In Java, is there anything that works like an array but takes less memory?

Question

I'm programming a genetic algorithm. Right now, I'm using arrays for everything: my individuals are composed of arrays of ints, my populations are arrays of individuals, I store information inside an array to keep track of it.

A huge limitation I'm encountering is running out of memory. I know GAs are memory intensive, but i wonder if my first step should be to make an easy change, by using something better than an array.

I can't think of a more efficient way of storing a large number of ints than an array of ints. But do they need to be ints? Are you using all 32 bits? Or would shorts or bytes be an option? — Dawood ibn Kareem, Apr 11 '14 at 03:41
@MattBall Out of curiosity, what were you going to suggest if they were? — Sotirios Delimanolis, Apr 11 '14 at 03:44
@SotiriosDelimanolis really depends on the use case. Anything from a `Map`/`Set` to a `BitSet` to a bloom filter. — Matt Ball, Apr 11 '14 at 03:46
How much memory are you giving the JVM? Could you... just give it more? That would be _by far_ the easiest change to make. — Matt Ball, Apr 11 '14 at 03:48
@DavidWallace, no, I'm only storing 0s and 1s... I should really change my ints to bytes. Thanks for reminding me. — user3448821, Apr 11 '14 at 03:49
@MattBall, yes, I've tried giving more memory to the JVM. The memory demands of the genetic algorithm are getting rather ridiculous, though, so I'm trying to make my code better. — user3448821, Apr 11 '14 at 03:51

score 0 · Accepted Answer · edited May 23 '17 at 12:21

0

The answer to this question depends a lot on the nature of your data.

If you have sparse data (mostly 0's and very few 1's or vice versa), then creating an array of indices of 1's might do the trick for you. As David Wallace mentioned, a HashSet of indices would allow you to quickly check whether a particular index is 1 or 0.

If you do not have sparse data, then you might want a BitSet.

This discussion might also be useful to give you input.

edited May 23 '17 at 12:21

Community

1
1

answered Apr 11 '14 at 03:53

merlin2011

71,677
44
195
329

For sparse data, a `HashSet` of indices might work better than an array. – Dawood ibn Kareem Apr 11 '14 at 03:56

score 0 · Answer 2 · answered Apr 11 '14 at 05:21

You can put a triplet into one integer.

G = 0001

A = 0010

T = 0011

C = 0100

U = 0101 (RNA)

N = 0111 (G or C)

Q = 1000 (A or T/U)

...

3 x 4 bits fits in one 32 bit int. A triplet fits good into the genetic context. Write a Helper class to encode/decode the base and add it to an list array. Consider initial size and load factor.

In Java, is there anything that works like an array but takes less memory?

2 Answers2