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Covid-19 vaccines and treatments: we must have raw data, now

bmj.com

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Re: Covid-19 vaccines and treatments: we must have raw data, now

#231

Post by throwawaygh »

rvnx wrote: post #188
throwawaygh wrote: post #134

Earlier quoted context omitted.

Why don't you include a step where you ask patients if they're ok with their medical history being put in a public s3 bucket ? I'm fully supportive of the right to pseudonymous speech, but it strikes me that you are in an awfully awkward position of speaking anonymously while demanding that you should have access a trove of patient history without signing any sort of data use agreement and without even the most basic…

Ok, why not, this is what I propose: Asking the user: "This record is going to be shared publicly, do you agree to share this information (without revealing your name and address) ? > [...] This information can help researchers, doctors and people interested into science to discover new information about drugs and diseases interaction."

And how do you ensure that statistical tests on the original data set are INVARIANT TO THE DE-ANONMYIZATION PROTOCOL WITH RESPECT TO ANY RELEVANT QUERY?

That is WAY harder that it sounds. When you add public disclosure of mismatch between results on public data and private (full) data things are even harder.

Specifically: suppose an independent researcher determines X is true via statistical test Y on the public dataset. Officials must respond, and say "True" or "False".

A small number of queries via this process can be used to infer data that makes re-identification possible. And there will be many more than a small number of queries, including from adversarial agents specifically designing queries to maximize information gain based on previous (public) revelations.

This is a game, in the game theory sense, in which the goal is to exploit the mathematical properties of statistical tests and social dynamics to force public revelations of binary assessments that yield information about individual cells or sets of cells and make re-id possible.

Have you actually studied this stuff, designed de-anonymization protocols, developed re-id threat models, thought about privacy budgets in public disclosure mandates, and at last put your reputation and your customer's privacy on the line when asserting that your statistical methods are resilient against attacks? Or are you just a jawboning know-it-all anonymous coward without any actual experience balancing privacy against public disclosure?

To be honest, all of your posts read like "just stop writing vulnerable software and then there will be no more hackers mmmkay?"

Re: Covid-19 vaccines and treatments: we must have raw data, now

#232

Post by andreskytt »

rvnx wrote: post #149
throwawaygh wrote: post #146

Earlier quoted context omitted.

Notice that this is a policy document outlining a process, and that one outcome of following that process can be not sharing the data ! It's not as simple as "follow these rules and you can share the data". It can also be "follow these rules, which tell you not to share the data". It's also possible to reach an outcome that the data can be shared but must be de-identified in a way that precludes important statistical…

The thing is; in practice, how can you re-id someone that has a very rare medical condition if you don't already know that the person has this very rare medical condition ?

What this boils down to is a set of observable factors being multiplied. Probably millions of people got the shot in August. From them, probably tens of thousands were overweight. From them, hundreds had diabetes. Add a few other factors like rough age and gender and you get to that one person along with all of their medical history. If we are not talking about the entire US but can know the state, for example, the task becomes so much easier.

Re: Covid-19 vaccines and treatments: we must have raw data, now

#233

Post by diroussel »

Fogest wrote: post #80
diroussel wrote: post #47

Earlier quoted context omitted.

I'm a pro vax person, and I've had three vaccine doses. But I have a few anti-vaxers around in friends and family, and it can be hard to argue with them that vaccines are totally safe and effective for them (not talking about the population as a whole). I would like safe and effective vaccines, and I would like to know that the vaccines I have been administered have really got the backing of truly scientific trials.…

This is my thing as well. I work at vaccine clinics and obviously am onboard with the vaccines, however I still feel bad helping administer these vaccines to people who are hesitant. Because of government vaccine mandates or employer vaccine mandates it has made some people who come in feeling "forced" to get a vaccine. And it honestly does not feel like this is the proper scientific or medical way. It sucks to give…

As far as I can see, in the UK, these adverse effects are not being logged or recorded in such a way that any analysis could be done to determine the scale, or even existence of any problem.

I heard that there was a public database in US for this sort of thing. But it has it’s own problems about data quality.

Re: Covid-19 vaccines and treatments: we must have raw data, now

#234

Post by raxxorrax »

someguydave wrote: post #79
bryanlarsen wrote: post #33

Who's responsible when it turns out that the anonymization of highly confidential patient data in the raw data is flawed, as it inevitably is?

There is a tradeoff between an individual’s absolute right to “health secrecy” and advancing treatments. I think the pendulum has swung too far towards privacy.

I disagree, I think we see a lot of condemnation for having had a treatment or not. On the contrary, we should bring privacy back and make health a private issue completely.

I also worked on medical devices and respective medical advisory boards. Getting people to share their data is just a question away. If you fail at that, I doubt any further inquiry would net any benefit.

Re: Covid-19 vaccines and treatments: we must have raw data, now

#235

Post by diroussel »

ashtonkem wrote: post #218
diroussel wrote: post #47

Earlier quoted context omitted.

I'm a pro vax person, and I've had three vaccine doses. But I have a few anti-vaxers around in friends and family, and it can be hard to argue with them that vaccines are totally safe and effective for them (not talking about the population as a whole). I would like safe and effective vaccines, and I would like to know that the vaccines I have been administered have really got the backing of truly scientific trials.…

> and it can be hard to argue with them that vaccines are totally safe and effective for them (not talking about the population as a whole). Right, and do you believe that a full release of the phase 3 trial data would convince them? I sure don't. Anti-vaxx is a fundamentally anti-expert stance, and most people have not logically convinced themselves into that position. Give them the full data set and I bet 9 out of…

I don’t believe it will convince those that don’t want to be convinced. But I want to be convinced, and I want transparency in the science that my taxes are funding and in the enlightened society in which I wish to live.

Transparency in science should include publishing raw data, as apart from re-creating the statistics in the report there is no other way the trial is repeatable.

Re: Covid-19 vaccines and treatments: we must have raw data, now

#236

Post by yread »

pfisherman wrote: post #171

Ummm… no. In IRB applications and informed consent documents you have to be very clear and specific about who you might share their data with under what circumstances. And these documents tend to be legally binding. So this editorial is kind of nutty. To give you an idea, this is kind of like asking banks to release customer account data to the public.

IRBs implement the law. Here in the Netherlands the law specifically has exceptions for releasing data if it's in the interest of public health. It's weighed against other concerns of course but it's not impossible

Re: Covid-19 vaccines and treatments: we must have raw data, now

#237

Post by cogman10 »

geoduck14 wrote: post #216
cogman10 wrote: post #131

Earlier quoted context omitted.

Frankly, putting up my name with my medical history has far less to do with having the two linked and far more to do with "I'd rather not have a future employer have an easy link to my social media information". Oh genetic disorders, you didn't ask about that earlier. My family is a carrier for cystic fibrosis. Is that something that's supposed to be super terrible to share? I'm not the GP, but frankly I think it's a…

>I think it's a little crazy how worried everyone is about being identified through round about methods in medical data Do you realize that people were murdered because of their medical history? Like mental illness and ADD were reasons for killing people in America just a couple of decades ago? And currently, today there places where it is acceptable to drown your own babies if they demonstrate delayed development. I…

> Like mental illness and ADD were reasons for killing people in America just a couple of decades ago?

Citation needed.

You realize a couple of decades ago was 2000, right? The closest I can think of what you might be talking about is the eugenics programs ran up to the early 1960s. Even so, those weren't executions, but rather sterilizations. Barbaric, but not murder.

> And currently, today there places where it is acceptable to drown your own babies if they demonstrate delayed development.

And what part of making health recorders more accessible would influence that one way or another? Do you think it's the fact that heath records are hard to access that protects us from parents murdering their children? How are other nations in the EU managing to not kill all their kids for defects!

Re: Covid-19 vaccines and treatments: we must have raw data, now

#238

Post by ceras »

soupfordummies wrote: post #219
jacquesm wrote: post #138

Earlier quoted context omitted.

See also: the AOL search CD ROM set and many other releases where it turned out that anonymous data isn't.

I’m intrigued. Got any more info on this or something I can google?

I think the AOL search leak reference is this: https://en.m.wikipedia.org/wiki/AOL_search_data_leak

Even if you take more care than AOL did in anonymizing your data, the unfortunate reality is that any publication of data increases the knowledge an adversary has at identifying somebody. Anonymizing is more about reducing the chance someone is identified than guaranteeing they never will be. And high dimensional data is particularly hard to do so in a way that retains the data's usefulness.

33 bits is an old defunct blog on this topic, but it has some interesting posts and academic papers if you want to go down the rabbit hole: https://33bits.wordpress.com/about/

Specific paper on Netflix deanonymization: https://33bits.wordpress.com/about/netflix-paper-home-page/

Re: Covid-19 vaccines and treatments: we must have raw data, now

#239

Post by macilacilove »

bsder wrote: post #165

One thing I haven't seen is the "raw data" people being willing to pay for their own government certified consultants to anonymize the data. I presume this would actually be the solution if the "raw data" people were making good faith requests. Is there any reason why this wouldn't be viable?

The public needs the data, so the public need to pay for it. We absolutely can. Yet the FDA says "sorry only 500 pages a month" which means 110 months.

Re: Covid-19 vaccines and treatments: we must have raw data, now

#240

Post by jacquesm »

ceras wrote: post #238
soupfordummies wrote: post #219

Earlier quoted context omitted.

I’m intrigued. Got any more info on this or something I can google?

I think the AOL search leak reference is this: https://en.m.wikipedia.org/wiki/AOL_search_data_leak Even if you take more care than AOL did in anonymizing your data, the unfortunate reality is that any publication of data increases the knowledge an adversary has at identifying somebody. Anonymizing is more about reducing the chance someone is identified than guaranteeing they never will be. And high dimensional data…

They key is to combine more than one anonymized dataset, this vastly increases your chances at de-anonymization.

This paper is a very good starting point:

https://papers.ssrn.com/sol3/papers.cfm?abstract_id=1450006

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