[HN Gopher] Prostate cancer can be precisely diagnosed using a u...
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Prostate cancer can be precisely diagnosed using a urine test with
AI
Author : samizdis
Score : 177 points
Date : 2021-01-21 16:06 UTC (6 hours ago)
(HTM) web link (phys.org)
(TXT) w3m dump (phys.org)
| m3kw9 wrote:
| How does a test get standardized? Is there something like drug
| trials where you need to show accuracy instead of efficacy?
| rozab wrote:
| So they used a neural net with only 4 parameters?? And they
| haven't compared the performance to a simple regression?
| zerof1l wrote:
| This article reads more like PR than research. Research is based
| on 76 urine samples which is way too little. In the paper,
| there's little info on model hyper-parameters as well as how they
| trained and tested them. I suspect they overfitted their model,
| meaning it just learned all the samples. If that's not the case,
| the only other explanation for such high accuracy is that there's
| a very obvious correlation and a human would be able to diagnose
| cancer with high accuracy also, meaning you don't need any AI.
| trhway wrote:
| >The team developed an ultrasensitive semiconductor sensor
| system capable of simultaneously measuring trace amounts of
| four selected cancer factors in urine for diagnosing prostate
| cancer.
|
| it would be interesting if they run as a control a human
| looking at those measurements.
|
| One can also wonder how many other cancers can be detected by
| dipping a chip in urine and whether those chips can be just
| made into a smartphone accessory for home/field use.
| Nowado wrote:
| > there's a very obvious correlation and a human would be able
| to diagnose cancer with high accuracy also, meaning you don't
| need any AI
|
| IF (big if) that's the case, arguably you still prefer
| something that runs on some electricity in few servers instead
| of having thousands of human diagnosticians who need to be
| housed, fed, educated, entertained and later retired.
| caycep wrote:
| Granted...through some weird HHS/medicare loophole, this is
| commercializable. Our center has a AI "stroke/clot" detector
| algorithm software, that's based on a training set of 50 CTs.
| It's ok, say at a 2nd year medical student level at reading
| images, i.e. not to the point anyone would trust them. But if
| the clinical writes in their documentation that the software
| was utilized to analyze the images, the hospital gets an extra
| couple grand of reimbursement from the insurance company,
| apparently. Exactly what rules apply here, I don't know.
| ttymck wrote:
| > Research is based on 76 urine samples which is way too little
|
| I'm sure I'm out of my depth, but I feel compelled to point out
| that reputable clinical research can be done on even smaller
| samples[0].
|
| I want to make sure we aren't conflating the training set and
| the test/validation/holdout set [1] -- I interpreted the
| article as stating "76 samples in the test set" and assumed the
| training set is far larger.
|
| [0]: https://stats.stackexchange.com/questions/2541/what-
| referenc....
|
| [1]: https://www.datarobot.com/wiki/training-validation-
| holdout/
| z77dj3kl wrote:
| It really depends on the model. If you're estimating a mean
| from a distribution with low variance, 76 can be quite
| enough. But for any even half-involved ML model, that's
| nothing.
| ska wrote:
| Your interpretation is wrong, unfortunately.
|
| The paper is really about developing a multi-marker sensor
| approach for screening.
|
| The analysis, however was done on a small set "Obtained data
| from 76 urine specimens were partitioned randomly into a
| training data set (70% of total) and a test data set (30% of
| total). " Later on it states the 76 samples are from 51
| individuals.
|
| So the GP complaint is correct in this case. They are
| comparing a RF approach and a NN approach - there isn't much
| detail in the paper but it's most likely the analysis is
| problematic. I suspect this was done because the group is a
| collection of hardware and clinical folks, not statisticians,
| and the paper would have benefited by review by a biostats
| person.
|
| You are quite right generally that for some models and some
| effects, a relatively small verification set can be
| effective.
| thegginthesky wrote:
| That's right, sample size can vary a lot depending on several
| factors such as:
|
| * Experiment design
|
| * Sampling techniques
|
| * Methodology being used on the model
|
| But normally with a small sample size a bigger emphasis
| should be put on performing the appropriate statistical tests
| on the sample and validating it carefully, before applying
| any model. There are a lot of assumptions that should be
| validated if you are working with small data.
|
| Unfortunately, I don't have access to the complete paper to
| verify the methodology used, so take it all with a grain of
| salt.
| samizdis wrote:
| The paper may be read here:
|
| https://sci-
| hub.do/https://pubs.acs.org/doi/10.1021/acsnano....
| dekhn wrote:
| There's a great paper about small sample sizes in the context
| of experimental surgeries (where usually the work is done at
| a single regional hospital on 3 patients): "If nobody died,
| is everything OK?" It's cited in Glantz's Primer on
| Biostatistics.
| Blikkentrekker wrote:
| "significant results" can be yielded from 76 samples,
| provided they all be independent, and one can practically bet
| that they are not.
|
| But this is a claim of accurate diagnosis which requires more
| than simple significance. The a.i. being demonstrated to
| simply be better than chance would be a significant result,
| which is obviously not a spectacular standard for diagnoses.
|
| The issue is that the meaning of "significant" is very often
| overrated. It means nothing more than " _We are highly
| confident that there is a stronger effect than zero._ "; --
| this does not mean this effect is particularly large, and
| most importantly, it does not mean the effect is universal.
| mbreese wrote:
| From Supplemental Table S2 in the paper:
|
| Non cancer patients: 26, Cancer patients: 25
|
| So, they only had 51 individuals in the study. Then they
| actually divided the patients in to 3 groups: normal, PCa
| with pre-DRE, and PCa with post-DRE. The cancer patients
| thus had 2 samples, pre and post-exam: 26 + (2*25) = 76.
|
| Given the false positive rate of PSA screening, I would
| imagine that including more normal samples would have been
| more beneficial here. The method of analysis is pretty
| interesting though, which is where I think the novelty is
| for this paper. I assume that a more thorough clinical
| trial is planned with better numbers. This paper looks like
| it is more of a validation of the device than anything
| else.
| ghastmaster wrote:
| Agreed. This article raises more questions than answers. How
| were the samples obtained? What does "almost 100 percent
| accuracy" mean? What was the source of non positive samples?
| How many total samples were there?
| bcatanzaro wrote:
| This isn't AI. It's a random forest with FOUR inputs and ONE
| output. The fact they put a huge big blue AI brain in their paper
| to represent this algorithm tells me this is mostly hype.
| plaidfuji wrote:
| What's the cutoff on number of inputs/outputs/parameters for an
| empirical model to be considered "AI"?
| williesleg wrote:
| Just put your mouth diaper back on.
| brundolf wrote:
| How do clinical trials work for ML? Since the system is largely a
| black-box, I imagine that the slightest alteration (training on
| more data, tweaking any parameters) would require totally re-
| doing a full gamut of trials, wouldn't it?
| Kuinox wrote:
| A lot of thing are blackbox. There also things that we think we
| understand, but we do not, thats why we have methodologies like
| double blind testing to assert that the blackbox is indeed
| working, and it's behavior is stable enough to be used as a
| tool.
| swsieber wrote:
| I'm not sure why you would need to re-do a full gamut of trials
| for anything except deciding that the current type of data
| collected was insufficient.
|
| Presumably you record all data, and just split it into test and
| train sets, and you're off to the races.
| brundolf wrote:
| I guess it makes sense that unlike for actual treatments, for
| diagnostic systems you could just "re-use" the test data from
| past trials and not have to gather a whole new dataset
| 5440 wrote:
| I'm a regulatory consultant for AI software and submit several
| AI/ML FDA submissions per week. Overall, I've submitted 100+
| AI/ML submissions to date. Generally, FDA has been really
| focused on locked algorithms even though there has been some
| guidance lately stating the the new Good Machine Learning
| Practice (GMLP) will provide some allowance for iterations
| without submitting new 510ks. I will say that a number of
| companies are slightly tuning their algorithms without FDA
| resubmission within the confines of the FDA Guidance
| "https://www.fda.gov/regulatory-information/search-fda-
| guidan...". That said, most companies most companies are just
| leaving their specifications at sensitivity/specificity of 80%
| which gives them some leeway to improve above those limits. In
| truth most companies are above 97%-99%. While most of the
| submissions I work on are MRI/CT image related, I'm starting to
| get a lot more in the predictive space centered around ovarian
| (CA125), breast or PSA cancer scores. Lately pathology AI is
| escalating rapidly.
| brundolf wrote:
| Thanks for the informed and informative answer! I love how
| common it is on HN to hear from someone with first-hand
| knowledge of a topic
| m00dy wrote:
| where can I find their paper ?
|
| note: I've got the link
| https://pubs.acs.org/doi/10.1021/acsnano.0c06946
| ackbar03 wrote:
| You can read it on a boat; You can read it with a goat; You can
| read it in the rain; You can read it on a train; You can read
| it in a box; You can read it with a fox; You can read it in a
| house; You can read it with a mouse; You can read it here or
| there; You can read it anywhere!
| harveywi wrote:
| I would recommend a quiet, distraction-free environment.
| samizdis wrote:
| https://sci-hub.do/https://pubs.acs.org/doi/10.1021/acsnano....
| boogies wrote:
| ([PDF], if blocked paste your url into sci-hub.st or .se, or
| whatever URLs are listed on
| https://en.wikipedia.org/wiki/Sci-Hub -- which got them from
| https://nitter.dark.fail/sci_hub before
| https://news.ycombinator.com/item?id=25779367. They came for
| the big bad orange man, too few spoke up, and now they've
| come for open access to other knowledge.)
| [deleted]
| gfxgirl wrote:
| So this is super awesome if true and I hope they can use the
| technique for other cancers.
|
| I'm curious though, my bf says his doctor asks if he wants a PSA
| at his checkup. His doctor then goes on to explain that pretty
| much all men eventually get prostate cancer and there's not much
| you can do about it and you're far more likely to die of
| something else first so, not really much reason to get the PSA
|
| Anyone have any other info? Is there actually treatment and is it
| worth while?
| aclsid wrote:
| That doesn't seem to match reality, where you have some men
| living past 100+ years. But I'm not a doctor so...
| inglor_cz wrote:
| Not every cancer is created equal. I helped an urologist
| typeset his PhD thesis about prostate cancer treatment in TeX
| (he used some math equations within) and he told me the same.
|
| Some cancers are aggressive and some are slooooow. In younger
| patients, cancers tend to move fast and kill fast. But a slow
| prostate cancer in a 70 y.o. may be better left as it is,
| because the risks of the operation may actually be higher.
|
| This, of course, is a difficult judgment call and belongs to
| the experts only.
| ChefboyOG wrote:
| I always wonder about bias in these statistics around age.
|
| It makes intuitive sense to me that a cancer diagnosed in a
| young patient, who is below the common screening age, is
| probably being diagnosed because it is presenting serious
| symptoms (i.e. is growing fast).
|
| Cancers diagnosed in a 70 year old, on the other hand,
| would seem much more likely to be diagnosed while they are
| asymptomatic and relatively contained, or to be cancers
| that have been growing slowly for a long time (more likely
| as the 70 year old has been alive longer).
|
| Obviously, I don't know if this is the case or not. If
| anyone has experience in this field, I'd love to hear about
| it.
| e40 wrote:
| NAD, but male. That's bad advice. Prostate cancer found in old
| men is likely to go untreated, but certainly not younger men.
|
| Your bf should switch Dr's.
| vharuck wrote:
| There are things that can be done, especially if the tumor is
| small and hasn't spread to adjacent organs. I'm not an expert,
| but in general, solid tumors are _much_ more easily treated if
| caught early. Still, "watchful waiting" is a totally valid
| option for early-staged prostate tumors.
|
| That said, the doctor might be trying to benevolently prevent
| unnecessary tests, stress, and treatment. Some people hear
| "cancer" and rush into risky treatments. This is part of the
| reason the United States Preventative Services Task Force
| "demoted" asymptomatic PSA screening from "recommended" to
| "have a talk with your doctor." Their review of the studies
| didn't show that screening asymptomatic men resulted in a large
| reduction in mortality. Mostly because prostate cancer is so
| common and often develops slowly. Somewhat because treatment
| can bring its own dangers.
|
| At first, in 2012, they recommended against it. Then doctors
| and patients' groups protested, so now it's "have a talk." We
| are now starting to see the result of that first decision in
| the increasing incidence of late-staged prostate cancer.
|
| All this is to say: PSA screening's not a bad idea as long as
| you can keep perspective if it comes back positive. Out of the
| major cancer types, prostate cancer has one of the highest
| 5-year net survival rates [0]. It's over 95% in my state[1].
|
| [0] Net survival tries to exclude the risk of death from other
| causes. So 100% net survival for a cancer diagnosis means
| there's no difference from a similar person who didn't have
| cancer.
|
| [1] The official statistic from the CDC may be lower, but I
| disagree with some adjustments they make. I believe they force
| the data to fit their mental model.
| gumby wrote:
| It's basically true that most men have it and live with it for
| a long time (even decades) -- one can see the evolutionary
| reasons not to select against it.
|
| However some cases are more aggressive and will have a negative
| impact or even kill them.
|
| The problem, as with most cancers, is to figure out which ones
| are worth treating rather than risk iatrogenic consequences.
| DanBC wrote:
| https://www.hardingcenter.de/en/early-detection-of-cancer/ea...
|
| Take 1000 men over the age of 50 and give them PSA and DRA for
| about 15 years. Take 1000 other men over 50 don't give them PSA
| nor DRA over the same time.
|
| > About 10 out of every 1,000 men with screening, and 12 out of
| every 1,000 men without screening died from prostate cancer
| within 16 years. This means that 2 out of every 1,000 people
| could be saved from death from prostate cancer by early
| detection using PSA testing. This was not reflected in overall
| mortality.
|
| Over all about 322 men died in both groups, so it doesn't seem
| to make much difference to all cause mortality.
|
| However, in the group who was screened we see 155 people had a
| false alarm (and that includes unnecessary tissue removal), and
| 51 men with non-progressive cancer had unnecessary treatment
| (that sometimes includes impotence or incontinence).
|
| The most important question you can ask a doctor is _what
| happens if we don 't do this?_
|
| There are different types of prostate cancer. Some are very
| slow growing and people tend to die with it, not of it. There
| are aggressive types of prostate cancer that do kill people,
| but these tend not to be found in time to make much difference
| to populations at the moment.
| ChefboyOG wrote:
| I think it's important to have some conception of a personal
| "risk tolerance" when it comes to screenings.
|
| Personally, I've had false alarms and dealt with that stress,
| and I still find that screenings are worthwhile. Having seen
| family members/friends die of cancer, I don't find the
| additional and potentially unnecessary discomfort of
| screenings to be too much of a cost.
|
| At the same time, I'd never judge someone for feeling the
| opposite, particularly in cases like prostate cancer, wherein
| most people die "with it, not of it" as they say.
| ohazi wrote:
| A PSA test is easy and non-invasive and I personally wouldn't
| skip it. But keep in mind that it doesn't have a lot of
| diagnostic accuracy by itself, and the false positive rate can
| lead you to do things that are more invasive than necessary.
| Family history should be considered.
|
| If the numbers are low, you're probably good. If the numbers
| are high, it isn't necessarily bad, but it could be good excuse
| to keep a closer eye on things. You might do additional PSA
| tests and look at whether it's trending up or down. A biopsy
| might be suggested, which is more invasive, and _can_ be more
| accurate, but it also depends on where the doctor is able to
| collect the tissue -- if they miss the spot, a biopsy could be
| inconclusive or contradictory.
|
| Finally, if you have prostate cancer and the numbers are bad
| and your doctor tells you that it needs treatment, the common
| treatment seems to be high intensity focused ultrasound (HIFU),
| which is unpleasant and invasive, but it isn't surgery, and it
| isn't anywhere near as damaging as radiation, and apparently it
| works rather well.
| LinuxBender wrote:
| There is probably some truth in all men eventually getting it,
| but there are for sure contributing factors that increase and
| decrease risk. I've run across many of these by mistake in my
| nutritional research on nih.gov. That is a great starting place
| to find some of the research.
| zwieback wrote:
| I had prostate cancer 10 years ago when I was 42, prostate
| surgically removed and doing fine now.
|
| I also heard from urologists that everyone eventually gets it
| but normally you can outrun it. If you have an aggresive
| variety or get it when you're young you should definitely do
| something about it.
|
| The tricky part is that the current PSA test is not specific
| enough to avoid the stress and extra human cost of
| overtreatment so a better test would be great.
|
| Everything else is pretty straightforward in terms of diagnosis
| and there are decent treatment techniques, I had a simple
| needle biopsy that confirmed the cancer but for many men this
| test (although easy-peasy in my case) is scary, expensive and
| often confirms there's no cancer at all.
| randcraw wrote:
| Your BF's doctor is uninformed and offering bad advice.
|
| Fact is, most men over age 70 do have elevated PSA due to small
| amounts of low grade prostate cancer cells (Gleason score of
| 3+3). Usually it advances slowly, never growing beyond the
| bounds of the prostate gland before the patient dies from some
| other cause.
|
| But an elevated PSA (over 1 and below 10) in someone younger
| than 70 should not be ignored. Often a second PSA test is done
| perhaps a month later to confirm the first score and to see if
| the number is rising quickly. If repeated tests do not show PSA
| elevation AND the score is low, often the urologist will
| recommend a "monitor it, and wait and see" strategy.
|
| If the PSA number is high or is rising, the next step is to get
| a biopsy where 12 to 18 samples of tissue are taken from the
| prostate to see how much of the gland has cancerous cells
| (Gleason 3, 4, or 5).
|
| I know something about this topic because a routine PSA test at
| age 55 showed that I had asymptomatic cancer in 80% of my
| prostate. Luckily it was removed surgically. But if my doctor
| was as casually unconcerned as your BF's doctor, my cancer
| would have metastasized and by now it would be incurable.
| fasteo wrote:
| >>> Your BF's doctor is uninformed and offering bad advice.
|
| I wouldn't go that far. In your n=1 case it seems clear that
| not monitoring PSA would have been an error, but there exists
| a debate on the risk/benefit of this test. Namely, the
| unnecessary suffering that it can inflict to a healthy person
| with elevated PSA.
|
| This is a good review [1]
|
| "To screen or not to screen for prostate cancer? This remains
| an important question. Screening relies on a highly imperfect
| measure, the prostate-specific antigen (PSA) blood test,
| which is prone to false-positive results. And with mounting
| evidence that survival benefits from screening pale in
| comparison with the harms from overtreatment -- particularly
| incontinence and impotence -- the pendulum has steadily swung
| away from it. Still, screening research continues, in the
| hopes that some lifesaving benefits may be found."
|
| [1] https://www.health.harvard.edu/blog/new-study-once-again-
| cas...
| randcraw wrote:
| I'm keenly aware of the PSA debate. Policy about its proper
| use been see-sawing back and forth for a decade.
|
| Starting about 10 years ago, just before it mattered to me,
| official policy decided to NOT screen using the PSA test.
| The belief was that underinformed primary care docs were
| overreacting to a high PSA number and ordering too many
| biopsies which often led to "unnecessary" infections. Of
| course, the right response was to do a better job of
| interpreting the test results, ideally to refer the results
| to a more expert urologist _before_ doing a biopsy, not to
| cut back on the test.
|
| Given its low cost ($50) and very high sensitivity, the PSA
| test provided a very valuable service that could be
| equalled by no other test. Physical exam is often wrong,
| missing a large fraction of positive cases of cancer. And
| biopsies introduce infection most often in older patients.
| Younger ones can tolerate biopsy better, but were
| disallowed from PSA screening entirely due to this
| overprotective policy.
|
| The right solution was clearly to interpret the PSA test
| results more judiciously by introducing more expertise
| prior to biopsy, knowing that PSA is overly sensitive for
| diagnosing cancer. Fortunately the official policy has
| since been reversed, and PSA has returned to routine use --
| now with inclusion of a second test or a urologist prior to
| biopsy.
|
| The same blunder took place in mammographies at about the
| same time. Too many false positives led to too many
| biopsies and thus routine screening with mammography was
| deemed unacceptable and it was deprecated as well.
| Fortunately that overreaction has also ended.
|
| Sensitive medical tests are essential. Overreaction to
| possible misinterpretation of positive results by inexpert
| GPs is the problem, not the test itself. I routinely thank
| the stars above that my GP was expert enough to know that.
| oleander73 wrote:
| It is true that in old men there is a large percentage of slow
| growing mostly harmless prostate cancers, but you can also get
| it if you are younger (or it can be aggressive) and then
| treatment is possible (and required). The advantage of doing a
| PSA test is however not clear cut, because having a (slightly)
| elevated PSA can be caused by a benign enlarged prostate or
| prostatitis. This is why this new test is worthwhile (if it
| really works).
|
| Source: I'm 47 and have prostate cancer (metastasized, so
| incurable but there are still a number of treatment options to
| improve quality and quantity of life).
| singingfish wrote:
| The way PSA is a useful marker is not the absolute value but
| the rate at which it increases. If the doubling time of your
| PSA is too high it means you're at risk of prostate cancer
| and need further investigation. Get it done twice in your 30s
| and 40s and more regularly when older than that.
| btam wrote:
| What exactly do you mean by "a large percentage"?
| Cancer.org[1] says that it's 1 in 8 men during their
| lifetimes, the parent post says "almost all men get it at
| some point" -- where is this info coming from?
|
| [1]: https://www.cancer.org/cancer/prostate-cancer/about/key-
| stat...
| the-dude wrote:
| My father was treated for prostate cancer with internal
| radation pellets.
|
| I don't know the time between the 'treatment' and his death,
| could be anything from 12 - 24 months. I know at least one of
| the pellets had started 'wandering'.
|
| He died of acute leukemia and I suspect that had to do with the
| radation. However, I am not pursuing research into this, it
| won't bring him back. He was 63 years old.
| ojbyrne wrote:
| Unless your boyfriend is 70+, this is lots of bad advice.
|
| 1. 1 in 8 men are diagnosed with prostate cancer.
|
| 2. Second leading cause of cancer death among men.
|
| 3. There are treatment options. With treatment, 15 year
| survival rate is 95%.
|
| All of that info can be found here:
| https://www.cancer.org/cancer/prostate-cancer/treating.html
| randcraw wrote:
| This news begs a big question: How much does this new test cost?
| That will decide how it might be adopted.
|
| This test requires a chip rather than a simple lab assay. If the
| cost of the test is comparably as low as PSA ($50) it could
| entirely replace PSA for screening. However, if the chip is more
| expensive than PSA, it still may be very useful -- as a second
| test _after_ a PSA screening test reports a high number but
| _before_ a biopsy.
|
| If this new test could diminish the number of infections from
| unnecessary biopsies that worry policymakers, routine PSA
| screening combined with this test could become a low-risk no-
| brainer new standard.
| elicash wrote:
| My dad had prostate cancer a few years ago, which was treated
| successfully with radiation. He now gets his PSA score twice a
| year -- once with his annual physical, and 6 months later with
| his cancer doc.
|
| I wonder whether the biosensor could be something patients like
| him could have at home. (Also, now I'm imagining Apple telling
| customers they can urinate on the next generation of the
| watch.)
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