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Genomic profiles of cancer cells provide valuable information on genetic alterations in cancer. Several recent studies employed these data to predict the response of cancer cell lines to drug treatment. Nonetheless, due to the multifactorial phenotypes and intricate mechanisms of cancer, the accurate prediction of the effect of pharmacotherapy on a specific cell line based on the genetic information alone is problematic. Emphasizing on the system-level complexity of cancer, we devised a procedure to integrate multiple heterogeneous data, including biological networks, genomics, inhibitor profiling, and gene-disease associations, into a unified graph structure. In order to construct compact, yet information-rich cancer-specific networks, we developed a novel graph reduction algorithm. Driven by not only the topological information, but also the biological knowledge, the graph reduction increases the feature-only entropy while preserving the valuable graph-feature information. Subsequent comparative benchmarking simulations employing a tissue level cross-validation protocol demonstrate that the accuracy of a graph-based predictor of the drug efficacy is 0.68, which is notably higher than those measured for more traditional, matrix-based techniques on the same data. Overall, the non-Euclidean representation of the cancer-specific data improves the performance of machine learning to predict the response of cancer to pharmacotherapy. The generated data are freely available to the academic community athttps://osf.io/dzx7b/.

 

The performance of partially synchronous BFT-based consensus protocols is highly dependent on the primary node. All participant nodes in the network are blocked until they receive a proposal from the primary node to begin the consensus process. Therefore, an honest but slack node (with limited bandwidth) can adversely affect the performance when selected as primary. Hermes decreases protocol dependency on the primary node and minimizes transmission delay induced by the slack primary while keeping low message complexity and latency with high scalability. Hermes achieves these performance improvements by relaxing strong BFT agreement (safety) guarantees only for a specific type of Byzantine faults (also called equivocated faults). Interestingly, we show that in Hermes equivocating by a Byzantine primary is expensive and ineffective. Therefore, the safety of Hermes is comparable to the general BFT consensus. We deployed and tested Hermes on 190 Amazon EC2 instances. In these tests, Hermes's performance was comparable to the state-of-the-art BFT protocol for blockchains (when the network size is large) in the absence of slack nodes. Whereas, in the presence of slack nodes, Hermes outperforms the state-of-the-art BFT protocol significantly in terms of throughput and latency. 

We investigate scheduling algorithms for distributed transactional memory systems where transactions residing at nodes of a communication graph operate on shared, mobile objects. A transaction requests the objects it needs, executes once those objects have been assembled, and then sends the objects to other waiting transactions. We study scheduling algorithms with provable performance guarantees. Previously, only the offline batch scheduling setting was considered in the literature where transactions and the objects they access are known a priori. Minimizing execution time, even for the offline batch scheduling, is known to be NP-hard for arbitrary communication graphs. In this paper, we analyze for the very first time scheduling algorithms in the online dynamic scheduling setting where transactions and the objects they access are not known a priori and the transactions may arrive online over time. We provide efficient and near-optimal execution time schedules for dynamic scheduling in many specialized network architectures. The core of our technique is a method to convert offline schedules to online. We first describe a centralized scheduler which we then adapt it to a purely distributed scheduler. To our knowledge, these are the first attempts to obtain provably efficient online execution schedules for distributed transactional memory.