Emmanuel Jeannot

Ritvik Prabhu, Emil Vatai, Bernard Moussad et al.

Cancer typically arises not from a single genetic mutation (i.e., hit) but from multi-hit combinations that accumulate within cells. However, enumerating multi-hit combinations becomes exponentially more expensive computationally as the number of candidate hit gene combinations grow, i.e. on the order of 20,000 choose h, where 20,000 is the number of genes in the human genome and h is the number of hits. To address this challenge, we present an algorithmic framework, called Pruned Depth-First Search (P-DFS) that leverages the high sparsity in tumor mutation data to prune large portions of the search space. Specifically, P-DFS (the main contribution of this paper) - a pruning technique that exploits sparsity to drastically reduce the otherwise exponential h-hit search space for candidate combinations used by Weighted Set Cover - which is grounded in a depth-first search backtracking technique, prunes infeasible gene subsets early, while a weighted set cover formulation systematically scores and selects the most discriminative combinations. By intertwining these ideas with optimized bitwise operations and a scalable distributed algorithm on high-performance computing clusters, our algorithm can achieve approximately 90 - 98% reduction in visited combinations for 4-hits, and roughly a 183x speedup over the exhaustive set cover approach(which is algorithmically NP-complete) measured on 147,456 ranks. In doing so, our method can feasibly handle four-hit and even higher-order gene hits, achieving both speed and resource efficiency.

Nathan Grinsztajn, Olivier Beaumont, Emmanuel Jeannot et al.

In practice, it is quite common to face combinatorial optimization problems which contain uncertainty along with non-determinism and dynamicity. These three properties call for appropriate algorithms; reinforcement learning (RL) is dealing with them in a very natural way. Today, despite some efforts, most real-life combinatorial optimization problems remain out of the reach of reinforcement learning algorithms. In this paper, we propose a reinforcement learning approach to solve a realistic scheduling problem, and apply it to an algorithm commonly executed in the high performance computing community, the Cholesky factorization. On the contrary to static scheduling, where tasks are assigned to processors in a predetermined ordering before the beginning of the parallel execution, our method is dynamic: task allocations and their execution ordering are decided at runtime, based on the system state and unexpected events, which allows much more flexibility. To do so, our algorithm uses graph neural networks in combination with an actor-critic algorithm (A2C) to build an adaptive representation of the problem on the fly. We show that this approach is competitive with state-of-the-art heuristics used in high-performance computing runtime systems. Moreover, our algorithm does not require an explicit model of the environment, but we demonstrate that extra knowledge can easily be incorporated and improves performance. We also exhibit key properties provided by this RL approach, and study its transfer abilities to other instances.