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seamossfet commented on A Primer on Molecular Dynamics   owlposting.com/p/a-primer... · Posted by u/EvgeniyZh
seamossfet · 6 months ago
Great write up, we're working on a drug discovery CAD tool and MD has been one of our focal points. Extremely challenging and fun problem to work on!

What complicates things is the experimental data we get back from labs to validate MD behavior is extremely tricky to work with. Most of what we're working with is NMR data which shows flexibility in areas of the proteins, but even then we're left with these mathematical models to attempt to "make sense" of the flexibility and infer dynamics from that. Sometimes it feels like an art and a science trying to get meaningful insights for lab data like this.

It's extremely difficult to experimentally verify any MD model since, as mentioned in the article, most of the data we're working with are static mugshots in the form of crystal structures.

seamossfet commented on Aspartame aggravates atherosclerosis through insulin-triggered inflammation   cell.com/cell-metabolism/... · Posted by u/tu7001
lotsofpulp · 9 months ago
https://pmc.ncbi.nlm.nih.gov/articles/PMC10096725/

>People with little saliva and a habit of frequently consuming acidic beverages are at increased risk for enamel erosion. The basic recommendations are to drink water as the first choice and eat fresh fruits as an integral part of a healthy and balanced diet.

>Health professionals should motivate the population to change their behavior regarding the consumption of acidic drinks, and recommendations should be made at the policy level to discourage the consumption of sugary drinks. Interventions that would improve oral health and overall health are widely available.

seamossfet · 9 months ago
From that same study:

>The increased amounts of calcium, phosphate, and fluoride in the drinks limited the severity of erosion by changing the solubility of the enamel [82]. The decline in enamel’s surface microhardness and mineral loss were both dramatically halted by the addition of CaGP to the carbonated drinks.

Most seltzer water has fluoride in it, and your tap water has fluoride in it (if you're making your own at home).

Also the methodology in this study was purely in vitro, not real world conditions. Notably, the lack of saliva.

>Under normal circumstances, human saliva forms a physical barrier, a film, and prevents direct contact between the tooth enamel surface and acidic beverages, thus protecting teeth from erosive attack by acids [45,84,85,86]. However, the erosion tests were carried out without saliva

Also, seems like the study was more on soft drinks in particular and not "other acidic drinks" which may include seltzer water.

>Soft drink consumption during meals was linked to mild to severe tooth damage [65]. No matter when they were consumed, other acidic meals and beverages were not linked to tooth damage [40].

Anyway, net is this: I'm not saying sparkling water carries absolutely no risk, but linking a study like this and cherry picking quotes to make it sound like sparkling water is going to destroy your teeth is misleading.

If drinking sparkling water helps you kick your soda habit, please definitely make the switch. It's so much better for you. The increased risk from drinking sparkling water compared to still water is not worth worrying about if sparkling water provides a quality of life increase for you.

Everything in healthcare is about moderated risk and counterbalancing it against lifestyle.

seamossfet commented on Product Development Processes You Might Not Have Heard of (2022)   departmentofproduct.com/b... · Posted by u/lgunsch
adamtaylor_13 · 10 months ago
My team (3 devs) has been using Shape Up since January and it’s been amazing. I don’t think I can ever go back to scrum.

It allows devs to be creative, do what needs to be done, and ship a real feature. All without any product managers, and zero meetings.

Corporate companies could never imagine not counting all their beans, but man it is so freeing if you have the option.

seamossfet · 10 months ago
Same! I run the engineering department for a medium sized software consultancy, we're on contract with several large enterprises. In terms of output, we run circles around their internal delivery teams. Not because our engineers are better than them, we've just fully embraced shape up as our development process.

This has also let us bid on projects as fixed rate instead of T&M since we budget time as appetite instead of how long we think something will take to build.

There are still some hurdles we have to overcome, like we can still run into unexpected things that we didn't know about during the betting process, but deep behind the philosophy of Shape Up it feels like something that translates extremely well to more creative R&D development projects like what we do.

seamossfet commented on Reddit is mass purging NSFW subs   old.reddit.com/r/BannedSu... · Posted by u/morkalork
seamossfet · 10 months ago
Seems like they're protecting themselves from the current administration. Wonder if they'll say anything on this or if they're hoping it slides under the radar.
seamossfet commented on Show HN: DeepSeek Your HN Profile   hn-wrapped.kadoa.com/... · Posted by u/hubraumhugo
seamossfet · a year ago
It told me F# is my favorite language and I am personally offended by that.
seamossfet commented on The Untouched Goldmine of F#   rm4n0s.github.io/posts/7-... · Posted by u/rmanolis
seamossfet · a year ago
God I remember having to deal with F# when I was an intern, what a nightmare. It's like the worst parts of Java and C# smashed into one esoteric language.
seamossfet commented on Venvstacks: Virtual Environment Stacks for Python   lmstudio.ai/blog/venvstac... · Posted by u/ingve
seamossfet · a year ago
It's crazy to me that in 2025 we still haven't figured out python dependency management
seamossfet commented on PayloadCMS: Open-Source, Fullstack Next.js Framework   github.com/payloadcms/pay... · Posted by u/stefankuehnel
seamossfet · a year ago
How does this handle threejs content? I've been looking for a good CMS for making interactive articles.
seamossfet commented on Differential Transformer   arxiv.org/abs/2410.05258... · Posted by u/weirdcat
phire · a year ago
Noise cancelling headphones are probably the wrong analogy here.

The better example is the differential signalling used in professional audio and many digital signaling protocols like Ethernet, HDMI and USB.

Instead of using one wire, referencing to ground, they send the signal as the difference between both wires. Both wires end up carrying the same signal with inverted polarity. Because both wires are running next to each-other any external noice will be applied to both equally.

The voltage will change, but the difference in voltage between both wires is untouched. And when you subtract the two voltages at the receiver end, any noise simply gets subtracted out.

seamossfet · a year ago
I think when they bring up differential amplifiers they're referring more to the DSP technique of how headphone noise cancelling works but the actual electrical properties of how a differential amplifier does that muddies the message a bit.

It sort of feels closer to heterodyning and "demodulating" the signal encoded in the softmax. Those tiny little errors we're trying to denoise with this technique are almost closer to carrier waves (when encoded to softmax) than noise imo. This wouldn't get rid of noise in the training data or noise in the dimensionality of the key / value space. It's really only removing noise introduced by the process itself.

seamossfet commented on Differential Transformer   arxiv.org/abs/2410.05258... · Posted by u/weirdcat
msoad · a year ago
Like most things in this new world of Machine Learning, I'm really confused why this works?

The analogy to noise-cancelling headphones is helpful but in that case we clearly know which is signal and which is noise. Here, if we knew why would we even bother to the noise-cancelling work?

seamossfet · a year ago
It sounds like they're just splitting the query / key space down the middle. We don't know which dimensions are encoded in each matrix, but they're assuming the "noise" introduced in one query / key space is equivalent to noise introduced in the other space.

If that is the case, then the "signal" in this case would be the softmax that encodes the dimensions captured by the query / key space. Since the noise ideally is the same in both softmax encodings, subtracting them should "cancel out" the noise.

u/seamossfet

KarmaCake day31January 21, 2023View Original