(Tissue) P Systems with Vesicles of Multisets

We consider tissue P systems working on vesicles of multisets with the very simple operations of insertion, deletion, and substitution of single objects. With the whole multiset being enclosed in a vesicle, sending it to a target cell can be indicated in those simple rules working on the multiset. As derivation modes we consider the sequential mode, where exactly one rule is applied in a derivation step, and the set maximal mode, where in each derivation step a non-extendable set of rules is applied. With the set maximal mode, computational completeness can already be obtained with tissue P systems having a tree structure, whereas tissue P systems even with an arbitrary communication structure are not computationally complete when working in the sequential mode. Adding polarizations (-1, 0, 1 are sufficient) allows for obtaining computational completeness even for tissue P systems working in the sequential mode.Comment: In Proceedings AFL 2017, arXiv:1708.0622

Metabolic Network Alignments and their Applications

The accumulation of high-throughput genomic and proteomic data allows for the reconstruction of the increasingly large and complex metabolic networks. In order to analyze the accumulated data and reconstructed networks, it is critical to identify network patterns and evolutionary relations between metabolic networks. But even finding similar networks becomes computationally challenging. The dissertation addresses these challenges with discrete optimization and the corresponding algorithmic techniques. Based on the property of the gene duplication and function sharing in biological network,we have formulated the network alignment problem which asks the optimal vertex-to-vertex mapping allowing path contraction, vertex deletion, and vertex insertions. We have proposed the first polynomial time algorithm for aligning an acyclic metabolic pattern pathway with an arbitrary metabolic network. We also have proposed a polynomial-time algorithm for patterns with small treewidth and implemented it for series-parallel patterns which are commonly found among metabolic networks. We have developed the metabolic network alignment tool for free public use. We have performed pairwise mapping of all pathways among five organisms and found a set of statistically significant pathway similarities. We also have applied the network alignment to identifying inconsistency, inferring missing enzymes, and finding potential candidates

A Survey on Causal Discovery: Theory and Practice

Understanding the laws that govern a phenomenon is the core of scientific progress. This is especially true when the goal is to model the interplay between different aspects in a causal fashion. Indeed, causal inference itself is specifically designed to quantify the underlying relationships that connect a cause to its effect. Causal discovery is a branch of the broader field of causality in which causal graphs is recovered from data (whenever possible), enabling the identification and estimation of causal effects. In this paper, we explore recent advancements in a unified manner, provide a consistent overview of existing algorithms developed under different settings, report useful tools and data, present real-world applications to understand why and how these methods can be fruitfully exploited

SoK: Cryptographically Protected Database Search

Protected database search systems cryptographically isolate the roles of reading from, writing to, and administering the database. This separation limits unnecessary administrator access and protects data in the case of system breaches. Since protected search was introduced in 2000, the area has grown rapidly; systems are offered by academia, start-ups, and established companies. However, there is no best protected search system or set of techniques. Design of such systems is a balancing act between security, functionality, performance, and usability. This challenge is made more difficult by ongoing database specialization, as some users will want the functionality of SQL, NoSQL, or NewSQL databases. This database evolution will continue, and the protected search community should be able to quickly provide functionality consistent with newly invented databases. At the same time, the community must accurately and clearly characterize the tradeoffs between different approaches. To address these challenges, we provide the following contributions: 1) An identification of the important primitive operations across database paradigms. We find there are a small number of base operations that can be used and combined to support a large number of database paradigms. 2) An evaluation of the current state of protected search systems in implementing these base operations. This evaluation describes the main approaches and tradeoffs for each base operation. Furthermore, it puts protected search in the context of unprotected search, identifying key gaps in functionality. 3) An analysis of attacks against protected search for different base queries. 4) A roadmap and tools for transforming a protected search system into a protected database, including an open-source performance evaluation platform and initial user opinions of protected search.Comment: 20 pages, to appear to IEEE Security and Privac

Observability Robustness under Sensor Failures: Complexities and algorithms

The problem of determining the minimal number of sensors whose removal destroys observability of a linear time invariant system is studied. This problem is closely related to the ability of unique state reconstruction of a system under adversarial sensor attacks, and the dual of it is the inverse to the recently studied minimal controllability problems. It is proven that this problem is NP-hard both for a numerically specific system, and for a generic system whose nonzero entries of its system matrices are unknown but can take values freely (also called structured system). Two polynomial time algorithms are provided to solve this problem, respectively, on a numerical system with bounded maximum geometric multiplicities, and on a structured system with bounded matching deficiencies, which are often met by practical engineering systems. The proposed algorithms can be easily extended to the case where each sensor has a non-negative cost. Numerical experiments show that the structured system based algorithm could be alternative when the exact values of system matrices are not accessible.Comment: 8 pages, 2 figures, add some materials, fix some type error