linkstream2 microblog

Quantifying the local resolution of #cryoEM density maps
https://www.Nature.com/articles/nmeth.2727 “Theory…based on the following idea: a L Angstrom feature exists at a pt…if a 3D local sinusoid of wavelength L is statistically detectable above noise at that point.”

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We propose a mathematical theory and an efficient algorithm for measuring local resolution that address all of the above limitations. The theory (Online Methods) is based on the following idea: a λ-Å feature exists at a point in the volume if a three-dimensional (3D) local sinusoid of wavelength λ is statistically detectable above noise at that point. A likelihood-ratio hypothesis test of the local sinusoid versus noise can detect this feature at a given P value (typically P = 0.05). We define the local resolution at a point as the smallest λ at which the local sinusoid is detectable, and we account for multiple testing with an FDR procedure.
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New Theory Cracks Open the Black Box of #DeepLearning
https://www.QuantaMagazine.org/new-theory-cracks-open-the-black-box-of-deep-learning-20170921/ Highlights the importance of a compression phase for generalization

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“Then learning switches to the compression phase. The network starts to shed information about the input data, keeping track of only the strongest features — those correlations that are most relevant to the output label. This happens because, in each iteration of stochastic gradient descent, more or less accidental correlations in the training data tell the network to do different things, dialing the strengths of its neural connections up and down in a random walk. This
randomization is effectively the same as compressing the system’s representation of the input data. As an example”
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Why these powerful health care gurus left the East Coast for California https://www.StatNews.com/2017/11/06/california-startup-culture/ Quotes T Insel, ex-director of NIMH: “What I was doing was providing lots of additional funding to people whose major goal was to get a paper in Nature & get tenure.”

““What I was doing was providing lots of additional funding to people whose major goal was to get a paper in Nature and get tenure.” Dr. Tom Insel, Mindstrong Health co-founder”

Reading by the Numbers: When #BigData Meets Literature
https://www.NYTimes.com/2017/10/30/arts/franco-moretti-stanford-literary-lab-big-data.html Distant reading as a complement to close reading for literary texts. Perhaps a useful dichotomy for biosequences too!

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“Literary criticism typically tends to emphasize the singularity of exceptional works that have stood the test of time. But the canon, Mr. Moretti argues, is a distorted sample. Instead, he says, scholars need to consider the tens of thousands of books that have been forgotten, a task that computer algorithms and enormous digitized databases have now made possible.

“We know how to read texts,” he wrote in a much-quoted essay included in his book “Distant Reading,” which won the 2014 National Book Critics Circle Award for Criticism. “Now let’s learn how to not read them.””

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Cancer’s Invasion Eqn, by @DrSidMukherjee
https://www.NewYorker.com/magazine/2017/09/11/cancers-invasion-equation terms: Soil-v-seed, metastasis matching + overcoming “denominator” problem

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“This is medicine’s “denominator problem.” The numerator is you—the person who gets ill. The denominator is everyone at risk, including all the other passengers who were exposed. Numerators are easy to study. Denominators are hard. Numerators come to the doctor’s office, congested and miserable. They get blood tests and prescriptions. Denominators go home from the subway station, heat up dinner, and watch “The Strain.” The numerator persists. The denominator vanishes.” “}}

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But it’s the very specificity of genomic data that threatens privacy. Although most genomic databases strip away any information linking a name to a genome, such information is very hard to keep anonymous. “I’m not convinced you can truly de-identify the data,” says Mark Gerstein, a Yale professor who studies large genetic databases and is a fierce privacy advocate. He is concerned about whether even the most cutting-edge protections can safeguard personal data. “I am not a believer that large-scale technical solutions or ‘super-encryption’ will solely work,” he says. “There also needs to be a process for credentialing the individuals who access this data.”
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Threats to privacy could multiply once there is an active market for genetic data. Wood speculates that it could be valuable to life insurance companies, which could use it to raise your premiums; or it could become a tool for those who want to prove or disprove paternity. White nationalist groups, who have become preoccupied with genetic testing, might find a way to weaponize the ancestry data the tests can show. It would not be the first time genetic information was used against a race or races. “Genetics has a very troubled history, from Darwin on,” says Yale’s Mark Gerstein.
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Yet Columbia’s Yaniv Erlich and others, including Church, fear differential privacy could compromise biomedical research, with smudged data making it harder to get clear results. Mark Gerstein at Yale believes that scientists would be better off testing hypotheses on small amounts of publicly available but pure data, even if it’s not representative of the overall population, rather than using larger quantities of imperfect data.
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Is Genetic Privacy a Myth?
http://protomag.com/articles/genetic-privacy-myth
Genetic tests and genome sequencing are generating terabytes of sensitive private data. How can they be kept safe?

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“The 4D Nucleome, a major research consortium funded by the US National Institutes of Health (NIH), is now requiring that all manuscripts related to its US$120-million, five-year programme are posted to an online preprint server ahead of peer review. And a privately funded, US$600-million biomedical research initiative in California is considering whether to demand its investigators do the same.”
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http://www.nature.com/news/big-biology-projects-warm-up-to-preprints-1.21074

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“The Advanced Protection Program incorporates a physical security key (a small USB or wireless device that costs around $25) to protect against phishing. The key, which participants need to buy themselves, uses public-key cryptography and digital signatures. Without the key, even someone with your password would be unable to access your account. Advanced Protection limits your Google data access to only Google apps and adds additional safeguards in the account recovery process to prevent someone from social engineering their way into your account. It also performs additional scans on files and attachments to ensure no malware is piggybacking on the download.”
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#Google’s New Super-Secure Email Is Designed For High-Profile Targets http://www.Slate.com/blogs/future_tense/2017/10/17/google_introduces_super_secure_email_to_prevent_high_profile_hacks_could.html Appears to be open to all. Anyone tried this?

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"Wikipedia is one of the world’s most popular websites, but scientists rarely cite it in their papers. Despite this, the online encyclopedia seems to be shaping the language that researchers use in papers, according to an experiment showing that words and phrases in recently published Wikipedia articles subsequently appeared more frequently in scientific papers"
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“Thompson and co-author Douglas Hanley, an economist at the University of Pittsburgh in Pennsylvania, commissioned PhD students to write 43 chemistry articles on topics that weren’t yet on Wikipedia. In January 2015, they published a randomized set of half of the articles to the site. The other half, which served as control articles, weren’t uploaded.
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Using text-mining techniques to measure the frequency of words, they found that the language in the scientific papers drifted over the study period as new terms were introduced into the field. This natural drift equated to roughly one new term for every 250 words, Thompson told Nature. On top of those natural changes in language over time, the authors found that, on average, another 1 in every 300 words in a scientific paper was influenced by language in the Wikipedia article.”

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#Wikipedia shapes lang. in science https://www.Nature.com/news/wikipedia-shapes-language-in-science-papers-1.22656 Seeding it with new pages & watching them evolve (v ctrls) as a type of soc. expt

https://productforums.google.com/forum/#!topic/chrome/PaMriZC-Kuo

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OK — This isn’t a real fix, but I turned off "swipe between pages" in System Preferences -> Trackpad -> More Gestures.

Apparently "between pages" of a PDF or whatever is seen as back-forward in the browser. I wish you could keep the page turning and kill the browsing hiccup.

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