Binary weights spanning trees and the kk-red spanning tree problem in linear time

We address here spanning tree problems on a graph with binary edge weights. For a general weighted graph the minimum spanning tree is solved in super-linear running time, even when the edges of the graph are pre-sorted. A related problem, of finding a spanning tree with a pre-specified sum of weights, is NP-hard. In contrast, for a graph with binary weights associated with the edges, it is shown that the minimum spanning tree and finding a spanning tree with a given total sum, are solvable in linear time with simple algorithms

Multiflow Transmission in Delay Constrained Cooperative Wireless Networks

This paper considers the problem of energy-efficient transmission in multi-flow multihop cooperative wireless networks. Although the performance gains of cooperative approaches are well known, the combinatorial nature of these schemes makes it difficult to design efficient polynomial-time algorithms for joint routing, scheduling and power control. This becomes more so when there is more than one flow in the network. It has been conjectured by many authors, in the literature, that the multiflow problem in cooperative networks is an NP-hard problem. In this paper, we formulate the problem, as a combinatorial optimization problem, for a general setting of $k$-flows, and formally prove that the problem is not only NP-hard but it is $o(n^{1/7-\epsilon})$ inapproxmiable. To our knowledge*, these results provide the first such inapproxmiablity proof in the context of multiflow cooperative wireless networks. We further prove that for a special case of k = 1 the solution is a simple path, and devise a polynomial time algorithm for jointly optimizing routing, scheduling and power control. We then use this algorithm to establish analytical upper and lower bounds for the optimal performance for the general case of $k$ flows. Furthermore, we propose a polynomial time heuristic for calculating the solution for the general case and evaluate the performance of this heuristic under different channel conditions and against the analytical upper and lower bounds.Comment: 9 pages, 5 figure

Efficient algorithms to discover alterations with complementary functional association in cancer

Recent large cancer studies have measured somatic alterations in an unprecedented number of tumours. These large datasets allow the identification of cancer-related sets of genetic alterations by identifying relevant combinatorial patterns. Among such patterns, mutual exclusivity has been employed by several recent methods that have shown its effectivenes in characterizing gene sets associated to cancer. Mutual exclusivity arises because of the complementarity, at the functional level, of alterations in genes which are part of a group (e.g., a pathway) performing a given function. The availability of quantitative target profiles, from genetic perturbations or from clinical phenotypes, provides additional information that can be leveraged to improve the identification of cancer related gene sets by discovering groups with complementary functional associations with such targets. In this work we study the problem of finding groups of mutually exclusive alterations associated with a quantitative (functional) target. We propose a combinatorial formulation for the problem, and prove that the associated computation problem is computationally hard. We design two algorithms to solve the problem and implement them in our tool UNCOVER. We provide analytic evidence of the effectiveness of UNCOVER in finding high-quality solutions and show experimentally that UNCOVER finds sets of alterations significantly associated with functional targets in a variety of scenarios. In addition, our algorithms are much faster than the state-of-the-art, allowing the analysis of large datasets of thousands of target profiles from cancer cell lines. We show that on one such dataset from project Achilles our methods identify several significant gene sets with complementary functional associations with targets.Comment: Accepted at RECOMB 201

A Fully Polynomial Time Approximation Scheme for the Replenishment Storage Problem

The Replenishment Storage problem (RSP) is to minimize the storage capacity requirement for a deterministic demand, multi-item inventory system where each item has a given reorder size and cycle length. The reorders can only take place at integer time units within the cycle. This problem was shown to be weakly NP-hard for constant joint cycle length (the least common multiple of the lengths of all individual cycles). When all items have the same constant cycle length, there exists a Fully Polynomial Time Approximation Scheme (FPTAS), but no FPTAS has been known for the case when the individual cycles are different. Here we devise the first known FPTAS for the RSP with different individual cycles and constant joint cycle length

The Max-Cut Decision Tree: Improving on the Accuracy and Running Time of Decision Trees

Decision trees are a widely used method for classification, both by themselves and as the building blocks of multiple different ensemble learning methods. The Max-Cut decision tree involves novel modifications to a standard, baseline model of classification decision tree construction, precisely CART Gini. One modification involves an alternative splitting metric, maximum cut, based on maximizing the distance between all pairs of observations belonging to separate classes and separate sides of the threshold value. The other modification is to select the decision feature from a linear combination of the input features constructed using Principal Component Analysis (PCA) locally at each node. Our experiments show that this node-based localized PCA with the novel splitting modification can dramatically improve classification, while also significantly decreasing computational time compared to the baseline decision tree. Moreover, our results are most significant when evaluated on data sets with higher dimensions, or more classes; which, for the example data set CIFAR-100, enable a 49% improvement in accuracy while reducing CPU time by 94%. These introduced modifications dramatically advance the capabilities of decision trees for difficult classification tasks.Comment: 12 pages, 8 figures, 5 table