11276211
PDC: Pattern discovery with confidence in DNA sequences
Pattern discovery in DNA sequences is one of the most challenging tasks in molecular biology and computer science. The main goal of pattern discovery in DNA sequences is to identify sequences of important biological function hidden in the huge amounts of genomic sequences. Several methods and techniques have been proposed and implemented in this field. However, in order to reduce computational time and complexity, most of them either focus on finding short DNA patterns or require explicit specification of pattern lengths in advance. Scientists need to find longer patterns without specifying pattern lengths in advance and still have good performance.In this paper, we propose a pattern discovery algorithm called Pattern Discovery with Confidence (PDC). Based on biological studies, we propose a new measurement system that can identify overrepresented patterns inside DNA sequences. Using this measurement, PDC algorithm can narrow the search space by checking dependency along the pattern, thus extending the pattern as long as possible without the need to restrict or specify the length of a pattern in advance. Experimental tests demonstrate that this approach can find long, interesting patterns within a reasonable computation time.
13092959
Whodunit? Causal Analysis for Counterexamples
Although the counterexample returned by a model checker can help in reproducing the symptom related to a defect, a significant amount of effort is often required for the programmer to interpret it in order to locate the cause. In this paper, we provide an automated procedure to zoom in to potential software defects by analyzing a single concrete counterexample. Our analysis relies on extracting from the counterexample a syntactic-level proof of infeasibility, i.e., a minimal set of word-level predicates that contradict with each other. The procedure uses an efficient weakest pre-condition algorithm carried out on a single concrete execution path, which is significantly more scalable than other model checking based approaches. Unlike most of the existing methods, we do not need additional execution traces other than the buggy one. We use public-domain examples to demonstrate the effectiveness of our new algorithm.
6254649
Disjunctive Image Computation for Embedded Software Verification
Finite state models generated from software programs have unique characteristics that are not exploited by existing model checking algorithms. In this paper, we propose a novel disjunctive image computation algorithm and other simplifications based on these characteristics. Our algorithm divides an image computation into a disjunctive set of easier ones that can be performed in isolation. Hypergraph partitioning is used to minimize the number of live variables in each disjunctive component. We use the live variables to simplify transition relations and reachable state subsets. Our experiments on a set of real-world C programs show that the new algorithm achieves orders-of-magnitude performance improvement over the best known conjunctive image computation algorithm
193663
SAT-Based Image Computation with Application in Reachability Analysis
Image computation nds wide application in VLSI CAD, such as state reachability analysis in formal veri cation and synthesis, combinational veri cation, combinational and sequential test. Existing BDD-based symbolic algorithms for image computation are limited by memory resources in practice, while SAT-based algorithms that can obtain the image by enumerating satisfying assignments to a CNF representation of the Boolean relation are potentially limited by time resources. We propose new algorithms that combine BDDs and SAT in order to exploit their complementary bene ts, and to o er a mechanism for trading o space vs. time. In particular, (1) our integrated algorithm uses BDDs to represent the input and image sets, and a CNF formula to represent the Boolean relation, (2) a fundamental enhancement called BDD Bounding is used whereby the SAT solver uses the BDDs for the input set and the dynamically changing image set to prune the search space of all solutions, (3) BDDs are used to compute all solutions below intermediate points in the SAT decision tree, (4) a ne-grained variable quanti cation schedule is used for each BDD subproblem, based on the CNF representation of the Boolean relation. These enhancements coupled with more engineering heuristics lead to an overall algorithm that can potentially handle larger problems. This is supported by our preliminary results on exact reachability analysis of ISCAS benchmark circuits.
361158
Efficient Distributed SAT and SAT-Based Distributed Bounded Model Checking
SAT-based Bounded Model Checking (BMC), though a robust and scalable verification approach, still is computationally intensive, requiring large memory and time. Interestingly, with the recent development of improved SAT solvers, it is frequently the memory limitation of a single server rather than time that becomes a bottleneck for doing deeper BMC search. Distributing computing requirements of BMC over a network of workstations can overcome the memory limitation of a single server, albeit at increased communication cost. In this paper, we present: a) a method for distributed-SAT over a network of workstations using a Master/Client model where each Client worsktation has an exclusive partition of the SAT problem and uses knowledge of partition topology to communicate with other Clients, b) a method for distributing SAT-based BMC using the distributed-SAT. For the sake of scalability, at no point in the BMC computation does a single workstation have all the information. We experimented on a network of heterogenous workstations interconnected with a standard Ethernet LAN. To illustrate, on an industrial design with 13K FFs and 0.5M gates, the non-disributed BMC on a single workstation (with 4 Gb memory) ran out of memroy after reaching a depth of 120; on the otherhand, our SAT-based distributed BMC over 5 similar workstations was able to go upto 323 steps with a communication overhead of only 30%.
25613636
Efficient distributed SAT and SAT-based distributed Bounded Model Checking
SAT-based Bounded Model Checking (BMC), though a robust and scalable verification approach, still is computationally intensive, requiring large memory and time. Even with the recent development of improved SAT solvers, the memory limitation of a single server rather than time can become a bottleneck for doing deeper BMC search for large designs. Distributing computing requirements of BMC over a network of workstations can overcome the memory limitation of a single server, albeit at increased communication cost. In this paper, we present (a) a method for distributed SAT over a network of workstations using a Master/Client model where each Client workstation has an exclusive partition of the SAT problem and uses knowledge of partition topology to communicate with other Clients, (b) a method for distributing SAT-based BMC using the distributed SAT. For the sake of scalability, at no point in the BMC computation does a single workstation have all the information. We experimented on a network of heterogeneous workstations interconnected with a standard Ethernet LAN. To illustrate, on an industrial design with ∼13 K FFs and ∼0.5 million gates, the non-distributed BMC on a single workstation (with 4 GB memory) ran out of memory after reaching a depth of 120; on the other hand, our SAT-based distributed BMC over 5 similar workstations was able to go up to 323 steps with a communication overhead of only 30%.
11052169
Privacy-Preserving Classification of Customer Data without Loss of Accuracy
Privacy has become an increasingly important issue in data mining. In this paper, we consider a scenario in which a data miner surveys a large number of customers to learn classiflcation rules on their data, while the sensitive attributes of these customers need to be protected. Solutions have been proposed to address this problem using randomization techniques. Such solutions exhibit a tradeofi of accuracy and privacy: the more each customer’s private information is protected, the less accurate result the miner obtains; conversely, the more accurate the result, the less privacy for the customers. In this paper, we propose a simple cryptographic approach that is e‐cient even in a many-customer setting, provides strong privacy for each customer, and does not lose any accuracy as the cost of privacy. Our key technical contribution is a privacy-preserving method that allows a data miner to compute frequencies of values or tuples of values in the customers’ data, without revealing the privacy-sensitive part of the data. Unlike general-purpose cryptographic protocols, this method requires no interaction between customers, and each customer only needs to send a single ∞ow of communication to the data miner. However, we are still able to ensure that nothing about the sensitive data beyond the desired frequencies is revealed to the data miner. To illustrate the power of our approach, we use our frequency mining computation to obtain a privacypreserving naive Bayes classifler learning algorithm. Initial experimental results demonstrate the practical e‐ciency of our solution. We also suggest some other applications of privacy-preserving frequency mining.
62782878
Anonymity-preserving data collection
Protection of privacy has become an important problem in data mining. In particular, individuals have become increasingly unwilling to share their data, frequently resulting in individuals either refusing to share their data or providing incorrect data. In turn, such problems in data collection can affect the success of data mining, which relies on sufficient amounts of accurate data in order to produce meaningful results. Random perturbation and randomized response techniques can provide some level of privacy in data collection, but they have an associated cost in accuracy. Cryptographic privacy-preserving data mining methods provide good privacy and accuracy properties. However, in order to be efficient, those solutions must be tailored to specific mining tasks, thereby losing generality.In this paper, we propose efficient cryptographic techniques for online data collection in which data from a large number of respondents is collected anonymously, without the help of a trusted third party. That is, our solution allows the miner to collect the original data from each respondent, but in such a way that the miner cannot link a respondent's data to the respondent. An advantage of such a solution is that, because it does not change the actual data, its success does not depend on the underlying data mining problem. We provide proofs of the correctness and privacy of our solution, as well as experimental data that demonstrates its efficiency. We also extend our solution to tolerate certain kinds of malicious behavior of the participants.
2501005
Coordinating Multiple Agents via Reinforcement Learning
In this paper, we attempt to use reinforcement learning techniques to solve agent coordination problems in task-oriented environments. The Fuzzy Subjective Task Structure model (FSTS) is presented to model the general agent coordination. We show that an agent coordination problem modeled in FSTS is a Decision-Theoretic Planning (DTP) problem, to which reinforcement learning can be applied. Two learning algorithms, ‘‘coarse-grained’’ and ‘‘fine-grained’’, are proposed to address agents coordination behavior at two different levels. The ‘‘coarse-grained’’ algorithm operates at one level and tackle hard system constraints, and the ‘‘fine-grained’’ at another level and for soft constraints. We argue that it is important to explicitly model and explore coordination-specific (particularly system constraints) information, which underpins the two algorithms and attributes to the effectiveness of the algorithms. The algorithms are formally proved to converge and experimentally shown to be effective.
45395929
An Operational Investigation of the CPS Hierarchy
We explore the hierarchy of control induced by successive transformations into continuation-passing style (CPS) in the presence of "control delimiters" and "composable continuations". Specifically, we investigate the structural operational semantics associated with the CPS hierarchy. 
 
To this end, we characterize an operational notion of continuation semantics. We relate it to the traditional CPS transformation and we use it to account for the control operator shift and the control delimiter reset operationally. We then transcribe the resulting continuation semantics in ML, thus obtaining a native and modular implementation of the entire hierarchy. We illustrate it with several examples, the most significant of which is layered monads.
17075655
Privacy-enhancing k-anonymization of customer data
In order to protect individuals' privacy, the technique of k-anonymization has been proposed to de-associate sensitive attributes from the corresponding identifiers. In this paper, we provide privacy-enhancing methods for creating k-anonymous tables in a distributed scenario. Specifically, we consider a setting in which there is a set of customers, each of whom has a row of a table, and a miner, who wants to mine the entire table. Our objective is to design protocols that allow the miner to obtain a k-anonymous table representing the customer data, in such a way that does not reveal any extra information that can be used to link sensitive attributes to corresponding identifiers, and without requiring a central authority who has access to all the original data. We give two different formulations of this problem, with provably private solutions. Our solutions enhance the privacy of k-anonymization in the distributed scenario by maintaining end-to-end privacy from the original customer data to the final k-anonymous results.