Towards running complex models on big data

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1 Towards running complex models on big data Working with all the genomes in the world without changing the model (too much) Daniel Lawson Heilbronn Institute, University of Bristol / 17

2 Motivation For Large datasets Statistics doesn t work estimates get worse as we get more data! (for linear compute) Simple analytics can extract many useful features e.g. PageRank [Page 1999], K-medians clustering, etc Informative in practice - and still hard to get working! Exploit averaging over lots of data But many interesting quantities are subtle... or local, so we only have a small amount of data about them Always a place for models closer matching reality 2 / 17

3 Example applications 1. Genetics: Model-based clustering for all the genomes in the world (2. Cyber security: finding timing coincidences in event processes a large graph)... In both cases we have a complex model per pair of objects but can use a simpler model to find out whether they are at all close Linked by use of a similarity model Other applications exist 3 / 17

4 Similarity: a worked example p(d S)p(S Q)p(Q) N Data D N Similarity S Structure N Q L N K Compare N items about which we have a large amount of data D (trivial extension: to M = O(N) other items). Similarity S(i, j) is computationally costly to evaluate S structured by a model Q i.e. Similarity model p(d S) separates the data D from the structure model p(s Q) If rows of Q sum to 1 this is a mixture model if only 1 element is non-zero it is a partitioning 4 / 17

5 Random or convenience filtering See big data 1 as better sampling of data Why not throw away elements from D? Convenience sampling - what can we actually measure? Systematic sampling - retain every n-th data point Simple random sampling - retain fraction p Stratified sampling etc For example: Use L L Use N N Inference shouldn t get worse with more data! 1: Big data: any data that can t be processed in memory on a single high spec computer 5 / 17

6 Emulated Likelihood Models (ELMs) Fundamental idea: Replace p(d S, θ) in p(d S, θ)p(θ)p(s Q, φ)p(q, φ) using S computed and S emulated similarities, s.t. S = S S : ˆp(D S, θ) = p(d S S, θ) = p(d S S, θ, ψ)p(s S, ψ)dψ S ij is costly to compute, and needed for S Q But are highly structured (e.g. clusters) So can emulate S ij rather than computing Choose S to be approximately sufficient for p(d S, θ) 6 / 17

7 The oracle Which NT elements S of S should we evaluate? Natural solution using oracle knowledge of the true S. Use a loss function L(S ) Seek argmin S (T )L(S (T )) Choices for L might be: KL divergence between the true and the emulated posterior A loss based on model usage (e.g. is the clustering correct? Control the false positive rate, etc) Choose T based on acceptable loss 7 / 17

8 Building blocks of a real Emulated Likelihood Model The oracle is too costly. We instead must: Iteratively choose the next S ij to add to S From a limited set produced by a restriction operator R(S ) Construct an estimator ˆL for L Decide on the ( next point to) evaluate using argmin Sij E ˆL(S S ij ) S We can consider different histories to evaluate performance Stopping rule: convergence of ˆL ˆL can be implicit from R, if it returns points ordered by E( ˆL) 8 / 17

9 The emulator Machine learning emulator with the usual caveats: Rarely optimal, rarely unbiased Prediction error estimated using online cross validation Respects computational constraints: L N: Consider O(N 2 + LN) algorithms N L: Consider O(LN) algorithms Massive data: Consider O(LN α + N) algorithms with α < 1. 9 / 17

10 Fast finestructure - outline Emulator: Decision model parameters D S* S [N,L] [N,T] [N,N] D' S' S [N,L'] [N,N] [N,N] θ Thinning model Parameters Simple model parameters Emulator model parameters Empirical Bayes S becomes the data for inferring Q: [ ] p(d Ŝ, ˆθ) p(s Q, φ)p(q, φ) 10 / 17

11 Fast finestructure - decision and emulation Decision R: Choose item to evaluate i t using the point most distant to all evaluated points We are evaluating S in entire rows Emulation: Predict S i : mixture model Si = MM(Si ), and regression on Ŝ ij = LM(Sij, S ij ) Implicit loss function L: Minimise the maximum prediction error Finds outliers and clusters S form convex hull of S 11 / 17

12 Fast finestructure - in practice Computation of S costs O(N 2 L + NT 2 L) O(N 2 L) Current datasets: L = 10, 000, 000, N = 5000, L = 10, 000 T = 100, predicted saving ratio is 100 We can save up to factor by reducing T, the cost of the linearised model on the reduced dataset. L will not grow beyond this, but N will - can introduce an emulation step for S 12 / 17

13 Fast finestructure - Parallel MCMC algorithm A parallel tempering algorithm for when MCMC parallelises poorly Evaluate the unlinked model S Master node: perform MCMC clustering to find ˆQ t using Ŝ t, when there are t rows St computed Worker nodes compute S i in the order chosen by the master Stopping rule: posterior distribution of ˆQ converges No new information added when increasing t (Or if the MCMC is slower than the evaluation of S, sometime afterwards) 13 / 17

14 14 / 17

15 15 / 17

16 Emulated Likelihood Models for general Bayesian problems General emulation for big (but not so big) problems ˆp(D S, θ) = p(d S S, θ)p(s S, θ, ψ)dψ i.e. Can use θ to emulate S (θ) - e.g. regression in (S, θ) space Gaussian Process for Sij (θ) is a natural choice If S is an unbiased estimator of S this is a pseudo-marginal approach (and hence targeting the correct posterior) 16 / 17

17 Discussion Goal: Approximate answers to the right questions using exact answers to the wrong questions Machine learning is increasingly important for large datasets Statistical modelling still has a place Proposed the Emulated Likelihood Model: Full statistical modelling Machine learning algorithms used for the calculation Statistical estimation of parameters is retained but approximated 17 / 17

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