Given an edge-weighted graph and a set of potentially overlapping vertex groups, a group Steiner tree (GST) is a minimum weight tree that includes at least one vertex in each group. Finding GSTs serves as a classical approach to keyword search in relational databases. Existing studies use CPUs to find optimal GSTs in a serial way, and remain slow in some cases. No prior work has applied GPUs to meet this challenge. To fill this gap, first, we propose a parallel-friendly GST solution framework, by breaking the traditional bottom-up dynamic programming order. Second, since a direct execution of this framework on GPUs faces a severe workload imbalance problem, we develop a GST-customized load balancing approach. Specifically, we employ kernel fusion and global memory coalescing techniques to efficiently utilize different parallel granularities to match divergent tree construction workloads. Third, since existing pruning methods cannot be directly applied to a parallel scheme, we modify feasible pruning procedures to reduce the computation burden, and rigorously prove the solution correctness. Furthermore, inspired by recent applications, we present a novel dynamic programming algorithm for finding optimal diameter-bounded GSTs on GPUs. Experiments on various real datasets show that the proposed techniques achieve a speedup of 48-2390× over state-of-the-art methods, and can handle some large weighted graphs where existing solutions are too slow to be applied, and thus could greatly improve the user experience in related applications.

Given a time interval and a graph where vertices exhibit a property of interest (PoI) dynamically, an interesting question is: where (i.e., which part of the graph) and when (i.e., which time sub-interval) does the PoI occur frequently? To our knowledge, no work has been done to answer this question to date. We address this issue in this paper. Specifically, given (i) a time interval composed of multiple time slots and (ii) a graph where each vertex either exhibits or does not exhibit the PoI in each time slot, our objective is to find a pair of a connected sub-graph and a time sub-interval (which we refer to as a temporal bump), such that the discrepancy between the numbers of times that vertices in this sub-graph exhibit and do not exhibit the PoI during this time sub-interval is maximized. Due to the NP-hardness of this problem, initially, we propose two approximation algorithms. The first one achieves a tight approximation guarantee, at the cost of a weak scalability to the number of time slots. The second one achieves a strong scalability to the number of time slots, at the price of a loose approximation guarantee. Then, we propose two heuristic algorithms that have no non-trivial approximation guarantee, but produce similar solutions with, and are considerably faster than, the two approximation algorithms. Experiments on real datasets show that, in comparison with baselines built using related existing techniques, our algorithms hunt bumps with significantly higher discrepancies, while scaling well to large graphs, and thus are more suitable for answering the aforementioned question.

Consider an edge-weighted graph, and a number of properties of interests (PoIs). Each vertex has a probability of exhibiting each PoI. The joint probability that a set of vertices exhibits a PoI is the probability that this set contains at least one vertex that exhibits this PoI. The probabilistic group Steiner tree problem is to find a tree such that (i) for each PoI, the joint probability that the set of vertices in this tree exhibits this PoI is no smaller than a threshold value, e.g. , 0.97; and (ii) the total weight of edges in this tree is the minimum. Solving this problem is useful for mining various graphs with uncertain vertex properties, but is NP-hard. The existing work focuses on certain cases, and cannot perform this task. To meet this challenge, we propose 3 approximation algorithms for solving the above problem. Let |Γ| be the number of PoIs, and ξ be an upper bound of the number of vertices for satisfying the threshold value of exhibiting each PoI. Algorithms 1 and 2 have tight approximation guarantees proportional to |Γ| and ξ, and exponential time complexities with respect to ξ and |Γ|, respectively. In comparison, Algorithm 3 has a looser approximation guarantee proportional to, and a polynomial time complexity with respect to, both |Γ| and ξ. Experiments on real and large datasets show that the proposed algorithms considerably outperform the state-of-the-art related work for finding probabilistic group Steiner trees in various cases.

Given an undirected graph and a number of vertex groups, the group Steiner trees problem is to find a tree such that (i) this tree contains at least one vertex in each vertex group; and (ii) the sum of vertex and edge weights in this tree is minimized. Solving this problem is useful in various scenarios, ranging from social networks to knowledge graphs. Most existing work focuses on solving this problem in vertex-unweighted graphs, and not enough work has been done to solve this problem in graphs with both vertex and edge weights. Here, we develop several algorithms to address this issue. Initially, we extend two algorithms from vertex-unweighted graphs to vertex- and edge-weighted graphs. The first one has no approximation guarantee, but often produces good solutions in practice. The second one has an approximation guarantee of |Γ| - 1, where |Γ| is the number of vertex groups. Since the extended (|Γ| - 1)-approximation algorithm is too slow when all vertex groups are large, we develop two new (|Γ| - 1)-approximation algorithms that overcome this weakness. Furthermore, by employing a dynamic programming approach, we develop another (|Γ| - h + 1)-approximation algorithm, where h is a parameter between 2 and |Γ|. Experiments show that, while no algorithm is the best in all cases, our algorithms considerably outperform the state of the art in many scenarios.

Bump hunting is an important approach to the extraction of insights from Euclidean datasets. Recently, it has been explored for graph datasets for the first time, and a single bump is hunted in an unweighted graph in this exploration. Here, we extend this exploration by hunting multiple bumps in a weighted graph. Given a weighted graph and a set of query nodes exhibiting a property of interest, our objective is to find k non-overlapping and connected subgraphs, i.e., bumps, in which the discrepancy between the numbers of query and non-query nodes is maximized and the sum of edge costs is minimized simultaneously. We prove that our extended bump hunting problem can be transformed to a recently formulated Prize-Collecting Steiner Forest Problem (PCSFP). We further prove that PCSFP is NP-hard even in trees. Then, we propose a fast approximation algorithm for solving PCSFP in trees. Based on this algorithm, we improve the state-of-the-art approximation algorithm for solving PCSFP in graphs, and prove that the solutions of our improvement are always better than or equal to those of the state-of-the-art algorithm. Moreover, we adapt the existing bump hunting algorithms for solving our extended bump hunting problem. We evaluate our methodology via real datasets, and show that 1) our improvement scales well to large graphs, while producing solutions that dominate those of the state-of-the-art algorithm; and 2) our adaptation of an existing bump hunting algorithm can also produce solutions that are better than those of the state-of-the-art algorithm in some cases.

Relay node placement, which aims to connect pre-deployed sensor nodes to base stations, is essential in minimizing the costs of wireless sensor networks. In this paper, we formulate the new Node-Weighted Partial Terminal Steiner Tree Problem (NWPTSTP) for minimum-cost relay node placement in two-tiered wireless sensor networks. The objective is to minimize the sum of heterogeneous production and placement costs of relay nodes and the sum of outage probabilities of transmission routes in a routing tree simultaneously. This extends the previous work that considers the costs of relay nodes to be homogeneous. After formulating NWPTSTP for this purpose, we prove that it can be transformed to the existing node-weighted Steiner tree problem. Subsequently, we conduct some theoretical analyses on the emerging Physarum-inspired algorithms to reveal their potential of computing Steiner trees. Based on these analyses, we propose a new Physarum-inspired algorithm for solving NWPTSTP. We conduct computational trials to show that: 1) in comparison to a state-of-the-art approximation algorithm for solving the node-weighted Steiner tree problem, our Physarum-inspired algorithm can produce better solutions in a smaller amount of time; and 2) in comparison to two state-of-the-art relay node placement algorithms, our Physarum-inspired algorithm can design wireless sensor networks with 25% lower relay cost and similar quality of service (specifically, 5% shorter network lifetime, 2% longer delay, and 0% loss of goodput). This indicates the usefulness of our Physarum-inspired algorithm for minimum-cost relay node placement in budget-limited scenarios.

It is challenging to design large and low-cost communication networks. In this paper, we formulate this challenge as the prize-collecting Steiner Tree Problem (PCSTP). The objective is to minimize the costs of transmission routes and the disconnected monetary or informational profits. Initially, we note that the PCSTP is MAX SNP-hard. Then, we propose some post-processing techniques to improve suboptimal solutions to PCSTP. Based on these techniques, we propose two fast heuristic algorithms: the first one is a quasilinear time heuristic algorithm that is faster and consumes less memory than other algorithms; and the second one is an improvement of a state-of-the-art polynomial time heuristic algorithm that can find high-quality solutions at a speed that is only inferior to the first one. We demonstrate the competitiveness of our heuristic algorithms by comparing them with the state-of-the-art ones on the largest existing benchmark instances (169 800 vertices and 338 551 edges). Moreover, we generate new instances that are even larger (1 000 000 vertices and 10 000 000 edges) to further demonstrate their advantages in large networks. The state-of-the-art algorithms are too slow to find high-quality solutions for instances of this size, whereas our new heuristic algorithms can do this in around 6 to 45s on a personal computer. Ultimately, we apply our post-processing techniques to update the best-known solution for a notoriously difficult benchmark instance to show that they can improve near-optimal solutions to PCSTP. In conclusion, we demonstrate the usefulness of our heuristic algorithms and post-processing techniques for designing large and low-cost communication networks.

BACKGROUND: Cancer constitutes a momentous health burden in our society. Critical information on cancer may be hidden in its signaling pathways. However, even though a large amount of money has been spent on cancer research, some critical information on cancer-related signaling pathways still remains elusive. Hence, new works towards a complete understanding of cancer-related signaling pathways will greatly benefit the prevention, diagnosis, and treatment of cancer. RESULTS: We propose the node-weighted Steiner tree approach to identify important elements of cancer-related signaling pathways at the level of proteins. This new approach has advantages over previous approaches since it is fast in processing large protein-protein interaction networks. We apply this new approach to identify important elements of two well-known cancer-related signaling pathways: PI3K/Akt and MAPK. First, we generate a node-weighted protein-protein interaction network using protein and signaling pathway data. Second, we modify and use two preprocessing techniques and a state-of-the-art Steiner tree algorithm to identify a subnetwork in the generated network. Third, we propose two new metrics to select important elements from this subnetwork. On a commonly used personal computer, this new approach takes less than 2 s to identify the important elements of PI3K/Akt and MAPK signaling pathways in a large node-weighted protein-protein interaction network with 16,843 vertices and 1,736,922 edges. We further analyze and demonstrate the significance of these identified elements to cancer signal transduction by exploring previously reported experimental evidences. CONCLUSIONS: Our node-weighted Steiner tree approach is shown to be both fast and effective to identify important elements of cancer-related signaling pathways. Furthermore, it may provide new perspectives into the identification of signaling pathways for other human diseases.

Recently it has been shown that Physarum-inspired algorithms can solve some network optimization problems. However, it is not yet shown that Physarum-inspired algorithm can solve Node Weighted Steiner Tree Problem (NWSTP). Two new Physarum-inspired algorithms are proposed in this paper to solve NWSTP for the first time. Since all the existing NWSTP benchmark instances have an empty terminal set, new benchmark instances with non-empty terminal sets are generated to cover the shortage of existing benchmark instances. Both proposed algorithms are compared with Genetic Algorithm (GA) and Discrete Particle Swarm Optimization (DPSO) in these benchmark instances. Furthermore, an adapted Dijkstra's algorithm is proposed to provide the optimal solutions for part of these benchmark instances where there are two terminals and the node weights are negative. Simulation results show that our first proposed algorithm can find the optimal solutions for NWSTP with two terminals in graphs with negative node weights, and our second proposed algorithm can find close approximate solutions for NWSTP with multiple terminals in any node weighted graph. Both proposed algorithms provide faster and better NWSTP solutions than GA and DPSO.