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MATH 1020: Mathematics For Non-science Chapter 3.1: Information in a networked age Instructor: Dr. Ken Tsang Room E409-R9 Email: [email protected] 1 Transmitting Information – Binary codes – Encoding with parity-check sums – Data compression – Cryptography – Model the genetic code 2 The Challenges Mathematical Challenges in the Digital Revolution How to correct errors in data transmission How to electronically send and store information economically How to ensure security of transmitted data How to improve Web search efficiency 3 Binary Codes A binary code is a system for encoding data made up of 0’s and 1’s Examples – Postnet (tall = 1, short = 0) – UPC (universal product code, dark = 1, light = 0) – Morse code (dash = 1, dot = 0) – Braille (raised bump = 1, flat surface = 0) – Yi-jing易经 (Yin=0, yang=1) Binary Codes are Everywhere CD, MP3, and DVD players, digital TV, cell phones, the Internet, GPS system, etc. all represent data as strings of 0’s and 1’s rather than digits 0-9 and letters A-Z Whenever information needs to be digitally transmitted from one location to another, a binary code is used Transmission Problems What are some problems that can occur when data is transmitted from one place to another? The two main problems are – transmission errors: the message sent is not the same as the message received – security: someone other than the intended recipient receives the message Transmission Error Example Suppose you were looking at a newspaper ad for a job, and you see the sentence “must have bive years experience” We detect the error since we know that “bive” is not a word Can we correct the error? Why is “five” a more likely correction than “three”? Why is “five” a more likely correction than “nine”? Another Example Suppose NASA is directing one of the Mars rovers by telling it which crater to investigate There are 16 possible signals that NASA could send, and each signal represents a different command NASA uses a 4-digit binary code to represent this information 0000 0001 0010 0100 0101 0110 1000 1001 1010 1100 1101 1110 0011 0111 1011 1111 Lost in Transmission The problem with this method is that if there is a single digit error, there is no way that the rover could detect or correct the error If the message sent was “0100” but the rover receives “1100”, the rover will never know a mistake has occurred This kind of error – called “noise” – occurs all the time BASIC IDEA The details of techniques used to protect information against noise in practice are sometimes rather complicated, but basic principles are easily understood. The key idea is that in order to protect a message against a noise, we should encode the message by adding some redundant information to the message. In such a case, even if the message is corrupted by a noise, there will be enough redundancy in the encoded message to recover, or to decode the message completely. 10 Adding Redundancy to our Messages To decrease the effects of noise, we add redundancy to our messages. First method: repeat the digits multiple times. Thus, the computer is programmed to take any five-digit message received and decode the result by majority rule. Majority Rule So, if we sent 00000, and the computer receives any of the following, it will still be decoded as 0. 00000 11000 Notice that for the 10000 10100 computer to decode 01000 10010 incorrectly, at least 00010 10001 three errors must be 00001 etc. made. Independent Errors Using the five-time repeats, and assuming the errors happen independently, it is less likely that three errors will occur than two or fewer will occur. This is called the maximum likelihood decoding. Why don’t we use this? Repetition codes have the advantage of simplicity, both for encoding and decoding But, they are too inefficient! In a five-fold repetition code, 80% of all transmitted information is redundant. Can we do better? Yes! More Redundancy Another way to try to avoid errors is to send the same message twice This would allow the rover to detect the error, but not correct it (since it has no way of knowing if the error occurs in the first copy of the message or the second) Parity-Check Sums Sums of digits whose parities determine the check digits. Even Parity – Even integers are said to have even parity. Odd Parity – Odd integers are said to have odd parity. Decoding The process of translating received data into code words. Example: Say the parity-check sums detects an error. The encoded message is compared to each of the possible correct messages. This process of decoding works by comparing the distance between two strings of equal length and determining the number of positions in which the strings differ. The one that differs in the fewest positions is chosen to replace the message in error. In other words, the computer is programmed to automatically correct the error or choose the “closest” permissible answer. Error Correction Over the past 40 years, mathematicians and engineers have developed sophisticated schemes to build redundancy into binary strings to correct errors in transmission! One example can be illustrated with Venn diagrams! Claude Shannon (1916-2001) “Father of Information Theory” 17 Computing the Check Digits The original message is four digits long We will call these digits I, II, III, and IV We will add three new digits, V, VI, and VII Draw three intersecting circles as shown here Digits V, VI, and VII should be chosen so that each circle contains an even number of ones Venn Diagrams V I III IV II VII VI A Hamming (7,4) code A Hamming code of (n,k) means the message of k digits long is encoded into the code word of n digits. The 16 possible messages: 0000 1010 0011 0001 1100 1110 0010 1001 1101 0100 0110 1011 1000 0101 0111 1111 Binary Linear Codes The error correcting scheme we just saw is a special case of a Hamming code. These codes were first proposed in 1948 by Richard Hamming (1915-1998), a mathematician working at Bell Laboratories. Hamming was frustrated with losing a week’s worth of work due to an error that a computer could detect, but not correct. 20 Appending Digits to the Message The message we want to send is “0100” Digit V should be 1 so that the first circle has two ones Digit VI should be 0 so that the second circle has zero ones (zero is even!) Digit VII should be 1 so that the last circle has two ones Our message is now 0100101 1 0 0 0 1 1 0 22 23 Encoding those messages Message codeword 0000 0000000 0110 0110010 0001 0001011 0101 0101110 0010 0010111 0011 0011100 0100 0100101 1110 1110100 1000 1000110 1101 1101000 1010 1010001 1011 1011010 1100 1100011 0111 0111001 1001 1001101 1111 1111111 25 Detecting and Correcting Errors Now watch what happens when there is a single digit error We transmit the message 0100101 and the rover receives 0101101 The rover can tell that the second and third circles have odd numbers of ones, but the first circle is correct So the error must be in the digit that is in the second and third circles, but not the first: that’s digit IV Since we know digit IV is wrong, there is only one way to fix it: change it from 1 to 0 1 0 0 1 1 1 0 27 Try It! Encode the message 1110 using this method You have received the message 0011101. Find and correct the error in this message. Extending This Idea This method only allows us to encode 4 bits (16 possible) messages, which isn’t even enough to represent the alphabet! However, if we use more digits, we won’t be able to use the circle method to detect and correct errors We’ll have to come up with a different method that allows for more digits Parity Check Sums The circle method is a specific example of a “parity check sum” The “parity” of a number is 1 is the number is odd and 0 if the number is even For example, digit V is 0 if I + II + III is even, and 1 if I + II + III is odd Conventional Notation Instead of using Roman numerals, we’ll use a1 to represent the first digit of the message, a2 to represent the second digit, and so on We’ll use c1 to represent the first check digit, c2 to represent the second, etc. Old Rules in the New Notation Using this notation, our rules for our check digits become – c1 = 0 if a1 + a2 + a3 is even – c1 = 1 if a1 + a2 + a3 is odd – c2 = 0 if a1 + a3 + a4 is even – c2 = 1 if a1 + a3 + a4 is odd c1 a1 – c3 = 0 if a2 + a3 + a4 is even a3 a 4 a2 – c3 = 1 if a2 + a3 + a4 is odd c3 c2 An Alternative System If we want to have a system that has enough code words for the entire alphabet, we need to have 5 message digits: a1, a2, a3, a4, a5 We will also need more check digits to help us decode our message: c1, c2, c3, c4 Rules for the New System We can’t use the circles to determine the check digits for our new system, so we use the parity notation from before c1 c2 is the parity of a1 + a2 + a3 + a4 is the parity of a2 + a3 + a4 + a5 c3 is the parity of a1 + a2 + a4 + a5 c4 is the parity of a1 + a2 + a3 + a5 Making the Code Using 5 digits in our message gives us 32 possible messages, we’ll use the first 26 to represent letters of the alphabet On the next slide you’ll see the code itself, each letter together with the 9 digit code representing it The Code Letter Code Letter Code A 000000000 N 011010101 B 000010111 O 011101100 C 000101110 P 011111011 D 000111001 Q 100001011 E 001001101 R 100011100 F 001011010 S 100100101 G 001100011 T 100110010 H 001110100 U 101000110 I 010001111 V 101010001 J 010011000 W 101101000 K 010100001 X 101111111 L 010110110 Y 110000100 M 011000010 Z 110010011 Using the Code Now that we have our code, using it is simple When we receive a message, we simply look it up on the table But what happens when the message we receive isn’t on the list? Then we know an error has occurred, but how do we fix it? We can’t use the circle method anymore Beyond Circles Using this new system, how do we decode messages? Simply compare the (incorrect) message with the list of possible correct messages and pick the “closest” one What should “closest” mean? The distance between the two messages is the number of digits in which they differ The Distance Between Messages What is the distance between 1100101 and 1010101? – The messages differ in the 2nd and 3rd digits, so the distance is 2 What is the distance between 1110010 and 0001100? – The messages differ in all but the 7th digit, so the distance is 6 Hamming Distance Def: The Hamming distance between two vectors of a vector space is the number of components in which they differ, denoted d(u,v). Hamming Distance Ex. 1: The Hamming distance between v=[1011010] u=[0111100] d(u, v) = 4 Notice: d(u,v) = d(v,u) 42 Hamming weight of a Vector Def: The Hamming weight of a vector is the number of nonzero components of the vector, denoted wt(u). Hamming weight of a code Def: The Hamming weight of a linear code is the minimum weight of any nonzero vector in the code. Hamming Weight The Hamming weight of v=[1011010] u=[0111100] w=[0100101] are: wt(v) = 4 wt(u) = 4 wt(w) = 3 Nearest-Neighbor Decoding The nearest neighbor decoding method decodes a received message as the code word that agrees with the message in the most positions Trying it Out Suppose that, using our alphabet code, we receive the message 010100011 We can check and see that this message is not on our list How far away is it from the messages on our list? Distances From 010100011 Code Distance Code Distance 000000000 4 011010101 5 000010111 4 011101100 5 000101110 4 011111011 3 000111001 4 100001011 4 001001101 6 100011100 8 001011010 6 100100101 4 001100011 2 100110010 4 001110100 6 101000110 6 010001111 3 101010001 6 010011000 5 101101000 6 010100001 1 101111111 6 010110110 3 110000100 5 011000010 3 110010011 3 Fixing the Error Since 010100001 was closest to the message that we received, we know that this is the most likely actual transmission We can look this corrected message up in our table and see that the transmitted message was (probably) “K” This might still be incorrect, but other errors can be corrected using context clues or check digits Distances From 1010 110 The distances between message “1010 110” and all possible code words: v 1010 110 1010 110 1010 110 1010 110 1010 110 1010 110 1010 110 1010 110 code word 0000 000 0001 011 0010 111 0100 101 1000 110 1100 011 1010 001 1001 101 distance 4 5 2 5 1 4 3 4 v 1010 110 1010 110 1010 110 1010 110 1010 110 1010 110 1010 110 1010 110 code word 0110 010 0101 110 0011 100 1110 100 1101 000 1011 010 0111 001 1111 111 distance 3 4 3 2 5 2 6 3 50 Transmitting Information – Binary codes – Encoding with parity-check sums – Data compression – Cryptography – Model the genetic code 51 Data compression Data compression is important to storage systems because it allows more bytes to be packed into a given storage medium than when the data is uncompressed. Some storage devices (notably tape) compress data automatically as it is written, resulting in less tape consumption and significantly faster backup operations. Compression also reduces file transfer time, saving time and communications bandwidth. 53 Compression There are two main categories – Lossless – Lossy Compression ratio: 54 Compression factor A good metric for compression is the compression factor (or compression ratio) given by: If we have a 100KB file that we compress to 40KB, we have a compression factor of: 55 Information Theory Shannon, C.E. (1948). A mathematical theory of communication. Bell System Technical Journal 30, 50-64. Very precise definition of information as a message made up of symbols from some finite alphabet. Shannon’s definition of information ignores the meaning conveyed by the message 56 Information Theory cont. Information content is a quantifiable amount The information content of some message is inversely related to the probability that that message will be received from the set of all possible messages. The message with the lowest probability of being received contains the highest information content. 57 Information content Compression is achieved by removing data redundancy while preserving information content. The information content of a group of bytes (a message) is its entropy. – Data with low entropy permit a larger compression ratio than data with high entropy. Entropy 熵, H, is a function of symbol frequency. It is the weighted average of the number of bits required to encode the symbols of a message. For a single symbol x: H= -P(x) log2P(x) 58 Entropy of a message The entropy of the entire message is the sum of the individual symbol entropies. i -P(xi) log2P(xi) where xi is the i-th symbol Information and entropy are measures of unexpectedness. Entropy effectively limits the strongest lossless compression possible. 59 Entropy Entropy is a measure of information content: the minimum number of bits required to store data without any loss of information. Entropy is sometimes called a measure of surprise, the uncertainty associated with the message – A highly predictable sequence contains little actual information Example: 11011011011011011011011011 (what’s next?) – A completely unpredictable sequence of n bits contains n bits of information Example: 01000001110110011010010000 (what’s next?) – Note that nothing says the information has to have any “meaning” (whatever that is) A fair coin has an entropy of one. If the coin is not fair, then the uncertainty is lower and the entropy is also lower. 60 Entropy of a coin flip Entropy H(X) of a coin flip, measured in bits; graphed versus the fairness of the coin Pr(X=1). Note the maximum of the graph depends on the distribution: Here, at most 1 bit is required to communicate the outcome of a fair coin flip; but the result of a fair die would require at most log2(6) bits. 61 62 Inefficiency of ASCII Realization: In many natural (English) files, we are much more likely to see the letter ‘e’ than the character ‘&’, yet they are both encoded using 7 bits! Solution: Use variable length encoding! The encoding for ‘e’ should be shorter than the encoding for ‘&’. 63 ASCII (cont.) Here are the ASCII bit strings for the capital letters in our alphabet: Letter ASCII Letter ASCII A 0100 0001 N 0100 1110 B 0100 0010 O 0100 1111 C 0100 0011 P 0101 0000 D 0100 0100 Q 0101 0001 E 0100 0101 R 0101 0010 F 0100 0110 S 0101 0011 G 0100 0111 T 0101 0100 H 0100 1000 U 0101 0101 I 0100 1001 V 0101 0110 J 0100 1010 W 0101 0111 K 0100 1011 X 0101 1000 L 0100 1100 Y 0101 1001 M 0100 1101 Z 0101 1010 64 Variable Length Coding Assume we know the distribution of characters (‘e’ appears 1000 times, ‘&’ appears 1 time) Each character will be encoded using a number of bits that is inversely proportional to its frequency (made precise later). Need a ‘prefix free’ encoding: if ‘e’ = 001 than we cannot assign ‘&’ to be 0011. Since encoding is variable length, need to know when to stop. 65 Example: Morse code Morse code is a method of transmitting textual information as a series of on-off tones, lights, or clicks that can be directly understood by a skilled listener or observer without special equipment. Each character is a sequence of dots and dashes, with the shorter sequences assigned to the more frequently used letters in English – the letter 'E' represented by a single dot, and the letter 'T' by a single dash. Invented in the early 1840s. it was extensively used in the 1890s for early radio communication before it was possible to transmit voice. 66 A U.S. Navy seaman sends Morse code signals in 2005. Vibroplex semiautomatic key. The paddle, when pressed to the right by the thumb, generates a series of dits. When pressed to the left by the knuckle of the index finger, the paddle generates a dah. 67 International Morse Code 68 Relative Frequency of Letters in English Text 69 Encoding Trees Think of encoding as an (unbalanced) tree. Data is in leaf nodes only (prefix free). 1 0 e 0 1 a b ‘e’ = 0, ‘a’ = 10, ‘b’ = 11 How to decode ‘01110’? 70 Cost of a Tree For each character ci let fi be its frequency in the file. Given an encoding tree T, let di be the depth of ci in the tree (number of bits needed to encode the character). The length of the file after encoding it with the coding scheme defined by T will be C(T)= Σdi fi 71 Example Huffman encoding A=0 B = 100 C = 1010 D = 1011 R = 11 ABRACADABRA = 01001101010010110100110 This is eleven letters in 23 bits A fixed-width encoding would require 3 bits for 5 different letters, or 33 bits for 11 letters Notice that the encoded bit string can be decoded! 72 Why it works In this example, A was the most common letter In ABRACADABRA: – 5 As – 2 Rs – 2 Bs – 1C – 1D code for A is 1 bit long code for R is 2 bits long code for B is 3 bits long code for C is 4 bits long code for D is 4 bits long 73 Creating a Huffman encoding For each encoding unit (letter, in this example), associate a frequency (number of times it occurs) – Use a percentage or a probability Create a binary tree whose children are the encoding units with the smallest frequencies – The frequency of the root is the sum of the frequencies of the leaves Repeat this procedure until all the encoding units are in the binary tree 74 Example, step I Assume that relative frequencies are: A: 40 B: 20 C: 10 D: 10 R: 20 (I chose simpler numbers than the real frequencies) Smallest numbers are 10 and 10 (C and D), so connect those – – – – – 75 Example, step II and D have already been used, and the new node above them (call it C+D) has value 20 The smallest values are B, C+D, and R, all of which have value 20 C – Connect any two of these; it doesn’t matter which two 76 Example, step III The smallest values is R, while A and B+C+D all have value 40 Connect R to either of the others root leave 77 Example, step IV Connect the final two nodes 78 Example, step V Assign 0 to left branches, 1 to right branches Each encoding is a path from the root A=0 B = 100 C = 1010 D = 1011 R = 11 Each path terminates at a leaf Do you see why encoded strings are decodable? 79 Unique prefix property A=0 B = 100 C = 1010 D = 1011 R = 11 No bit string is a prefix of any other bit string For example, if we added E=01, then A (0) would be a prefix of E Similarly, if we added F=10, then it would be a prefix of three other encodings (B=100, C=1010, and D=1011) The unique prefix property holds because, in a binary tree, a leaf is not on a path to any other node 80 Practical considerations It is not practical to create a Huffman encoding for a single short string, such as ABRACADABRA – To decode it, you would need the code table – If you include the code table in the entire message, the whole thing is bigger than just the ASCII message Huffman encoding is practical if: – The encoded string is large relative to the code table, OR – We agree on the code table beforehand For example, it’s easy to find a table of letter frequencies for English (or any other alphabet-based language) 81 Data compression Huffman encoding is a simple example of data compression: representing data in fewer bits than it would otherwise need A more sophisticated method is GIF (Graphics Interchange Format) compression, for .gif files Another is JPEG (Joint Photographic Experts Group), for .jpg files – Unlike the others, JPEG is lossy—it loses information – Generally OK for photographs (if you don’t compress them too much) because decompression adds “fake” data very similar to the original 82 JPEG Compression Photographic images incorporate a great deal of information. However, much of that information can be lost without objectionable deterioration in image quality. With this in mind, JPEG allows user-selectable image quality, but even at the “best” quality levels, JPEG makes an image file smaller owing to its multiple-step compression algorithm. It’s important to remember that JPEG is lossy, even at the highest quality setting. It should be used only when the loss can be tolerated. 83 2. Run Length Encoding (RLE) RLE: When data contain strings of repeated symbols (such as bits or characters), the strings can be replaced by a special marker, followed by the repeated symbol, followed by the number of occurrences. In general, the number of occurrences (length) is shown by a two digit number. If the special marker itself occurs in the data, it is duplicated (as in character stuffing). RLE can be used in audio (silence is a run of 0s) and video (run of a picture element having the same brightness and color). 84 An Example of Run-Length Encoding 85 2. Run Length Encoding (RLE) Example – # is chosen as the special marker. – Two-digit number is chosen for the repetition count. – Consider the following string of decimal digits 15000000000045678111111111111118 Using RLE algorithm, the above digital string would be encoded as: 15#01045678#1148 – The compression ration would be (1 – (16/32)) * 100% = 50% 86 87 Transmitting Information – Binary codes – Encoding with parity-check sums – Data compression – Cryptography – Model the genetic code 88 Model the genetic code The genome基因組 is the instruction manual for life, an information system that specifies the biological body. In its simplest form, it consists of a linear sequence of four extremely small molecules, called nucleotides. These nucleotides make up the “steps” of the spiral-staircase structure of the DNA and are the letters of the genetic code. 89 90 The structure of part of a DNA double helix DNA is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms. 91 A DNA double helix The main role of DNA (Deoxyribonucleic acid 脱 氧核糖核酸) molecules is the long-term storage of information. 92 Four bases found in DNA The DNA double helix is stabilized by hydrogen bonds between the bases attached to the two strands. The four bases (nucleotides) found in DNA are adenine (abbreviated A), cytosine (C), guanine (G) and thymine (T). These four bases are attached to the sugar/phosphate to form the complete nucleotide 93 Escherichia coli genome >gb|U00096|U00096 Escherichia coli 大腸桿菌 K-12 MG1655 complete genome基因組 AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTG TGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTG AACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATT GACTTAGGTCACTAAATACTTTAACCAATATAGGCAT AGCGCACAGACAGATAAAAATTACAGAGTACACAAC ATCCATGAAACGCATTAGCACCACCATTACCACCACC ATCACCATTACCACAGGTAACGGTGCGGGCTGACGCG TACAGGAAACACAGAAAAAAGCCCGCACCTGACAGT GCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAAC AACCATGCGAGTGTTGAA 94 Hierarchies of symbols English letter (26) word (1-28 letters) sentence book computer bit (2) byte (8 bits) line program genetics nucleotide核苷酸(4) codon (3 nucleotides) gene genome 95 A typical communication system Shannon (1948) DNA Message Information Source: Parents Signal Received Signal Receiver Transmitter Message Destination: Child Noise Source Mutation Information Theory 96 DNA from an Information Theory Perspective The “alphabet” for DNA is {A,C,G,T}. Each DNA strand is a sequence of symbols from this alphabet. These sequences are replicated and translated in processes reminiscent of Shannon’s communication model. There is redundancy in the genetic code that enhances its error tolerance. 97 The Central Dogma of Molecular Biology Replication Transcription Translation RNA DNA Protein Reverse Transcription Ribonucleic acid 核糖核酸 What Information Theory Contributes to Genetic Biology A useful model for how genetic information is stored and transmitted in the cell A theoretical justification for the observed redundancy of the genetic code Data Compression in gene sequences As an illustration of data compression, let’s use the idea of gene sequences. Biologists are able to describe genes by specifying sequences composed of the four letters A, T, G, and C, which stand for the four nucleotides adenine, thymine, guanine, and cytosine, respectively. Suppose we wish to encode the sequence AAACAGTAAC. 100 Data Compression (cont.) One way is to use the (fixed-length) code: A00, C01, T10, and G11. Then AAACAGTAAC is encoded as: 00000001001110000001. From experience, biologists know that the frequency of occurrence from most frequent to least frequent is A, C, T, G. Thus, it would more efficient to choose the following binary code: A0, C10, T110, and G111. With this new code, AAACAGTAAC is encoded as: 0001001111100010. Notice that this new binary code word has 16 letters versus 20 letters for the fixed-length code, a decrease of 20%. This new code is an example of data compression! 101 Data Compression (cont.) Suppose we wish to decode a sequence encoded with the new data compression scheme, such as 0001001111100010. Looking at groups of three digits at a time, we can decode this message! Since 0 only occurs at the end of a code word, and the codes words that end in 0 are 0, 10, and 110, we can put a mark after every 0, as this will be the end of a code word. The only time a sequence of 111 occurs is for the code word 111, so we can put a mark after every triple of 1’s. Thus, we have: 0,0,0,10,0,111,110,0,0,10, which is AAACAGTAAC. 102 103