1925819
Authentication of quantum messages
Authentication is a well-studied area of classical cryptography: a sender A and a receiver B sharing a classical secret key want to exchange a classical message with the guarantee that the message has not been modified or replaced by a dishonest party with control of the communication line. In this paper we study the authentication of messages composed of quantum states. We give a formal definition of authentication in the quantum setting. Assuming A and B have access to an insecure quantum channel and share a secret, classical random key, we provide a non-interactive scheme that enables A to both encrypt and authenticate an m qubit message by encoding it into m+s qubits, where the error probability decreases exponentially in the security parameter s. The scheme requires a secret key of size 2m+O(s). To achieve this, we give a highly efficient protocol for testing the purity of shared EPR pairs. It has long been known that learning information about a general quantum state will necessarily disturb it. We refine this result to show that such a disturbance can be done with few side effects, allowing it to circumvent cryptographic protections. Consequently, any scheme to authenticate quantum messages must also encrypt them. In contrast, no such constraint exists classically. This reasoning has two important consequences: It allows us to give a lower bound of 2m key bits for authenticating m qubits, which makes our protocol asymptotically optimal. Moreover, we use it to show that digitally signing quantum states is impossible.
1672422
Entropic Security and the Encryption of High Entropy Messages
We study entropic security, an information-theoretic notion of security introduced by Russell and Wang [24] in the context of encryption and by Canetti et al. [5,6] in the context of hash functions. Informally, a probabilitic map $Y = \mathcal{E}(X)$ (e.g., an encryption sheme or a hash function) is entropically secure if knowledge of Y does not help predicting any predicate of X, whenever X has high min-entropy from the adversary's point of view. On one hand, we strengthen the formulation of [5,6,24] and show that entropic security in fact implies that Y does not help predicting any function of X (as opposed to a predicate), bringing this notion closer to the conventioonal notion of semantic security [10]. On the other hand, we also show that entropic security is equivalent to indistinguishability on pairs of input distributions of sufficiently high entropy, which is in turn related to randomness extraction from non-uniform distributions [21]. 
 
We then use the equivalence above, and the connection to randomness extraction, to prove several new results on entropically-secure encryption. First, we give two general frameworks for constructing entropically secure encryption schemes: one based on expander graphs and the other on XOR-universal hash functions. These schemes generalize the schemes of Russell and Wang, yielding simpler constructions and proofs, as well as improved parameters. To encrypt an n-bit message of min-entropy t while allowing at most e-advantage to the adversary, our best schemes use a shared secret key of length $k = n - t + 2{\rm log} (\frac {1}{\epsilon})$. Second, we obtain lower bounds on the key length k for entropic security and indistinguishability. In particular, we show near tightness of our constructions: k > n – t. For a large class of schemes — including all the schemes we study — the bound can be strengthened to $k \geq n - t+{\rm log} (\frac {1}{\epsilon})-O(1)$.
37361807
Robust Fuzzy Extractors and Authenticated Key Agreement from Close Secrets
Consider two parties holding correlated random variables W and W′, respectively, that are within distance t of each other in some metric space. These parties wish to agree on a uniformly distributed secret key R by sending a single message over an insecure channel controlled by an all-powerful adversary. We consider both the keyless case, where the parties share no additional secret information, and the keyed case, where the parties share a long-term secret SK that they can use to generate a sequence of session keys {Rj} using multiple pairs {(Wj, W′j)}. The former has applications to, e.g., biometric authentication, while the latter arises in, e.g., the bounded storage model with errors. 
 
Our results improve upon previous work in several respects: 
 
– The best previous solution for the keyless case with no errors (i.e., t=0) requires the min-entropy of W to exceed 2|W|/3. We show a solution when the min-entropy of W exceeds the minimal threshold |W|/2. 
 
– Previous solutions for the keyless case in the presence of errors (i.e., t>0) required random oracles. We give the first constructions (for certain metrics) in the standard model. 
 
– Previous solutions for the keyed case were stateful. We give the first stateless solution.
5424518
Round Efficiency of Multi-party Computation with a Dishonest Majority
We consider the round complexity of multi-party computation in the presence of a static adversary who controls a majority of the parties. Here, n players wish to securely compute some functionality and up to n - 1 of these players may be arbitrarily malicious. Previous protocols for this setting (when a broadcast channel is available) require O(n) rounds. We present two protocols with improved round complexity: The first assumes only the existence of trapdoor permutations and dense cryptosystems, and achieves round complexity O(log n) based on a proof scheduling technique of Chor and Rabin [13]; the second requires a stronger hardness assumption (along with the non-black-box techniques of Barak [2]) and achieves O(1) round complexity.
314094
Correcting errors without leaking partial information
This paper explores what kinds of information two parties must communicate in order to correct errors which occur in a shared secret string W. Any bits they communicate must leak a significant amount of information about W --- that is, from the adversary's point of view, the entropy of W will drop significantly. Nevertheless, we construct schemes with which Alice and Bob can prevent an adversary from learning any useful information about W. Specifically, if the entropy of W is sufficiently high, then there is no function f(W) which the adversary can learn from the error-correction information with significant probability.This leads to several new results: (a) the design of noise-tolerant "perfectly one-way" hash functions in the sense of Canetti et al. [7], which in turn leads to obfuscation of proximity queries for high entropy secrets W; (b) private fuzzy extractors [11], which allow one to extract uniformly random bits from noisy and nonuniform data W, while also insuring that no sensitive information about W is leaked; and (c) noise tolerance and stateless key re-use in the Bounded Storage Model, resolving the main open problem of Ding [10].The heart of our constructions is the design of strong randomness extractors with the property that the source W can be recovered from the extracted randomness and any string W' which is close to W.
7418837
Lower bounds for collusion-secure fingerprinting
Collusion-secure fingerprinting codes are an important primitive used by many digital watermarking schemes [1, 10, 9]. Boneh and Shaw [3] define a model for these types of codes and present an explicit construction. Their code has length <i>O</i>(<i>c</i><sup>3</sup> log(l/ε)) and attains security against coalitions of size <i>c</i> with ε error. Boneh and Shaw also present a lower bound of Ω (<i>c</i><sup>3</sup>log(1/<i>c</i>ε)) on the length of any collusion-secure code.We give new lower bounds on the length of collusion-secure codes by analyzing a weighted coinflipping strategy for the coalition. As an illustration of our methods, we give a simple proof that the Boneh-Shaw construction cannot be asymptotically improved. Next, we prove a general lower bound: no secure code can have length <i>O</i>(<i>c</i><sup>2</sup>1og(1/<i>c</i>ε)), which improves the previous known bound by a factor of <i>c</i>. In particular, we show that any secure code will have length Ω(<i>c</i><sup>2</sup> log(1/<i>c</i>ε)) as long as log(l/ε) ≥ <i>K</i> <i>k</i> log <i>c</i>, where <i>K</i> is a constant and <i>k</i> is the number of columns in the code (in some sense, a measure of the code's complexity). Finally, we describe a general paradigm for constructing fingerprinting codes which encompasses the construction of [3], and show that no secure code that follows this paradigm can have length <i>O</i>((c<sup>3</sup>/log c) log(1/<i>c</i>ε)) follows this (again, by showing a lower bound for large values of ln(1/ε)). This suggests that any attempts at improvement should be directed toward techniques that lie outside our paradigm.
4331453
Computational prediction of novel components of lung transcriptional networks
MOTIVATION
Little is known regarding the transcriptional mechanisms involved in forming and maintaining epithelial cell lineages of the mammalian respiratory tract.


RESULTS
Herein, a motif discovery approach was used to identify novel transcriptional regulators in the lung using genes previously found to be regulated by Foxa2 or Wnt signaling pathways. A human-mouse comparison of both novel and known motifs was also performed. Some of the factors and families identified here were previously shown to be involved epithelial cell differentiation (ETS family, HES-1 and MEIS-1), and ciliogenesis (RFX family), but have never been characterized in lung epithelia. Other unidentified over-represented motifs suggest the existence of novel mammalian lung transcription factors. Of the fraction of motifs examined we describe 25 transcription factor family predictions for lung. Fifteen novel factors were shown here to be expressed in mouse lung, and/or human bronchial or distal lung epithelial tissues or lung epithelial cell lineages.


AVAILABILITY
DME: http://rulai.cshl.edu/dme. MATCOMPARE: http://rulai.cshl.edu/MatCompare. MOTIFCLASS is available from the authors.
2433417
Logarithmic Opinion Pools for Conditional Random Fields
Recent work on Conditional Random Fields (CRFs) has demonstrated the need for regularisation to counter the tendency of these models to overfit. The standard approach to regularising CRFs involves a prior distribution over the model parameters, typically requiring search over a hyperparameter space. In this paper we address the overfitting problem from a different perspective, by factoring the CRF distribution into a weighted product of individual "expert" CRF distributions. We call this model a logarithmic opinion pool (LOP) of CRFs (LOP-CRFs). We apply the LOP-CRF to two sequencing tasks. Our results show that unregularised expert CRFs with an unregularised CRF under a LOP can outperform the unregularised CRF, and attain a performance level close to the regularised CRF. LOP-CRFs therefore provide a viable alternative to CRF regularisation without the need for hyperparameter search.
9985308
Analysis of shared memory misses and reference patterns
Shared bus computer systems permit the relatively simple and efficient implementation of cache consistency algorithms, but the shared bus is a bottleneck which limits performance. False sharing can be an important source of unnecessary traffic for invalidation-based protocols, elimination of which can provide significant performance improvements. For many multiprocessor workloads, however, most misses are true sharing plus cold start misses. Regardless of the cause of cache misses, the largest fraction of bus traffic are words transferred between caches without being accessed, which we refer to as dead sharing. We establish here new methods for characterizing cache block reference patterns, and we measure how these patterns change with variation in workload and block size. Our results show that 42 percent of 64-byte cache blocks are invalidated before more than one word has been read from the block and that 58 percent of blocks that have been modified only have a single word modified before an invalidation to the block occurs. Approximately 50 percent of blocks written and subsequently read by other caches show no use of the newly written information before the block is again invalidated. In addition to our general analysis of reference patterns, we also present a detailed analysis of dead sharing for each shared memory multiprocessor program studied. We find that the worst 10 blocks (based on most total misses) from each of our traces contribute almost 50 percent of the false shearing misses and almost 20 percent of the true sharing misses (on average). A relatively simple restructuring of four of our workloads based on analysis of these 10 worst blocks leads to a 21 percent reduction in overall misses and a 15 percent reduction in execution time. Permitting the block size to vary (as could be accomplished with a sector cache) shows that bus traffic can be reduced by 88 percent (for 64-byte blocks) while also decreasing the miss ratio by 35 percent.
5725147
Local search genetic algorithm for optimal design of reliable networks
This paper presents a genetic algorithm (GA) with specialized encoding, initialization, and local search operators to optimize the design of communication network topologies. This NP-hard problem is often highly constrained so that random initialization and standard genetic operators usually generate infeasible networks. Another complication is that the fitness function involves calculating the all-terminal reliability of the network, which is a computationally expensive calculation. Therefore, it is imperative that the search balances the need to thoroughly explore the boundary between feasible and infeasible networks, along with calculating fitness on only the most promising candidate networks. The algorithm results are compared to optimum results found by branch and bound and also to GA results without local search operators on a suite of 79 test problems. This strategy of employing bounds, simple heuristic checks, and problem-specific repair and local search operators can be used on other highly constrained combinatorial applications where numerous fitness calculations are prohibitive.
12460438
Evaluation of cache consistency algorithm performance
As more computer systems turn to multiprocessing for improved performance, additional research is needed to evaluate and improve the performance of cache consistency protocols. In this study, we use trace-driven simulation to examine the performance of several consistency protocols, including some new adaptive protocols which have not been examined in prior research. This study uses a wider variety of traces than have been previously analyzed, including some production applications from a vector mini-supercomputer system, and presents a wider variety of analyses than have been previously presented for a given workload. We find that the sharing characteristics of application programs have a large bearing on the relative performance of the different protocols. Update-based protocols outperform invalidate-based protocols when accesses so shared data are highly interleaved among different processors (fine-grain sharing), while invalidate-based protocols are superior if one processor performs all accesses to shared data over long periods of time (coarse-grain sharing). Adaptive protocols provide the best overall performance across all applications; we present a new protocol called Update-Once, which yields the highest average performance. In even the best cases, however, estimated processor utilizations are unacceptably low due to the overhead to maintain consistent caches. To extract good performance from multiprocessor systems, existing application programs must be recoded to reduce sharing between processors.