Sieve of Eratosthenes
Compute for every integer n between 0 and N (excluded), the minimum number of operations to reduce it to zero. Allowed operations: decrease by 1 or divide by a factor, not larger than its square root.
Key ingredient
The key ingredient is the sieve of Eratosthenes. This is simple procedure to find all prime numbers below some given integer N. Simply fill a boolean table T, which initially is all True, except for indexes 0 and 1. Process from index 2 to N (excluded). When processing p, if T[p] is True, then we know that p is a prime. Now set T[ap] to False for all integers a at least 2, (not exceeding the table size).
This procedure takes time $O(N \log N)$.
Model as a shortest path problem
We can model the problem as a shortest path problem in an acyclic directed graph, which therefore naturally leads to a dynamic program. For every vertex we wish to find the distance to the vertex 0.
Dynamic program using decomposition into prime factors
The idea is to compute for every n — in the range 0 to N — the distance d[n] between the vertices n and 0. Clearly we have d[0]=0 and d[n]= 1 + min(d[n-1], min(d[n/a])), where the second minimum is taken over all factors a of n with a*a <= n. The dynamic program simply fills the table in order of increasing indexes.
The key difficulty is to find the non-trivial factors for a given integer n. By non-trival we mean factors that are strictly between 1 and $n$. One possibility is to use the sieve of Eratosthenes. Let F[n] be the list of all primes dividing $n$. If $p^2$ divides n then p is present twice in the list. The table F is filled up in order of increasing indexes.
Side-note: we experimented using a dictionary instead of a list, associating the value 2 to the key p if $p^2$ divides $n$ but not $p^3$. This gave almost no improvement.
Initially all entries of F are empty. Then for every $p$ from 2 to $N$, we check if F[p] is empty. If it is the case, then $p$ is a prime number and we proceed as follows. For every integer multiple of $p$ not exceeding $N$, namely $p, 2p, 3p$ etc we add $p$ to its list stored in F. Then for every integer multiple of $p^2$ we add again $p$ to its list stored in F. And we repeat so for all integer powers of p, not exceeding $N$.
Just to create confusion we renamed F as decomp in the following implementation.
Now given $n$ we know the list F[n] of its prime numbers. Every strict and non-empty sublist L of F[n] corresponds to a factor of $n$, simply by multiplying all the primes in L.
In the implementation below we use a useful function from the module itertools, which iterates over all sublists of a given size.
Now we can implement the dynamic program.
Dynamic program using multiplicities
A much easier solution is to implement the dynamic program not by processing all arcs grouped by the source vertex, but grouped by the target vertex. Suppose that initially $d[n]=n$, which corresponds to repeated applications of the decrement operation, reducing $n$ to zero. We process $n$ from 2 to $N$, with the property that at the moment $n$ is processed, $d[n]$ contains the correct answer. At that moment, we consider all integer multiples of $n$, of the form $an$ with $a<=n$, and $an<=N$, and update $d[an]$ by $min(d[an], 1 + d[n])$, corresponding to a division of $an$ by its factor $a$.
Note that in the implementation below, we make sure that $a$ does not exceed $n$ and that $an$ is strictly smaller than $N$.
Complexity
The procedure above makes at most $N/n$ comparisons for every $n$, which sum up to $O(N \log N)$, using the harmonic number equality $H_N=1+1/2+…+1/N=O(\log N)$.
The Python implementation of the first versions takes 13 seconds, using the pypy interpreter, while the second one takes only 0.4 seconds.
This measures have to be considered with care as they are sensible to the machine environment.