I have got a data-management problem. I have a database where "EDSS.1","EDSS.2",... represent a numeric variable, scaled from 0 to 10 (0.5 scale), where higher number stand for higher disability. For each EDSS variable, I have a "VISITDATE.1", "VISITDATE.2",...
EDSS
VISITDATE
Now I am interested in assessing the CONFIRMED DISABILITY PROGRESSION (CDP), which is an increased i 1 poin on the EDSS. To make things more difficult, this increment need to be confirmed in the subsequent visit (e.g. EDSS.3) which has to be >= 6 months (which is, VISITDATE.3 - VISITDATE.2 > 6 months.
To do so, I am creating a nested ifelse statement, as showed below.
prova <- prova %>% mutate(
CDP = ifelse(EDSS.2 > EDSS.1 & EDSS.3>=EDSS.2 & difftime(VISITDATE.3,VISITDATE.2,
units = "weeks") > 48,
print(ymd(VISITDATE.2)),0))
However, I am facing the following main problems:
How can I print the VISIT.DATE of my interest instead of 1 or 0?
How can I shift my code to the EDSS.2,EDSS.3, and so on? I am interested in finding all the confirmed disability progressions (CDPs).
Many thanks to everyone who find the time to answer me.
Related
I'm reviewing for my midterm and this specific question is causing me some issues.
This is the following array to perform the binary search:
the value I want to search for is 150.
To start off, I take the first element which is 0, and the last element which is 15.
(start + end) / 2,
(0 + 15) / 2 = 7
The value at the array of 7 is 90.
90 < 150, so the value is contained in the right side of the array.
The array now looks like this:
Continuing with the same logic
(start + end) / 2
(8 + 15) / 2 = 11.
However, according to the professor I should be at the value 12 here. I'm not sure what i am doing wrong. Any help would be appreciated.
The algorithms were written even before the computers were invented.
Computers are simply a tool or a device which implements the algorithm in an efficient manner which is why it is fast.
The binary search which you are performing here is relevant to computers as the array are indexed from 0 (counting usually starts from 0 in computers), that is why you are getting 11 which is correct in point of computers.
But for the humans counting starts from 1 and the so the result according to professor is 12.
While writing algorithms we write in according to the perception of the human and we twist it a little to implement in our machine.
I was going through Google Interview Questions. to implement the random number generation from 1 to 7.
I did write a simple code, I would like to understand if in the interview this question asked to me and if I write the below code is it Acceptable or not?
import time
def generate_rand():
ret = str(time.time()) # time in second like, 12345.1234
ret = int(ret[-1])
if ret == 0 or ret == 1:
return 1
elif ret > 7:
ret = ret - 7
return ret
return ret
while 1:
print(generate_rand())
time.sleep(1) # Just to see the output in the STDOUT
(Since the question seems to ask for analysis of issues in the code and not a solution, I am not providing one. )
The answer is unacceptable because:
You need to wait for a second for each random number. Many applications need a few hundred at a time. (If the sleep is just for convenience, note that even a microsecond granularity will not yield true random numbers as the last microsecond will be monotonically increasing until 10us are reached. You may get more than a few calls done in a span of 10us and there will be a set of monotonically increasing pseudo-random numbers).
Random numbers have uniform distribution. Each element should have the same probability in theory. In this case, you skew 1 more (twice the probability for 0, 1) and 7 more (thrice the probability for 7, 8, 9) compared to the others in the range 2-6.
Typically answers to this sort of a question will try to get a large range of numbers and distribute the ranges evenly from 1-7. For example, the above method would have worked fine if u had wanted randomness from 1-5 as 10 is evenly divisible by 5. Note that this will only solve (2) above.
For (1), there are other sources of randomness, such as /dev/random on a Linux OS.
You haven't really specified the constraints of the problem you're trying to solve, but if it's from a collection of interview questions it seems likely that it might be something like this.
In any case, the answer shown would not be acceptable for the following reasons:
The distribution of the results is not uniform, even if the samples you read from time.time() are uniform.
The results from time.time() will probably not be uniform. The result depends on the time at which you make the call, and if your calls are not uniformly distributed in time then the results will probably not be uniformly distributed either. In the worst case, if you're trying to randomise an array on a very fast processor then you might complete the entire operation before the time changes, so the whole array would be filled with the same value. Or at least large chunks of it would be.
The changes to the random value are highly predictable and can be inferred from the speed at which your program runs. In the very-fast-computer case you'll get a bunch of x followed by a bunch of x+1, but even if the computer is much slower or the clock is more precise, you're likely to get aliasing patterns which behave in a similarly predictable way.
Since you take the time value in decimal, it's likely that the least significant digit doesn't visit all possible values uniformly. It's most likely a conversion from binary to some arbitrary number of decimal digits, and the distribution of the least significant digit can be quite uneven when that happens.
The code should be much simpler. It's a complicated solution with many special cases, which reflects a piecemeal approach to the problem rather than an understanding of the relevant principles. An ideal solution would make the behaviour self-evident without having to consider each case individually.
The last one would probably end the interview, I'm afraid. Perhaps not if you could tell a good story about how you got there.
You need to understand the pigeonhole principle to begin to develop a solution. It looks like you're reducing the time to its least significant decimal digit for possible values 0 to 9. Legal results are 1 to 7. If you have seven pigeonholes and ten pigeons then you can start by putting your first seven pigeons into one hole each, but then you have three pigeons left. There's nowhere that you can put the remaining three pigeons (provided you only use whole pigeons) such that every hole has the same number of pigeons.
The problem is that if you pick a pigeon at random and ask what hole it's in, the answer is more likely to be a hole with two pigeons than a hole with one. This is what's called "non-uniform", and it causes all sorts of problems, depending on what you need your random numbers for.
You would either need to figure out how to ensure that all holes are filled equally, or you would have to come up with an explanation for why it doesn't matter.
Typically the "doesn't matter" answer is that each hole has either a million or a million and one pigeons in it, and for the scale of problem you're working with the bias would be undetectable.
Using the same general architecture you've created, I would do something like this:
import time
def generate_rand():
ret = str(time.time()) # time in second like, 12345.1234
ret = ret % 8 # will return pseudorandom numbers 0-7
if ret == 0:
return 1 # or you could also return the result of another call to generate_rand()
return ret
while 1:
print(generate_rand())
time.sleep(1)
1) I have time series data and signals (indicators) that their value changes over time.
My question:
2) I need to do logical checking all the time, e.g. if signal 1 and 2 happened around the same time (were equal to a certain value e.g.=1) then I need to know the exact time in order to check what happened next.
3) to complicate things,e.g. if signal 3 happened in some time range after signal 1 and signal 2 were equal to 1, I would like to check other things.
4)The time series is very long and I need to deal with it segment by segment.
Please advice how to write it without inventing the wheel.
Is it recommended to write it in Matlab?, using a state machine? in C++?, using threads?
5) Does Matlab have a simulator ready for this kind of things?
How do I define the logical conditions in an efficient way?
6) Can I use data mining tools for this?
I saw this list of tools:
Data Mining open source tools
not sure where to start.
Thanks
The second and third question could be done like this in Matlab:
T = -range; % Assuming that t starts at 0.
for n = 1 : length(t)
if signal1(n) == 1 && signal2(n) == 1
T = t(n);
end
if t(n) - T < range && signal3(n) == 1
if % Conditions you want to get checked, could also be put in the previous if statement.
% Things you want to be executed if these coditions are met.
end
end
end
Using a lower level programming language like C++ would improve the rate at which it would be done. And if data is very long it could also reduce the amount of memory use by loading in an element of each array at the time.
Matlab has a simulator, called Simulink, but that is more meant for solving more complicated things, since you only conditionally want to do something.
I've got a classification system, which I will unfortunately need to be vague about for work reasons. Say we have 5 features to consider, it is basically a set of rules:
A B C D E Result
1 2 b 5 3 X
1 2 c 5 4 X
1 2 e 5 2 X
We take a subject and get its values for A-E, then try matching the rules in sequence. If one matches we return the first result.
C is a discrete value, which could be any of a-e. The rest are just integers.
The ruleset has been automatically generated from our old system and has an extremely large number of rules (~25 million). The old rules were if statements, e.g.
result("X") if $A >= 1 && $A <= 10 && $C eq 'A';
As you can see, the old rules often do not even use some features, or accept ranges. Some are more annoying:
result("Y") if ($A == 1 && $B == 2) || ($A == 2 && $B == 4);
The ruleset needs to be much smaller as it has to be human maintained, so I'd like to shrink rule sets so that the first example would become:
A B C D E Result
1 2 bce 5 2-4 X
The upshot is that we can split the ruleset by the Result column and shrink each independently. However, I cannot think of an easy way to identify and shrink down the ruleset. I've tried clustering algorithms but they choke because some of the data is discrete, and treating it as continuous is imperfect. Another example:
A B C Result
1 2 a X
1 2 b X
(repeat a few hundred times)
2 4 a X
2 4 b X
(ditto)
In an ideal world, this would be two rules:
A B C Result
1 2 * X
2 4 * X
That is: not only would the algorithm identify the relationship between A and B, but would also deduce that C is noise (not important for the rule)
Does anyone have an idea of how to go about this problem? Any language or library is fair game, as I expect this to be a mostly one-off process. Thanks in advance.
Check out the Weka machine learning lib for Java. The API is a little bit crufty but it's very useful. Overall, what you seem to want is an off-the-shelf machine learning algorithm, which is exactly what Weka contains. You're apparently looking for something relatively easy to interpret (you mention that you want it to deduce the relationship between A and B and to tell you that C is just noise.) You could try a decision tree, such as J48, as these are usually easy to visualize/interpret.
Twenty-five million rules? How many features? How many values per feature? Is it possible to iterate through all combinations in practical time? If you can, you could begin by separating the rules into groups by result.
Then, for each result, do the following. Considering each feature as a dimension, and the allowed values for a feature as the metric along that dimension, construct a huge Karnaugh map representing the entire rule set.
The map has two uses. One: research automated methods for the Quine-McCluskey algorithm. A lot of work has been done in this area. There are even a few programs available, although probably none of them will deal with a Karnaugh map of the size you're going to make.
Two: when you have created your final reduced rule set, iterate over all combinations of all values for all features again, and construct another Karnaugh map using the reduced rule set. If the maps match, your rule sets are equivalent.
-Al.
You could try a neural network approach, trained via backpropagation, assuming you have or can randomly generate (based on the old ruleset) a large set of data that hit all your classes. Using a hidden layer of appropriate size will allow you to approximate arbitrary discriminant functions in your feature space. This is more or less the same idea as clustering, but due to the training paradigm should have no issue with your discrete inputs.
This may, however, be a little too "black box" for your case, particularly if you have zero tolerance for false positives and negatives (although, it being a one-off process, you get an arbitrary degree of confidence by checking a gargantuan validation set).
I apologize for being a bit verbose in advance: if you want to skip all the background mumbo jumbo you can see my question down below.
This is pretty much a follow up to a question I previously posted on how to compare two 1D (time dependent) signals. One of the answers I got was to use the cross-correlation function (xcorr in MATLAB), which I did.
Background information
Perhaps a little background information will be useful: I'm trying to implement an Independent Component Analysis algorithm. One of my informal tests is to (1) create the test case by (a) generate 2 random vectors (1x1000), (b) combine the vectors into a 2x1000 matrix (called "S"), and multiply this by a 2x2 mixing matrix (called "A"), to give me a new matrix (let's call it "T").
In summary: T = A * S
(2) I then run the ICA algorithm to generate the inverse of the mixing matrix (called "W"), (3) multiply "T" by "W" to (hopefully) give me a reconstruction of the original signal matrix (called "X")
In summary: X = W * T
(4) I now want to compare "S" and "X". Although "S" and "X" are 2x1000, I simply compare S(1,:) to X(1,:) and S(2,:) to X(2,:), each which is 1x1000, making them 1D signals. (I have another step which makes sure that these vectors are the proper vectors to compare to each other and I also normalize the signals).
So my current quandary is how to 'grade' how close S(1,:) matches to X(1,:), and likewise with S(2,:) to X(2,:).
So far I have used something like: r1 = max(abs(xcorr(S(1,:), X(1,:)))
My question
Assuming that using the cross correlation function is a valid way to go about comparing the similarity of two signals, what would be considered a good R value to grade the similarity of the signals? Wikipedia states that this is a very subjective area, and so I defer to the better judgment of those who might have experience in this field.
As you might realize, I'm not coming from a EE/DSP/statistical background at all (I'm a medical student) so I'm going through a sort of "baptism through fire" right now, and I appreciate all the help I can get. Thanks!
(edit: as far as directly answering your question about R values, see below)
One way to approach this would be to use cross-correlation. Bear in mind that you have to normalize amplitudes and correct for delays: if you have signal S1, and signal S2 is identical in shape, but half the amplitude and delayed by 3 samples, they're still perfectly correlated.
For example:
>> t = 0:0.001:1;
>> y = #(t) sin(10*t).*exp(-10*t).*(t > 0);
>> S1 = y(t);
>> S2 = 0.4*y(t-0.1);
>> plot(t,S1,t,S2);
These should have a perfect correlation coefficient. A way to compute this is to use maximum cross-correlation:
>> f = #(S1,S2) max(xcorr(S1,S2));
f =
#(S1,S2) max(xcorr(S1,S2))
>> disp(f(S1,S1)); disp(f(S2,S2)); disp(f(S1,S2));
12.5000
2.0000
5.0000
The maximum value of xcorr() takes care of the time-delay between signals. As far as correcting for amplitude goes, you can normalize the signals so that their self-cross-correlation is 1.0, or you can fold that equivalent step into the following:
ρ2 = f(S1,S2)2 / (f(S1,S1)*f(S2,S2);
In this case ρ2 = 5 * 5 / (12.5 * 2) = 1.0
You can solve for ρ itself, i.e. ρ = f(S1,S2)/sqrt(f(S1,S1)*f(S2,S2)), just bear in mind that both 1.0 and -1.0 are perfectly correlated (-1.0 has opposite sign)
Try it on your signals!
with respect to what threshold to use for acceptance/rejection, that really depends on what kind of signals you have. 0.9 and above is fairly good but can be misleading. I would consider looking at the residual signal you get after you subtract out the correlated version. You could do this by looking at the time index of the maximum value of xcorr():
>> t = 0:0.001:1;
>> y = #(a,t) sin(a*t).*exp(-a*t).*(t > 0);
>> S1=y(10,t);
>> S2=0.4*y(9,t-0.1);
>> f(S1,S2)/sqrt(f(S1,S1)*f(S2,S2))
ans =
0.9959
This looks pretty darn good for a correlation. But let's try fitting S2 with a scaled/shifted multiple of S1:
>> [A,i]=max(xcorr(S1,S2)); tshift = i-length(S1);
>> S2fit = zeros(size(S2)); S2fit(1-tshift:end) = A/f(S1,S1)*S1(1:end+tshift);
>> plot(t,[S2; S2fit]); % fit S2 using S1 as a basis
>> plot(t,[S2-S2fit]); % residual
Residual has some energy in it; to get a feel for how much, you can use this:
>> S2res=S2-S2fit;
>> dot(S2res,S2res)/dot(S2,S2)
ans =
0.0081
>> sqrt(dot(S2res,S2res)/dot(S2,S2))
ans =
0.0900
This says that the residual has about 0.81% of the energy (9% of the root-mean-square amplitude) of the original signal S2. (the dot product of a 1D signal with itself will always be equal to the maximum value of cross-correlation of that signal with itself.)
I don't think there's a silver bullet for answering how similar two signals are with each other, but hopefully I've given you some ideas that might be applicable to your circumstances.
A good starting point is to get a sense of what a perfect match will look like by calculating the auto-correlations for each signal (i.e. do the "cross-correlation" of each signal with itself).
THIS IS A COMPLETE GUESS - but I'm guessing max(abs(xcorr(S(1,:),X(1,:)))) > 0.8 implies success. Just out of curiosity, what kind of values do you get for max(abs(xcorr(S(1,:),X(2,:))))?
Another approach to validate your algorithm might be to compare A and W. If W is calculated correctly, it should be A^-1, so can you calculate a measure like |A*W - I|? Maybe you have to normalize by the trace of A*W.
Getting back to your original question, I come from a DSP background, so I get to deal with fairly noise-free signals. I understand that's not a luxury you get in biology :) so my 0.8 guess might be very optimistic. Perhaps looking at some literature in your field, even if they aren't using cross-correlation exactly, might be useful.
Usually in such cases people talk about "false acceptance rate" and "false rejection rate".
The first one describes how many times algorithm says "similar" for non-similar signals, the second one is the opposite.
Selecting a threshold thus becomes a trade-off between these criteria. To make FAR=0, threshold should be 1, to make FRR=0 threshold should be -1.
So probably, you will need to decide which trade-off between FAR and FRR is acceptable in your situation and this will give the right value for threshold.
Mathematically this can be expressed in different ways. Just a couple of examples:
1. fix some of rates at acceptable value and minimize other one
2. minimize max(FRR,FAR)
3. minimize aFRR+bFAR
Since they should be equal, the correlation coefficient should be high, between .99 and 1. I would take the max and abs functions out of your calculation, too.
EDIT:
I spoke too soon. I confused cross-correlation with correlation coefficient, which is completely different. My answer might not be worth much.
I would agree that the result would be subjective. Something that would involve the sum of the squares of the differences, element by element, would have some value. Two identical arrays would give a value of 0 in that form. You would have to decide what value then becomes "bad". Make up 2 different vectors that "aren't too bad" and find their cross-correlation coefficient to be used as a guide.
(parenthetically: if you were doing a correlation coefficient where 1 or -1 would be great and 0 would be awful, I've been told by bio-statisticians that a real-life value of 0.7 is extremely good. I understand that this is not exactly what you are doing but the comment on correlation coefficient came up earlier.)