I've got the following task to do:
Given a rectangular chocolate bar, consisting of m x n small rectangles, and the wish of breaking it into its parts. At each step you can only pick one piece and break it either along any of its vertical lines or along its horizontal lines. How should you break the chocolate bar using the minimum number of steps?
I know you need exactly m x n - 1 steps to break the chocolate bar, but I'm asked to do it "the CS way:"
Define a predicate which selects the minimum number of steps among all alternative possibilities to break the chocolate bar into pieces. Construct a straucture on an additional argument position, which tells you where and how to break the bar and what to do with the resulting two pieces.
My thoughts: after breaking the piece of chocolate once, you have the choice of breaking it either on its vertical or its horizontal lines. So this is my code, but it doesn't work:
break_chocolate(Horizontal, Vertical, Minimum) :-
break_horizontal(Horizontal, Vertical, Min1),
break_vertical(Horizontal, Vertical, Min2),
Minimum is min(Min1, Min2).
break_horizontal(0,0,_).
break_vertical(0,0,_).
break_horizontal(0, V, Min) :-
V > 0,
break_horizontal(0, V, Min).
break_horizontal(H, V, Min) :-
H1 is H-1,
Min1 is Min + 1,
break_vertical(H1, V, Min1).
break_horizontal(H, V, Min) :-
H1 is H-1,
Min1 is Min + 1,
break_vertical(H1, V, Min).
break_vertical(H, V, Min) :-
V1 is V-1,
Min1 is Min + 1,
break_horizontal(H, V1, Min1).
break_vertical(H, V, Min) :-
V1 is V-1,
Min1 is Min + 1,
break_vertical(H, V1, Min1).
break_vertical(H, 0, Min) :-
H > 0,
break_horizontal(H, 0, Min).
Could anyone help me with this one?
This is not a complete answer, but should push you towards the right direction:
First an observation: every time you cut a chocolate bar, you end up with exactly one more pieces than you had before. So, actually, there is no "minimal" number of breaks you can have; you start with 1 piece (the whole bar), and you end up with m * n pieces, so you always have exactly m * n - 1 breaks. So either you have misunderstood your problem statement, or somehow misrepresented it in your question.
Second: once you break into two pieces, you will have to break each of the two in the same way that you have broken the previous one. One way to program that would be with a recursive call. I don't see this in your program, as it stands.
Third: so do you want to report the breaks that you make? How are you going to do this?
Whether you program in Prolog, C, or JavaScript, understanding your problem is a prerequisite to finding a solution.
Here are some additional hints for representing and solving your problem.
Each break separates one piece into two pieces (see Boris' second hint). You can, therefore, think of the collection of breaks as a binary tree of breaks which has the following characteristics:
The root node of the tree has the value M-N (the bar is M x N in dimension)
Suppose X-Y represents the value of any node in the tree representing a single X by Y piece that is not the single piece, 1-1. Since the two children of the node represents the piece of dimension X and Y being broken along one dimension, then the children of X-Y either have the values A-Y and B-Y where A + B = X, or the values X-A and X-B where A + B = Y
All of the leaf nodes of the tree have the value 1-1 (the smallest possible piece)
Each node of a binary tree consists of the node value, the left sub tree, and the right sub tree. An empty sub tree would have the value nil (or some other suitably chosen atom). A common representation of a tree would be something like, btree(X-Y, LeftSubTree, RightSubTree) (the term X-Y being the value of the top node of the tree, which in this problem, would be the dimensions of the piece in question). Using this scheme, the smallest piece of candy would be, btree(1-1, nil, nil), for example. A set of breaks for a 2 x 1 candy bar would be, btree(2-1, btree(1-1, nil, nil), btree(1-1, nil, nil)).
You can use the CLPFD library to constrain C #= A + B, A #> 0, B #> 0 and, to eliminate symmetrical cases, A #=< B.
As an algorithm (I'm not familiar with Prolog), I can't find any different answers in the number of breaks. I've tried 4x4, and been unable to come up with an answer other than 15 (either above or below); I've tried with a 5x2 and been unable to come up with an answer other than 9.
On this basis, I would suggest the simplest possible coding method:
while there is more than one column:
snap off the left-most column
while this column has more than one square:
snap off the top square
while the remaining column has more than one square:
snap off the top square
Depending on the situation, you may wish to change one or more of: (left, column)<->(top, row), left->right, top->bottom.
Related
I understand that there are mainly two approaches to dynamic programming solutions:
Fixed optimal order of evaluation (lets call it Foo approach): Foo approach usually goes from subproblems to bigger problems thus using results obtained earlier for subproblems to solve bigger problems, thus avoiding "revisiting" subproblem. CLRS also seems to call this "Bottom Up" approach.
Without fixed optimal order of evaluation (lets call it Non-Foo approach): In this approach evaluation proceeds from problems to their sub-problems . It ensures that sub problems are not "re-evaluated" (thus ensuring optimality) by maintaining results of their past evaluations in some data structure and then first checking if the result of the problem at hand exists in this data structure before starting its evaluation. CLRS seem to call this as "Top Down" approach
This is what is roughly conveyed as one of the main points by this answer.
I have following doubts:
Q1. Memoization or not?
CLRS uses terms "top down with memoization" approach and "bottom up" approach. I feel both approaches require memory to cache results of sub problems. But, then, why CLRS use term "memoization" only for top down approach and not for bottom up approach? After solving some problems by DP approach, I feel that solutions by top down approach for all problems require memory to caches results of "all" subproblems. However, that is not the case with bottom up approach. Solutions by bottom up approach for some problems does not need to cache results of "all" sub problems. Q1. Am I correct with this?
For example consider this problem:
Given cost[i] being the cost of ith step on a staircase, give the minimum cost of reaching the top of the floor if:
you can climb either one or two steps
you can start from the step with index 0, or the step with index 1
The top down approach solution is as follows:
class Solution:
def minCostAux(self, curStep, cost):
if self.minCosts[curStep] > -1:
return self.minCosts[curStep]
if curStep == -1:
return 0
elif curStep == 0:
self.minCosts[curStep] = cost[0]
else:
self.minCosts[curStep] = min(self.minCostAux(curStep-2, cost) + cost[curStep]
, self.minCostAux(curStep-1, cost) + cost[curStep])
return self.minCosts[curStep]
def minCostClimbingStairs(self, cost) -> int:
cost.append(0)
self.minCosts = [-1] * len(cost)
return self.minCostAux(len(cost)-1, cost)
The bottom up approach solution is as follows:
class Solution:
def minCostClimbingStairs(self, cost) -> int:
cost.append(0)
secondLastMinCost = cost[0]
lastMinCost = min(cost[0]+cost[1], cost[1])
minCost = lastMinCost
for i in range(2,len(cost)):
minCost = min(lastMinCost, secondLastMinCost) + cost[i]
secondLastMinCost = lastMinCost
lastMinCost = minCost
return minCost
Note that the top down approach caches result of all steps in self.minCosts while bottom up approach caches result of only last two steps in variables lastMinCost and secondLastMinCost.
Q2. Does all problems have solutions by both approaches?
I feel no. I came to this opinion after solving this problem:
Find the probability that the knight will not go out of n x n chessboard after k moves, if the knight was initially kept in the cell at index (row, column).
I feel the only way to solve this problem is to find successive probabilities in increasing number of steps starting from cell (row, column), that is probability that the knight will not go out of chessboard after step 1, then after step 2, then after step 3 and so on. This is bottom up approach. We cannot do it top down, for example, we cannot start with kth step and go to k-1th step, then k-2th step and so on, because:
We cannot know which cells will be reached in kth step to start with
We cannot ensure that all paths from kth step will lead to initial knight cell position (row,column).
Even one of the top voted answer gives dp solution as follows:
class Solution {
private int[][]dir = new int[][]{{-2,-1},{-1,-2},{1,-2},{2,-1},{2,1},{1,2},{-1,2},{-2,1}};
private double[][][] dp;
public double knightProbability(int N, int K, int r, int c) {
dp = new double[N][N][K + 1];
return find(N,K,r,c);
}
public double find(int N,int K,int r,int c){
if(r < 0 || r > N - 1 || c < 0 || c > N - 1) return 0;
if(K == 0) return 1;
if(dp[r][c][K] != 0) return dp[r][c][K];
double rate = 0;
for(int i = 0;i < dir.length;i++) rate += 0.125 * find(N,K - 1,r + dir[i][0],c + dir[i][1]);
dp[r][c][K] = rate;
return rate;
}
}
I feel this is still a bottom up approach since it starts with initial knight cell position (r,c) (and hence starts from 0th or no step to Kth step) despite the fact that it counts K downwads to 0. So, this is bottom up approach done recursively and not top down approach. To be precise, this solution does NOT first find:
probability of knight not going out of chessboard after K steps starting at cell (r,c)
and then find:
probability of knight not going out of chessboard after K-1 steps starting at cell (r,c)
but it finds in reverse / bottom up order: first for K-1 steps and then for K steps.
Also, I did not find any solutions in of top voted discussions in leetcode doing it in truly top down manner, starting from Kth step to 0th step ending in (row,column) cell, instead of starting with (row,column) cell.
Similarly we cannot solve the following problem with the bottom up approach but only with top down approach:
Find the probability that the Knight ends up in the cell at index (row,column) after K steps, starting at any initial cell.
Q2. So am I correct with my understanding that not all problems have solutions by both top down or bottom up approaches? Or am I just overthinking unnecessarily and both above problems can indeed be solved with both top down and bottom up approaches?
PS: I indeed seem to have done overthinking here: knightProbability() function above is indeed top down, and I ill-interpreted as explained in detailed above 😑. I have kept this explanation for reference as there are already some answers below and also as a hint of how confusion / mis-interpretaions might happen, so that I will be more cautious in future. Sorry if this long explanation caused you some confusion / frustrations. Regardless, the main question still holds: does every problem have bottom up and top down solutions?
Q3. Bottom up approach recursively?
I am pondering if bottom up solutions for all problems can also be implemented recursively. After trying to do so for other problems, I came to following conclusion:
We can implement bottom up solutions for such problems recursively, only that the recursion won't be meaningful, but kind of hacky.
For example, below is recursive bottom up solution for minimum cost climbing stairs problem mentioned in Q1:
class Solution:
def minCostAux(self, step_i, cost):
if self.minCosts[step_i] != -1:
return self.minCosts[step_i]
self.minCosts[step_i] = min(self.minCostAux(step_i-1, cost)
, self.minCostAux(step_i-2, cost)) + cost[step_i]
if step_i == len(cost)-1: # returning from non-base case, gives sense of
# not-so meaningful recursion.
# Also, base cases usually appear at the
# beginning, before recursive call.
# Or should we call it "ceil condition"?
return self.minCosts[step_i]
return self.minCostAux(step_i+1, cost)
def minCostClimbingStairs(self, cost: List[int]) -> int:
cost.append(0)
self.minCosts = [-1] * len(cost)
self.minCosts[0] = cost[0]
self.minCosts[1] = min(cost[0]+cost[1], cost[1])
return self.minCostAux(2, cost)
Is my quoted understanding correct?
First, context.
Every dynamic programming problem can be solved without dynamic programming using a recursive function. Generally this will take exponential time, but you can always do it. At least in principle. If the problem can't be written that way, then it really isn't a dynamic programming problem.
The idea of dynamic programming is that if I already did a calculation and have a saved result, I can just use that saved result instead of doing the calculation again.
The whole top-down vs bottom-up distinction refers to the naive recursive solution.
In a top-down approach your call stack looks like the naive version except that you make a "memo" of what the recursive result would have given. And then the next time you short-circuit the call and return the memo. This means you can always, always, always solve dynamic programming problems top down. There is always a solution that looks like recursion+memoization. And that solution by definition is top down.
In a bottom up approach you start with what some of the bottom levels would have been and build up from there. Because you know the structure of the data very clearly, frequently you are able to know when you are done with data and can throw it away, saving memory. Occasionally you can filter data on non-obvious conditions that are hard for memoization to duplicate, making bottom up faster as well. For a concrete example of the latter, see Sorting largest amounts to fit total delay.
Start with your summary.
I strongly disagree with your thinking about the distinction in terms of the optimal order of evaluations. I've encountered many cases with top down where optimizing the order of evaluations will cause memoization to start hitting sooner, making code run faster. Conversely while bottom up certainly picks a convenient order of operations, it is not always optimal.
Now to your questions.
Q1: Correct. Bottom up often knows when it is done with data, top down does not. Therefore bottom up gives you the opportunity to delete data when you are done with it. And you gave an example where this happens.
As for why only one is called memoization, it is because memoization is a specific technique for optimizing a function, and you get top down by memoizing recursion. While the data stored in dynamic programming may match up to specific memos in memoization, you aren't using the memoization technique.
Q2: I do not know.
I've personally found cases where I was solving a problem over some complex data structure and simply couldn't find a bottom up approach. Maybe I simply wasn't clever enough, but I don't believe that a bottom up approach always exists to be found.
But top down is always possible. Here is how to do it in Python for the example that you gave.
First the naive recursive solution looks like this:
def prob_in_board(n, i, j, k):
if i < 0 or j < 0 or n <= i or n <= j:
return 0
elif k <= 0:
return 1
else:
moves = [
(i+1, j+2), (i+1, j-2),
(i-1, j+2), (i-1, j-2),
(i+2, j+1), (i+2, j-1),
(i-2, j+1), (i-2, j-1),
]
answer = 0
for next_i, next_j in moves:
answer += prob_in_board(n, next_i, next_j, k-1) / len(moves)
return answer
print(prob_in_board(8, 3, 4, 7))
And now we just memoize.
def prob_in_board_memoized(n, i, j, k, cache=None):
if cache is None:
cache = {}
if i < 0 or j < 0 or n <= i or n <= j:
return 0
elif k <= 0:
return 1
elif (i, j, k) not in cache:
moves = [
(i+1, j+2), (i+1, j-2),
(i-1, j+2), (i-1, j-2),
(i+2, j+1), (i+2, j-1),
(i-2, j+1), (i-2, j-1),
]
answer = 0
for next_i, next_j in moves:
answer += prob_in_board_memoized(n, next_i, next_j, k-1, cache) / len(moves)
cache[(i, j, k)] = answer
return cache[(i, j, k)]
print(prob_in_board_memoized(8, 3, 4, 7))
This solution is top down. If it seems otherwise to you, then you do not correctly understand what is meant by top-down.
I found your question ( does every dynamic programming problem have bottom up and top down solutions ? ) very interesting. That's why I'm adding another answer to continue the discussion about it.
To answer the question in its generic form, I need to formulate it more precisely with math. First, I need to formulate precisely what is a dynamic programming problem. Then, I need to define precisely what is a bottom up solution and what is a top down solution.
I will try to put some definitions but I think they are not the most generic ones. I think a really generic definition would need more heavy math.
First, define a state space S of dimension d as a subset of Z^d (Z represents the integers set).
Let f: S -> R be a function that we are interested in calculate for a given point P of the state space S (R represents the real numbers set).
Let t: S -> S^k be a transition function (it associates points in the state space to sets of points in the state space).
Consider the problem of calculating f on a point P in S.
We can consider it as a dynamic programming problem if there is a function g: R^k -> R such that f(P) = g(f(t(P)[0]), f(t(P)[1]), ..., f(t(P)[k])) (a problem can be solved only by using sub problems) and t defines a directed graph that is not a tree (sub problems have some overlap).
Consider the graph defined by t. We know it has a source (the point P) and some sinks for which we know the value of f (the base cases). We can define a top down solution for the problem as a depth first search through this graph that starts in the source and calculate f for each vertex at its return time (when the depth first search of all its sub graph is completed) using the transition function. On the other hand, a bottom up solution for the problem can be defined as a multi source breadth first search through the transposed graph that starts in the sinks and finishes in the source vertex, calculating f at each visited vertex using the previous visited layer.
The problem is: to navigate through the transposed graph, for each point you visit you need to know what points transition to this point in the original graph. In math terms, for each point Q in the transition graph, you need to know the set J of points such that for each point Pi in J, t(Pi) contains Q and there is no other point Pr in the state space outside of J such that t(Pr) contains Q. Notice that a trivial way to know this is to visit all the state space for each point Q.
The conclusion is that a bottom up solution as defined here always exists but it only compensates if you have a way to navigate through the transposed graph at least as efficiently as navigating through the original graph. This depends essentially in the properties of the transition function.
In particular, for the leetcode problem you mentioned, the transition function is the function that, for each point in the chessboard, gives all the points to which the knight can go to. A very special property about this function is that it's symmetric: if the knight can go from A to B, then it can also go from B to A. So, given a certain point P, you can know to which points the knight can go as efficiently as you can know from which points the knight can come from. This is the property that guarantees you that there exists a bottom up approach as efficient as the top down approach for this problem.
For the leetcode question you mentioned, the top down approach is like the following:
Let P(x, y, k) be the probability that the knight is at the square (x, y) at the k-th step. Look at all squares that the knight could have come from (you can get them in O(1), just look at the board with a pen and paper and get the formulas from the different cases, like knight in the corner, knight in the border, knight in a central region etc). Let them be (x1, y1), ... (xj, yj). For each of these squares, what is the probability that the knight jumps to (x, y) ? Considering that it can go out of the border, it's always 1/8. So:
P(x, y, k) = (P(x1, y1, k-1) + ... + P(xj, yj, k-1))/8
The base case is k = 0:
P(x, y ,0) = 1 if (x, y) = (x_start, y_start) and P(x, y, 0) = 0 otherwise.
You iterate through all n^2 squares and use the recurrence formula to calculate P(x, y, k). Many times you will need solutions you already calculated for k-1 and so you can benefit a lot from memoization.
In the end, the final solution will be the sum of P(x, y, k) over all squares of the board.
The problem sounds like this: we get n-cubes. Each cube has a length (the edge's length) and a colour. The edges' lengths are distinct, but the culours are not, for instance: any two cubes can never have the same length, but it is possible to have the same colour. The colours are from 1 to p (p is given).
We have to build a cube-tower that has a maximum height, following these rules:
1) a cube cannot be placed upon a cube if they have the same colour;
2) a cube cannot pe placed upon a cube whose edge's length is smaller.
e.g: cube c1 has a length of 3, cube c2 has a length of 5. cube c1 can be placed on the top of c2, but cube c2 cannot be placed on the top of c1.
Alright, so the algorithm I came up with in order to solve this problem is this:
we sort the cubes by edge length, in descending order and we put them in an array;
we add the first cube in the array to the Tower;
we save the length of the last inserted cube( in this case, the first cube's length ) in variable l;
we save the colour of the last inserted cube( in this case, the first cube's colour ) in variable c;
we go through the rest of the array, inserting the first cube whose length is smaller than l and colour different than c and then we repeat 3-4-5;
Now what I'm having difficulties with is, how do I prove this greedy algorithm to be the optimal one? I guess that the proof has to somehow look like the ones here: http://www.cs.princeton.edu/~wayne/kleinberg-tardos/pdf/04GreedyAlgorithmsI-2x2.pdf
The question is:
Is there a case where picking the max-length cube is not optimal?
At each decision-node we have to decide if we pick a or b, given a>b:
Assume picking b is strictly optimal (implies max-height):
Case 1: col(a) == col(b)
b optimal => final tower: b, x0, x1, ...
but also valid by construction with equal height: a, x0, x1, ...
valid because: col(a) == col(b), (a > b) & (b > x0) => (a > x0) (transitivity)
contradiction!
Case 2 col(a) != col(b)
b optimal -> final tower: b, x0, x1, ...
but also valid construction with more height: a, b, x0, x1, ...
valid because: (a > b) & (col(a) != col(b)) => a before b
contradiction!
We assumed picking b is strictly optimal and showed contradictions. Picking b can only be equally good or worse than picking a (the max-length cube of the remaining ones).
I have pairs of series of timed measurements I want to align. I have
annotators judging and marking ambiguous events in a signal and want
to optimally match their times and events. The input is four columns:
the event onset times and labels for one annotator, and the times and
labels for the other annotator. For example (as rows):
annotator_1_times: .34, .39, .50, .68, .88
annotator_1_label: A, X, Q, L, Z
annotator_2_times: .33, .41, .67, .90
annotator_2_label: A, X, L, X
Annotators don't necessarily have the same number of events when they
interpret the same signal. Annotators in general are expected to have
similar but nonidentical labels, and similar but nonidentical times.
How this should be done depends on some sort of cost function --
something that will decide how "bad" it is for a time to be off a
certain amount, and for two labels to disagree.
A desirable output in my example case:
annotator_1_times: .34, .39, .50, .68, .88
annotator_1_label: A, X, Q, L, Z
annotator_2_times: .33, .41, [], .67, .90 <-note gap inserted
annotator_2_label: A, X, [], L, X
Stuff I would then do post hoc:
time_mismatch_dif: .01, .02, XX, .01, .02 <- for computing agreemt
label_mismatches_: 0, 0, ADD, 0, SUBST <- for computing agreemt
The hard part is to know where to insert the gaps.
If need be, I can do just the numerical alignments and separately just
the label alignments and then merge them somehow. I know there are
character alignment algorithms (e.g. in genetics) and there must be
time-series alignment algorithms.
Any suggestions welcome.
Your problem is very similar to Levenshtein distance problem, and you can adapt the same algorithm there.
Firstly define your cost function.
Then, run a dynamic programming on a quadratic table: for each i and j calculate ans[i][j], that is the 'cost of alignment' of first i events from the first annotator and first j events from the second. This can be done in three ways:
either you align i and j, then ans[i][j] becomes ans[i-1][j-1] + costAlignment(a[i],b[j])
either you align i and 'gap', then ans[i][j] becomes ans[i-1][j] + costGap(a[i])
either you align j and 'gap', then ans[i][j] becomes ans[i][j-1] + costGap(b[j])
You should choose minimum of three options.
I am trying to implement the Parallel Algorithm for Longest Common Subsequence Problem described in http://www.iaeng.org/publication/WCE2010/WCE2010_pp499-504.pdf
But i am having a problem with the variable C in Equation 6 on page 4
The paper refered to C on at the end of page 3 as
C as Let C[1 : l] bethe finite alphabet
I am not sure what is ment by this, as i guess it would it with the 2 strings ABCDEF and ABQXYEF be ABCDEFQXY. But what if my 2 stings is a list of objects (Where my match test for an example is obj1.Name = obj2.Name), what would my C be here? just a union on the 2 arrays?
Having read and studied the paper, I can say that C is supposed to be an array holding the alphabet of your strings, where the alphabet size (and, thus, the size of C) is l.
By the looks of your question, however, I feel the need to go deeper on this, because it looks like you didn't get the whole picture yet. What is P[i,j], and why do you need it? The answer is that you don't really need it, but it's an elegant optimization. In page 3, a little bit before Theorem 1, it is said that:
[...] This process ends when j-k = 0 at the k-th step, or a(i) =
b(j-k) at the k-th step. Assume that the process stops at the k-th
step, and k must be the minimum number that makes a(i) = b(j-k) or j-k
= 0. [...]
The recurrence relation in (3) is equivalent to (2), but the fundamental difference is that (2) expands recursively, whereas with (3) you never have recursive calls, provided that you know k. In other words, the magic behind (3) not expanding recursively is that you somehow know the spot where the recursion on (2) would stop, so you look at that cell immediately, rather than recursively approaching it.
Ok then, but how do you find out the value for k? Since k is the spot where (2) reaches a base case, it can be seen that k is the amount of columns that you have to "go back" on B until you are either off the limits (i.e., the first column that is filled with 0's) OR you find a match between a character in B and a character in A (which corresponds to the base case conditions in (2)). Remember that you will be matching the character a(i-1), where i is the current row.
So, what you really want is to find the last position in B before j where the character a(i-1) appears. If no such character ever appears in B before j, then that would be equivalent to reaching the case i = 0 or j-1 = 0 in (2); otherwise, it's the same as reaching a(i) = b(j-1) in (2).
Let's look at an example:
Consider that the algorithm is working on computing the values for i = 2 and j = 3 (the row and column are highlighted in gray). Imagine that the algorithm is working on the cell highlighted in black and is applying (2) to determine the value of S[2,2] (the position to the left of the black one). By applying (2), it would then start by looking at a(2) and b(2). a(2) is C, b(2) is G, to there's no match (this is the same procedure as the original, well-known algorithm). The algorithm now wants to find the value of S[2,2], because it is needed to compute S[2,3] (where we are). S[2,2] is not known yet, but the paper shows that it is possible to determine that value without refering to the row with i = 2. In (2), the 3rd case is chosen: S[2,2] = max(S[1, 2], S[2, 1]). Notice, if you will, that all this formula is doing is looking at the positions that would have been used to calculate S[2,2]. So, to rephrase that: we're computing S[2,3], we need S[2,2] for that, we don't know it yet, so we're going back on the table to see what's the value of S[2,2] in pretty much the same way we did in the original, non-parallel algorithm.
When will this stop? In this example, it will stop when we find the letter C (this is our a(i)) in TGTTCGACA before the second T (the letter on the current column) OR when we reach column 0. Because there is no C before T, we reach column 0. Another example:
Here, (2) would stop with j-1 = 5, because that is the last position in TGTTCGACA where C shows up. Thus, the recursion reaches the base case a(i) = b(j-1) when j-1 = 5.
With this in mind, we can see a shortcut here: if you could somehow know the amount k such that j-1-k is a base case in (2), then you wouldn't have to go through the score table to find the base case.
That's the whole idea behind P[i,j]. P is a table where you lay down the whole alphabet vertically (on the left side); the string B is, once again, placed horizontally in the upper side. This table is computed as part of a preprocessing step, and it will tell you exactly what you will need to know ahead of time: for each position j in B, it says, for each character C[i] in C (the alphabet), what is the last position in B before j where C[i] is found (note that i is used to index C, the alphabet, and not the string A. Maybe the authors should have used another index variable to avoid confusion).
So, you can think of the semantics for an entry P[i,j] as something along the lines of: The last position in B where I saw C[i] before position j. For example, if you alphabet is sigma = {A, E, I, O, U}, and B = "AOOIUEI", thenP` is:
Take the time to understand this table. Note the row for O. Remember: this row lists, for every position in B, where is the last known "O". Only when j = 3 will we have a value that is not zero (it's 2), because that's the position after the first O in AOOIUEI. This entry says that the last position in B where O was seen before is position 2 (and, indeed, B[2] is an O, the one that follows A). Notice, in that same row, that for j = 4, we have the value 3, because now the last position for O is the one that correspnds to the second O in B (and since no more O's exist, the rest of the row will be 3).
Recall that building P is a preprocessing step necessary if you want to easily find the value of k that makes the recursion from equation (2) stop. It should make sense by now that P[i,j] is the k you're looking for in (3). With P, you can determine that value in O(1) time.
Thus, the C[i] in (6) is a letter of the alphabet - the letter that we are currently considering. In the example above, C = [A,E,I,O,U], and C[1] = A, C[2] = E, etc. In equaton (7), c is the position in C where a(i) (the current letter of string A being considered) lives. It makes sense: after all, when building the score table position S[i,j], we want to use P to find the value of k - we want to know where was the last time we saw an a(i) in B before j. We do that by reading P[index_of(a(i)), j].
Ok, now that you understand the use of P, let's see what's happening with your implementation.
About your specific case
In the paper, P is shown as a table that lists the whole alphabet. It is a good idea to iterate through the alphabet because the typical uses of this algorithm are in bioinformatics, where the alphabet is much, much smaller than the string A, making the iteration through the alphabet cheaper.
Because your strings are sequences of objects, your C would be the set of all possible objects, so you'd have to build a table P with the set of all possible object instance (nonsense, of course). This is definitely a case where the alphabet size is huge when compared to your string size. However, note that you will only be indexing P in those rows that correspond to letters from A: any row in P for a letter C[i] that is not in A is useless and will never be used. This makes your life easier, because it means you can build P with the string A instead of using the alphabet of every possible object.
Again, an example: if your alphabet is AEIOU, A is EEI and B is AOOIUEI, you will only be indexing P in the rows for E and I, so that's all you need in P:
This works and suffices, because in (7), P[c,j] is the entry in P for the character c, and c is the index of a(i). In other words: C[c] always belongs to A, so it makes perfect sense to build P for the characters of A instead of using the whole alphabet for the cases where the size of A is considerably smaller than the size of C.
All you have to do now is to apply the same principle to whatever your objects are.
I really don't know how to explain it any better. This may be a little dense at first. Make sure to re-read it until you really get it - and I mean every little detail. You have to master this before thinking about implementing it.
NOTE: You said you were looking for a credible and / or official source. I'm just another CS student, so I'm not an official source, but I think I can be considered "credible". I've studied this before and I know the subject. Happy coding!
I have a list of elements, each one identified with a type, I need to reorder the list to maximize the minimum distance between elements of the same type.
The set is small (10 to 30 items), so performance is not really important.
There's no limit about the quantity of items per type or quantity of types, the data can be considered random.
For example, if I have a list of:
5 items of A
3 items of B
2 items of C
2 items of D
1 item of E
1 item of F
I would like to produce something like:
A, B, C, A, D, F, B, A, E, C, A, D, B, A
A has at least 2 items between occurences
B has at least 4 items between occurences
C has 6 items between occurences
D has 6 items between occurences
Is there an algorithm to achieve this?
-Update-
After exchanging some comments, I came to a definition of a secondary goal:
main goal: maximize the minimum distance between elements of the same type, considering only the type(s) with less distance.
secondary goal: maximize the minimum distance between elements on every type. IE: if a combination increases the minimum distance of a certain type without decreasing other, then choose it.
-Update 2-
About the answers.
There were a lot of useful answers, although none is a solution for both goals, specially the second one which is tricky.
Some thoughts about the answers:
PengOne: Sounds good, although it doesn't provide a concrete implementation, and not always leads to the best result according to the second goal.
Evgeny Kluev: Provides a concrete implementation to the main goal, but it doesn't lead to the best result according to the secondary goal.
tobias_k: I liked the random approach, it doesn't always lead to the best result, but it's a good approximation and cost effective.
I tried a combination of Evgeny Kluev, backtracking, and tobias_k formula, but it needed too much time to get the result.
Finally, at least for my problem, I considered tobias_k to be the most adequate algorithm, for its simplicity and good results in a timely fashion. Probably, it could be improved using Simulated annealing.
First, you don't have a well-defined optimization problem yet. If you want to maximized the minimum distance between two items of the same type, that's well defined. If you want to maximize the minimum distance between two A's and between two B's and ... and between two Z's, then that's not well defined. How would you compare two solutions:
A's are at least 4 apart, B's at least 4 apart, and C's at least 2 apart
A's at least 3 apart, B's at least 3 apart, and C's at least 4 apart
You need a well-defined measure of "good" (or, more accurately, "better"). I'll assume for now that the measure is: maximize the minimum distance between any two of the same item.
Here's an algorithm that achieves a minimum distance of ceiling(N/n(A)) where N is the total number of items and n(A) is the number of items of instance A, assuming that A is the most numerous.
Order the item types A1, A2, ... , Ak where n(Ai) >= n(A{i+1}).
Initialize the list L to be empty.
For j from k to 1, distribute items of type Ak as uniformly as possible in L.
Example: Given the distribution in the question, the algorithm produces:
F
E, F
D, E, D, F
D, C, E, D, C, F
B, D, C, E, B, D, C, F, B
A, B, D, A, C, E, A, B, D, A, C, F, A, B
This sounded like an interesting problem, so I just gave it a try. Here's my super-simplistic randomized approach, done in Python:
def optimize(items, quality_function, stop=1000):
no_improvement = 0
best = 0
while no_improvement < stop:
i = random.randint(0, len(items)-1)
j = random.randint(0, len(items)-1)
copy = items[::]
copy[i], copy[j] = copy[j], copy[i]
q = quality_function(copy)
if q > best:
items, best = copy, q
no_improvement = 0
else:
no_improvement += 1
return items
As already discussed in the comments, the really tricky part is the quality function, passed as a parameter to the optimizer. After some trying I came up with one that almost always yields optimal results. Thank to pmoleri, for pointing out how to make this a whole lot more efficient.
def quality_maxmindist(items):
s = 0
for item in set(items):
indcs = [i for i in range(len(items)) if items[i] == item]
if len(indcs) > 1:
s += sum(1./(indcs[i+1] - indcs[i]) for i in range(len(indcs)-1))
return 1./s
And here some random result:
>>> print optimize(items, quality_maxmindist)
['A', 'B', 'C', 'A', 'D', 'E', 'A', 'B', 'F', 'C', 'A', 'D', 'B', 'A']
Note that, passing another quality function, the same optimizer could be used for different list-rearrangement tasks, e.g. as a (rather silly) randomized sorter.
Here is an algorithm that only maximizes the minimum distance between elements of the same type and does nothing beyond that. The following list is used as an example:
AAAAA BBBBB CCCC DDDD EEEE FFF GG
Sort element sets by number of elements of each type in descending order. Actually only largest sets (A & B) should be placed to the head of the list as well as those element sets that have one element less (C & D & E). Other sets may be unsorted.
Reserve R last positions in the array for one element from each of the largest sets, divide the remaining array evenly between the S-1 remaining elements of the largest sets. This gives optimal distance: K = (N - R) / (S - 1). Represent target array as a 2D matrix with K columns and L = N / K full rows (and possibly one partial row with N % K elements). For example sets we have R = 2, S = 5, N = 27, K = 6, L = 4.
If matrix has S - 1 full rows, fill first R columns of this matrix with elements of the largest sets (A & B), otherwise sequentially fill all columns, starting from last one.
For our example this gives:
AB....
AB....
AB....
AB....
AB.
If we try to fill the remaining columns with other sets in the same order, there is a problem:
ABCDE.
ABCDE.
ABCDE.
ABCE..
ABD
The last 'E' is only 5 positions apart from the first 'E'.
Sequentially fill all columns, starting from last one.
For our example this gives:
ABFEDC
ABFEDC
ABFEDC
ABGEDC
ABG
Returning to linear array we have:
ABFEDCABFEDCABFEDCABGEDCABG
Here is an attempt to use simulated annealing for this problem (C sources): http://ideone.com/OGkkc.
I believe you could see your problem like a bunch of particles that physically repel eachother. You could iterate to a 'stable' situation.
Basic pseudo-code:
force( x, y ) = 0 if x.type==y.type
1/distance(x,y) otherwise
nextposition( x, force ) = coined?(x) => same
else => x + force
notconverged(row,newrow) = // simplistically
row!=newrow
row=[a,b,a,b,b,b,a,e];
newrow=nextposition(row);
while( notconverged(row,newrow) )
newrow=nextposition(row);
I don't know if it converges, but it's an idea :)
I'm sure there may be a more efficient solution, but here is one possibility for you:
First, note that it is very easy to find an ordering which produces a minimum-distance-between-items-of-same-type of 1. Just use any random ordering, and the MDBIOST will be at least 1, if not more.
So, start off with the assumption that the MDBIOST will be 2. Do a recursive search of the space of possible orderings, based on the assumption that MDBIOST will be 2. There are a number of conditions you can use to prune branches from this search. Terminate the search if you find an ordering which works.
If you found one that works, try again, under the assumption that MDBIOST will be 3. Then 4... and so on, until the search fails.
UPDATE: It would actually be better to start with a high number, because that will constrain the possible choices more. Then gradually reduce the number, until you find an ordering which works.
Here's another approach.
If every item must be kept at least k places from every other item of the same type, then write down items from left to right, keeping track of the number of items left of each type. At each point put down an item with the largest number left that you can legally put down.
This will work for N items if there are no more than ceil(N / k) items of the same type, as it will preserve this property - after putting down k items we have k less items and we have put down at least one of each type that started with at ceil(N / k) items of that type.
Given a clutch of mixed items you could work out the largest k you can support and then lay out the items to solve for this k.