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Group Testing and Coding Theory Atri Rudra University at Buffalo, SUNY Or, A Theoretical Computer Scientist’s (Biased) View of Group Testing

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Group testing overview Test soldier for a disease WWII example: syphillis 1

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Group testing overview Test an army for a disease WWII example: syphillis What if only one soldier has the disease? 2 Can we do better?

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3 Communicating with my 2 year old C(x) x y = C(x)+error x Give up “Code” C “Akash English” C(x) is a “codeword”

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4 The setup C(x) x y = C(x)+error x Give up Mapping C Error-correcting code or just code Encoding: x C(x) Decoding: y x C(x) is a codeword

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The fundamental tradeoff Correct as many errors as possible with as little redundancy as possible 5 Can one achieve the “optimal” tradeoff with efficient encoding and decoding ?

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The main message 6 Coding Theory Group Testing

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Asymptotic view n! 10n 2 n2n2

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O( ) notation ≤ is O with glasses poly(n) is O(n c ) for some fixed c

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Group testing overview Test an army for a disease WWII example: syphillis What if only one soldier has the disease? Can pool blood samples and check if at least one soldier has the disease 9

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Group testing Set of items: (Unknown) vector x in {0,1} n At most d positives: |x| ≤ d Tests: a subset S of {1,..,n} Result of a test: OR of x i ’s such that i in S Goal 1: Figure out x Goal 2: Minimize the number of tests t Non-adaptive tests: all tests are fixed a priori 123n ………… 1 2 3 t...... 1001 …………. 0010 0001 1110...... t = O(d 2 log n) is possible Tons of applications Output + items 10

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The decoding step 123n ………… 1 2 3 t...... 1001 …………. 0010 0001 1110...... x1x1 x2x2 x3x3 xnxn............ r1r1 r2r2 r3r3 rtrt...... unknown To be designed Observed How fast can this step be done? 11

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An application: heavy hitters Stream items are numbers in the range {1,…,n} Output all items that occur at least 1/d fraction of the times One pass, poly log space, poly log update, poly log report time One pass, poly log space, poly log update, poly log report time 12

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Cormode-Muthukrishnan idea Use group testing: maintain counters for each test Heavy tail property: Total frequency of non-heavy items < 1/d 123n ………… c1c1 c2c2 c3c3 ctct...... 1001 …………. 0010 0001 1110...... Maintain count of items in tests Maintain total count m r i = 1 iff c i ≥ m/d x j = 1 iff j is a heavy item (|x| ≤ d) r = M × x Reporting the heavy items is just decoding! 13

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Requirements from group testing 123n ………… c1c1 c2c2 c3c3 ctct...... 1001 …………. 0010 0001 1110...... Non-adaptiveness is crucial Minimize t (space) Strongly explicit matrix Minimize decoding time (report time) 14

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An overview of results # tests (t)Decoding time d is O(log n) O(d 2 log n)poly(t) [INR10, NPR11] O(d 2 log n)O(nt) [DR82], [PR08] O(d 4 log n)O(t) [GI04] O(d 2 log 2 n)poly(t) [GI04, implicit] Big savings 15

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Tackling the first row # tests (t)Decoding time O(d 2 log n)poly(t) [INR10, NPR11] O(d 2 log n)O(nt) [DR82], [PR08] O(d 4 log n)O(t) [GI04] O(d 2 log 2 n)poly(t) [GI04, implicit] 16

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d-disjunct matrices Sufficient condition for group testing d columns 1 0 0 0 …………….. 0 Exists True for every d subset of columns and a disjoint column Set of positives Test result=0 Every non- positive column has one 0 test result 17

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L columns Naïve decoder for d-disjunct matrices d columns 1 0 0 0 …………….. 0 Set of positives If r j = 0 then for every column i that is in test j, set x i = 0 If x i =1 then all tests column i participates in will have a 1 O(nt) time O(Lt) time 18

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What is known d columns 1 0 0 0 …………….. 0 Set of positives O(nt) time r1r1 r2r2 r3r3 rtrt...... d-disjunct matrix Strongly explicit d-disjunct matrix with t = O(d 2 log 2 n) [ Kautz-Singleton 1964 ] Deterministic d-disjunct matrix with t = O(d 2 log n) [ Porat-Rothschild 2008 ] Lower bound of Ω(d 2 log n/log d) [ Dyachkov-Rykov 1982 ] 19 Randomized d-disjunct matrix with t = O(d 2 log n) [ Dyachkov-Rykov 1982 ]

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Up next # tests (t)Decoding time O(d 2 log n)poly(t) [INR10, NPR11] O(d 2 log n)O(nt) [DR82], [PR08] O(d 4 log n)O(t) [GI04] O(d 2 log 2 n)poly(t) [GI04, implicit] 20

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Error-correcting codes 21 C(x) x y x Give up Mapping C : k m Dimension k, block length m m≥ k Rate R = k/m 1 Efficient means polynomial in m Decoding time complexity

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Noise model Errors are worst case (Hamming) error locations arbitrary symbol changes Limit on total number of errors 22

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Hamming’s 60 yr old observation 23 ≥ D D/2 Large “distance” is good

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All you need to remember about Reed- Solomon codes– Part I q is a prime power q q/(d+1) vectors from [q] q where every two agree in < q/(d+1) positions 24

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How do we get binary codes ? 25 Concatenation of codes [Forney 66] C 1 : ({0,1} k ) K ({0,1} k ) M (Outer code) C 2 : {0,1} k {0,1} m (Inner code) C 1 ° C 2 : {0,1} kK {0,1} mM Typically k=O(log M) x1x1 x2x2 wMwM w1w1 w2w2 xKxK x C 1 (x) C 2 (w 1 )C 2 (w 2 ) C 2 (w M ) C 1 ° C 2 (x)

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Disjunct matrices from RS codes n = q q/(d+1) Column i gets ith codeword x 0 0 1 …. 0 x x. q rows t = q 2 = O(d 2 log 2 n) d-disjunct matrix [Kautz,Singleton] Code Concatenation q 26

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A q=3 example 0 0 0 1 1 1 2 2 2 0 1 2 1 2 0 2 0 1 1 0 0 0 0 1 0 1 0 0 1 2 100100 100100 100100 010010 010010 010010 001001 001001 001001 100100 010010 001001 010010 001001 100100 001001 100100 010010 27

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1-Agreement between two columns 0 0 0 1 1 1 2 2 2 0 1 2 1 2 0 2 0 1 1 0 0 0 0 1 0 1 0 0 1 2 100100 100100 100100 010010 010010 010010 001001 001001 001001 100100 010010 001001 010010 001001 100100 001001 100100 010010 ≤ 1 agr Agreement in binary = Agreement among RS codewords < q/(d+1) Agreement in binary = Agreement among RS codewords < q/(d+1) 28

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d-disjunct matrices Sufficient condition for group testing d columns 1 0 0 0 …………….. 0 Exists True for every d subset of columns and a disjoint column Set of positives 29

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d-disjunctness of Kautz-Singleton d columns < q/(d+1) agr 1 1 1 1 1 1 1 1 1 1 1 1 1>q- q*d/(d+1)>0 rows 000 30

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Up next # tests (t)Decoding time O(d 2 log n)poly(t) [INR10, NPR11] O(d 2 log n)O(nt) [DR82], [PR08] O(d 4 log n)O(t) [GI04] O(d 2 log 2 n)poly(t) [GI04, implicit] 31

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The basic idea 123n ………… 1 2 3 t...... 1001 …………. 0010 0001 1110...... x1x1 x2x2 x3x3 xnxn............ r1r1 r2r2 r3r3 rtrt...... unknown Every column is a codeword Observed Show is same as `decoding’ the code 32 n= # codewords = exp(m) t = poly(m)

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Decoding C(x) sent, y received x k, y m How much of y must be correct to recover x ? At least k symbols must be correct At most (m-k)/m = 1-R fraction of errors 1-R is the information-theoretic limit : the fraction of errors decoder can handle Information theoretic limit implies 1-R 33 xC(x) y R = k/m

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Can we get to the limit or 1-R ? 34 Not if we always want to uniquely recover the original message Limit for unique decoding, (1-R)/2 (1-R)/2 1-R c1c1 c2c2 r R (1-R)/2

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35 List decoding [ Elias57, Wozencraft58 ] Always insisting on unique codeword is restrictive The “pathological” cases are rare “Typical” received word can be decoded beyond (1- R)/2 Better Error-Recovery Model Output a list of answers List Decoding Example: Spell Checker (1-R)/2 Almost all the space in higher dimension. All but an exponential (in m) fraction

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Information theoretic limit < 1 - R – Information- theoretic limit Can handle twice as many errors 36 Rate (R) Unique decoding Inf. theoretic limit Frac. of Errors ( ) Achievable by random codes. NOT ALGORITHMIC! Achievable by random codes. NOT ALGORITHMIC!

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37 Other applications of list decoding Cryptography Cryptanalysis of certain block-ciphers [ Jakobsen98 ] Efficient traitor tracing scheme [ Silverberg, Staddon, Walker 03 ] Complexity Theory Hardcore predicates from one way functions [ Goldreich,Levin 89; Impagliazzo 97; Ta-Shama, Zuckerman 01 ] Worst-case vs. average-case hardness [ Cai, Pavan, Sivakumar 99; Goldreich, Ron, Sudan 99; Sudan, Trevisan, Vadhan 99; Impagliazzo, Jaiswal, Kabanets 06 ] Other algorithmic applications IP Traceback [ Dean,Franklin,Stubblefield 01; Savage, Wetherall, Karlin, Anderson 00 ] Guessing Secrets [ Alon,Guruswami,Kaufman,Sudan 02; Chung, Graham, Leighton 01 ]

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Algorithmic list decoding results 1- R - > 0 Folded RS codes [Guruswami, R. 06] 38 Unique decoding Inf. theoretic limit Guruswami-Sudan 98 Parvaresh-Vardy 05 Frac. of Errors ( ) Rate (R) Folded RS

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Concatenated codes 39 Concatenation of codes [Forney 66] C 1 : ({0,1} k ) K ({0,1} k ) M (Outer code) C 2 : {0,1} k {0,1} m (Inner code) C 1 ° C 2 : {0,1} kK {0,1} mM Typically k=O(log M) x1x1 x2x2 wMwM w1w1 w2w2 xKxK x C 1 (x) C 2 (w 1 )C 2 (w 2 ) C 2 (w M ) C 1 ° C 2 (x) Brute force decoding for inner code

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40 List decoding C 1 ° C 2 y1y1 y2y2 yMyM How do we “list decode” from lists ? in {0,1} m S1S1 S2S2 SMSM in {0,1} k

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List recovery............. S1S1 S2S2 S3S3 SMSM ……………………… Output all codewords that agree with (all) the input lists S i subset of [q] ……………………… c1c1 c2c2 c3c3 cMcM |S i | ≤ d 41

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All you need to remember about (Reed-Solomon) codes-- Part II q is a prime power q q/(d+1) vectors from [q] q where every two agree in < q/(d+1) positions poly(q) time algorithm for list recovery............. S1S1 S2S2 S3S3 SqSq ……………………… Output all codewords that agree with all the input lists S i subset of [q] ……………………… c1c1 c2c2 c3c3 cqcq |S i | ≤ d 42

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Back to the example 0 0 0 1 1 1 2 2 2 0 1 2 1 2 0 2 0 1 1 0 0 0 0 1 0 1 0 0 1 2 100100 100100 100100 010010 010010 010010 001001 001001 001001 100100 010010 001001 010010 001001 100100 001001 100100 010010 101101 001001 011011 + items Result vector Result vector {1,2} {2} {0,2} 43

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All you ever needed to know about (Reed-Solomon) codes… at least for this talk q is a prime power q q/(d+1) vectors from [q] q where every two agree in < q/(d+1) positions poly(q) time algorithm for list recovery............. S1S1 S2S2 S3S3 SqSq ……………………… Output all codewords that agree with all the input lists S i subset of [q] ……………………… c1c1 c2c2 c3c3 cqcq |S i | ≤ d 44

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d 2 columns What does this imply? d columns 1 0 0 0 …………….. 0 Set of positives r1r1 r2r2 r3r3 rtrt...... KS matrix poly(t) time O(d 2 t) time t = O(d 2 log 2 n) Implicit in [Guruswami- Indyk 04] 45

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Up next # tests (t)Decoding time O(d 2 log n)poly(t) [INR10, NPR11] O(d 2 log n)O(nt) [DR82], [PR08] O(d 4 log n)O(t) [GI04] O(d 2 log 2 n)poly(t) [GI04, implicit] 46

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L columns Filter-evaluate decoding paradigm d columns 1 0 0 0 …………….. 0 Set of positives r1r1 r2r2 r3r3 rtrt...... d-disjunct matrix “Filtering” matrix y1y1 y2y2 y3y3 y t’...... poly(t’)time O(Lt) time 47

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So all we need to do o(d 2 log n/log d) tests 48 [Indyk, Ngo, R. 10] [Ngo, Porat, R. 11]

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Overview of the results # tests (t)Decoding time O(d 2 log n)poly(t) [INR10, NPR11] O(d 2 log n)O(nt) [DR82], [PR08] O(d 4 log n)O(t) [GI04] O(d 2 log 2 n)poly(t) [GI04, implicit] 49

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The main message 50 Coding Theory Group Testing

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Open Questions Close the gap between upper and lower bounds Other applications of group testing? Complexity Theory? Strongly explicit construction of optimal disjunct matrices ? 51

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More on Coding Theory 52 http://www.cse.buffalo.edu/~atri/courses/coding-theory/book/index.html

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Questions? 53

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d+L columns The filtering matrix New* object: (d,L)-list disjunct matrix d columns Set of positives Running naïve decoder returns ≤ L bogus columns Independently considered by [Cheraghchi 09] (d,d)-list disjunct matrices exists with O(d log n) tests 54

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Reed-Solomon codes 55 Message: (x 0,x 1,…,x k-1 ) F k View as poly. f(Y) = x 0 +x 1 Y+…+x k-1 Y k-1 Encoding, RS(f) = ( f( 1 ),f( 2 ),…,f( m ) ) F ={ 1, 2,…, m } f( 1 ) f( 2 ) f( 3 ) f( 4 )f( m ) Alphabet size is at least m

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r Revisiting the decoding algorithm.... 1 2 j q.............................. 1 x x ………… SjSj.. |S j |≤ d 1 3 q 2 1 1 1 ………....... 2 1 1 3 q d-disjunct matrix Naïve decoder Works but hits a d 3 barrier 56

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r Connection to List Recovery x 0 0 1 …. 0 x.... 1 2 j q.............................. Decoding: Output all codewords that match the test results 1 x x ………… SjSj... S1S1 S2S2 SqSq List recover from S 1,…,S t to get the positive codewords |S j |≤ d 57

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r Revisiting the decoding algorithm-II.... 1 2 j q.............................. 1 x x ………… SjSj.. |S j |≤ 2d 1 3 q 2 (d,d)-list disjunct Naïve decoder Need to change the parameters of the Reed- Solomon codes a bit. 58

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http://www.impawards.com/2007/are_we_done_yet.html 59

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How we get our hands on….... 1 2 j q.............................. 1 3 q 2 (d,d)-list disjunct n ~ q q/d RS codeword d log q rows t = q X (d log q) ~ (d X log n/ log q) X (d log q) = d 2 log n 60

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Solution 1 [Indyk, Ngo, R. 10] 1 3 q 2 (d,d)-list disjunct d log q rows Pick “inner” codes at random 61

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Solution 2 [Ngo, Porat, R. 10] 1 3 q 2 (d,d)-list disjunct d log q rows Use explicit expanders! Some comments: Left degree of the expander not important d 1+o(1) log q rows possible [ GUV 07, Cheraghchi 09 ] Use PV codes instead of RS codes 62

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Applied Algorithmics - week7

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