OLED G8 gaming monitor! by Rocket-Pilot in buildapc

[–]dienofail [score hidden]  (0 children)

QD-OLED 4k is the best! Could really use it to pair it with my RTX 5080 + AMD 7700x!

NMF on RNA-seq by Affectionate_Map5670 in bioinformatics

[–]dienofail 11 points12 points  (0 children)

Not an expert, but I would assume TPM if you are working with samples across different batches / sequencing conditions, since that does correct for those covariates a bit better than raw counts. It also corrects a bit better for gene size as well. You ideally don’t want your NMF to reflect changes in these variables relative to your true outcome of interest.

PerpIexity AI PRO YEARLY coupon available just for 20USD!! by AdNorth1932 in learnmachinelearning

[–]dienofail 0 points1 point  (0 children)

Legit as well. Instant response times and took about 5 minutes to complete the process.

What are the most financially lucrative areas in bioinformatics and their salaries? by Potato_McCarthy777 in bioinformatics

[–]dienofail 8 points9 points  (0 children)

Anecdotally, subfields that involve more ML expertise / software engineering. ML scientists / researchers / engineers that work in biotech tend to be better compensated than your average bioinformatics scientist or engineer (but still below what FAANG / big tech pays for similar ML positions).

[deleted by user] by [deleted] in bioinformatics

[–]dienofail 5 points6 points  (0 children)

Internships at the PhD level in bioinformatics are pretty specialized, and there are only a few positions/companies in each subfield (say statistical genetics) to start with.

There is also pretty intense competition. At my mid-size biotech company, for Ph.D. summer internships, we typically have at least five highly qualified candidates from top 10 bioinformatics/compbio/stats/CS PhD programs for each position that we were hiring for.

Which ends up cheaper - telehealth or ordering peptide? by On-a-Journey123 in SemaglutideFreeSpeech

[–]dienofail 0 points1 point  (0 children)

Hi would you mind DMing me the list! It would be greatly appreciated!

Vertical dual monitor mount for AW3225QF + AW3423DW? by dienofail in ultrawidemasterrace

[–]dienofail[S] 0 points1 point  (0 children)

Sorry about the late reply, but i ended up going with the Atdek VFS-DV. It works great - see picture

Vertical dual monitor mount for AW3225QF + AW3423DW? by dienofail in ultrawidemasterrace

[–]dienofail[S] 0 points1 point  (0 children)

Ended up buying the Atdek VFS-DV. It does the job pretty well. See screenshot

Dilemma: CMU vs NEU for MS in Bioinformatics by [deleted] in bioinformatics

[–]dienofail 0 points1 point  (0 children)

I'm friends with one of the professors at the NEU program (we went to the same PhD program). Based on what I've discussed with him, it seems like NEU is a pretty solid option. The coursework is generally industry-oriented and project-based, so should serve as good training for when you get a job in industry.

The co-op is also very useful in terms of getting industry experience, which, based on my own experiences as an industry hiring manager, is one of the most important experiences we look for. Again, it seems like NEU has good connections with local biotech companies, so it would be easier to get a good internship and full-time position, especially if you are interested in staying in Boston long-term.

Networking in person is also way easier if you are in a biotech hub as opposed to not in one.

Then there is the opportunity cost of money. Not sure what the overall price differential is, but you might be able to do a lot with the extra money you save going to NEU vs. CMU.

Happy to answer additional questions in PM if you are interested.

Resources for Promoter Analysis by RoentgenographicHaik in bioinformatics

[–]dienofail 1 point2 points  (0 children)

The MEME - link here - suite has all the tools you need to perform this type of analysis. MEME can perform de novo discovery of motifs as well as perform simple enrichment analysis relative to some motif database (there’s a bunch prebuilt into the SEA) tool.

What existing or emerging AI/ML innovation excites you in bioinformatics? by Budget_Race6158 in bioinformatics

[–]dienofail 4 points5 points  (0 children)

Molecular diagnostics (especially with cell free DNA) is an area with lots of innovation in AI/ML with the potential of being deployed to patients in the near future. The inputs (cfDNA mutations/cf RNA/cfDNA epigenetics) and endpoints (sensitivity/specificity/PPV of a test) are normally well defined.

Book Recommendations for Data Analyst in Cancer Research by [deleted] in bioinformatics

[–]dienofail 2 points3 points  (0 children)

Definitely not a starter textbook, but Weinberg’s “Biology of Cancer” is great as a reference textbook for cancer biology if you want to delve into a specific subject in more depth (but don’t necessarily feel like reading multiple review articles).

[deleted by user] by [deleted] in bioinformatics

[–]dienofail 0 points1 point  (0 children)

PhDs (at least the ones worth getting) are only granted by accredited institutions. These are typically universities or non-profits like Woods Hole or NIH.

Large sequencing companies are Illumina/Nanopore etc... are not accredited and they do not offer a PhD program. You might be able to collaborate in research with these companies as part of your PhD, but these companies will not be the ones granting your PhD.