1. Announcements: Project 5 Everything we have been learning thus far will enable us to solve interesting problems Project 5 will focus on applying the skills we have learned on a problem from biology, specifically computational biology Email your group / group requests by Friday Project 5 will be released tomorrow late afternoon

2. Announcements Midterm 2: Same curve as Midterm 1 Pre Lab 15 will be released next Friday Stale version of week 12 slides was accidently uploaded to the wiki (correct slides were presented in class) – this has been fixed, please re download

3. O(1) Example def isOdd(list): return (len(list)%2 == 1) >>> isOdd([0]) True >>> isOdd([0,1]) False

4. Clicker Question def getFirst(list): if len(list) == 0: return -1 return (list[0]) A: O(n) B: O(n 2 ) C: O(1) >>> getFirst([]) >>> getFirst([0,1,2,3]) 0 >>> getFirst(["a", "b", "c"]) 'a’

5. Building the Intuition Logic Puzzle: You have 9 marbles. 8 marbles weigh 1 ounce each, & one marble weighs 1.5 ounces. You are unable to determine which is the heavier marble by looking at them. How do you find the marble which weighs more?

6. Solution 1: Weigh one marble vs another What is the complexity of this solution?

7. Finding the complexity Step 1: What is our input? The marbles Step 2: How much work do we do per marble? We weight each marble once (except one) Step 3: What is the total work we did? 8 measurements What if we had 100 marbles or 1000?

8. Clicker Question: What is the complexity of this algorithm? A: O(n) B: O(n 2 ) C: O(1) D: O(log n)

9. We can do better! Lets pull some intuition from our search algorithm that was O(log n) We want a way to eliminated ½ (or more) of the marbles with each measurement How might we do this? What about weighing multiple marbles at once?

10. The Optimal Solution Split the marbles into three groups We can then weigh two of the groups

11. Finding the complexity of the optimal solution Step 1: What is our input? The marbles Step 2: How much work do we do per marble? Logarithmic Step 3: What is the total work we did? 2 measurements What if we had 100 marbles or 1000?

12. What happens at each step? We eliminated 2/3rds of the marbles

13. Clicker Question: What is the complexity of this algorithm? A: O(n) B: O(n 2 ) C: O(1) D: O(log n)

14. Sorting Motivation We can answer questions like min/max very efficiently We can search very efficiently What if we need to search many many times Many algorithms require their input to be sorted

15. Intuition behind bubble sort Background reading (homework): http://en.wikipedia.org/wiki/Bubble_sort Bubble sort takes a list and returns a sorted list Compare each pair of adjacent items and swap them if the one to the right is smaller Assumption: we want our list sorted from smallest to greatest

16. Intuition behind bubble sort [5, 7, 9, 0, 3, 5, 6] [5, 7, 0, 9, 3, 5, 6] [5, 7, 0, 3, 9, 5, 6] [5, 7, 0, 3, 5, 9, 6] [5, 7, 0, 3, 5, 6, 9]

17. Intuition behind bubble sort [5, 7, 0, 3, 5, 6, 9] [5, 0, 7, 3, 5, 6, 9] [5, 0, 3, 7, 5, 6, 9] [5, 0, 3, 5, 7, 6, 9] [5, 0, 3, 5, 6, 7, 9]

18. Intuition behind bubble sort How many passes do we have to do before we are guaranteed the list is sorted? n passes, where n is the length of the list In each pass we do how much work? n-1 comparisons What is the total work? Complexity?

19. Changing our Intuition into Code def BubbleSort(myList): swapped = True while swapped: swapped = False for i in range(len(myList)-1): if myList[i] > myList[i+1]: temp = myList[i] myList[i] = myList[i+1] myList[i+1] = temp swapped = True return myList The main loop Keep executing the loop IF we do a swap

20. Changing our Intuition into Code def BubbleSort(myList): swapped = True while swapped: swapped = False for i in range(len(myList)-1): if myList[i] > myList[i+1]: temp = myList[i] myList[i] = myList[i+1] myList[i+1] = temp swapped = True return myList The loop that executes the swaps

21. Changing our Intuition into Code def BubbleSort(myList): swapped = True while swapped: swapped = False for i in range(len(myList)-1): if myList[i] > myList[i+1]: temp = myList[i] myList[i] = myList[i+1] myList[i+1] = temp swapped = True return myList Check if the two numbers should be swapped

22. Changing our Intuition into Code def BubbleSort(myList): swapped = True while swapped: swapped = False for i in range(len(myList)-1): if myList[i] > myList[i+1]: temp = myList[i] myList[i] = myList[i+1] myList[i+1] = temp swapped = True return myList Swap!

23. Fast Swapping of Two Variables Python provides us the ability to perform the swap in a much more efficient manner >>> a = 5 >>> b = 7 >>> a, b = b, a >>> print a 7 >>> print b 5 variable1, variable 2 = variable2, variable1

24. Changing our Intuition into Code def BubbleSort(myList): swapped = True while swapped: swapped = False for i in range(len(myList)-1): if myList[i] > myList[i+1]: myList[i], myList[i+1] = myList[i+1], myList[i] swapped = True return myList Swap!

25. Homework Reach Chapter 11 from the text book

26. Can we sort faster? Bubble sort certainly will sort our data for us Unfortunately it simply is not fast enough We can sort faster! There are algorithms which sort in O(n log n) or log linear time Lets reason why this is the case

27. Observation 1: We can merge two sorted lists in linear time What is in the input? Both the lists, n = total amount of elements Why is the complexity linear? We must examine each element in each of the lists Its linear in the total amount of elements O(len(list1) + len(list2)) = O(n)

28. Observation 1: We can merge two sorted lists in linear time [5,9,10, 100, 555] [3,4,12, 88, 535] [3]

29. Observation 1: We can merge two sorted lists in linear time [5,9,10, 100, 555] [3,4,12, 88, 535] [3, 4]

30. Observation 1: We can merge two sorted lists in linear time [5,9,10, 100, 555] [3,4,12, 88, 535] [3,4,5]

31. Observation 1: We can merge two sorted lists in linear time [5,9,10, 100, 555] [3,4,12, 88, 535] [3,4,5,9]

32. Observation 1: We can merge two sorted lists in linear time [5,9,10, 100, 555] [3,4,12, 88, 535] [3,4,5,9,10]

33. Observation 1: We can merge two sorted lists in linear time [5,9,10, 100, 555] [3,4,12, 88, 535] [3,4,5,9,10,12]

34. Observation 1: We can merge two sorted lists in linear time [5,9,10, 100, 555] [3,4,12, 88, 535] [3,4,5,9,10,12, 88]

35. Observation 2 Notice that merging two lists of length one ends up producing a sorted list of length two [5] [3] [5] [3] [3,5] [5] [3] [3,5]

36. Lets build the intuition for Merge-Sort We know we can merge sorted lists in linear time We know that merging two lists of length one results in a sorted list of length two Lets split our unsorted list into a bunch of lists of length one and merge them into progressively bigger lists! We split a list into two smaller lists of equal parts Keep splitting until we have lists of length one

37. Visual Representation log(n) n elements merged

38. Putting it all together We know that there are log(n) splits At each “level” we split each list in two We know that we need to merge a total of n elements at each “level” n * log(n) thus O(n log n)

39. Synopsis Took a look at the code for bubble sort We learned an efficient way to swap the contents of two variables (or list locations) We built the intuition as to why we can sort faster than quadratic time Introduced the concept of merge sort

40. Homework Start working on Project 5 Play around with the concepts presented in recitation as well as the pre lab They will help both with the lab AND project 5 Review the project 4 solution Many of the same concepts will be used in project 5