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Cellular barcoding is a significant, recently developed, biotechnology tool that enables the familial identification of progeny of individual cells in vivo. Most existing approaches rely on ex vivo viral transduction of cells with barcodes, followed by adoptive transfer into an animal, which works well for some systems, but precludes barcoding cells in their native environment, such as those inside solid tissues. With a view to overcoming this limitation, we propose a new design for a genetic barcoding construct based on the Cre Lox system that induces randomly created stable barcodes in cells in situ by exploiting inherent sequence distance constraints during site-specific recombination. Leveraging this previously unused feature, we identify the cassette with maximal code diversity. This proves to be orders of magnitude higher than what is attainable with previously considered Cre Lox barcoding approaches and is well suited for its intended applications as it exceeds the number of lymphocytes or hematopoietic progenitor cells in mice. Moreover, it can be built using established technology.

Establishing a Large Deviation Principle (LDP) proves to be a powerful result for a vast number of stochastic models in many application areas of probability theory. The key object of an LDP is the large deviations rate function, from which probabilistic estimates of rare events can be determined. In order make these results empirically applicable, it would be necessary to estimate the rate function from observations. This is the question we address in this article for the best known and most widely used LDP: Cram\'er's theorem for random walks. We establish that even when only a narrow LDP holds for Cram\'er's Theorem, as occurs for heavy-tailed increments, one gets a LDP for estimating the random walk's rate function in the space of convex lower-semicontinuous functions equipped with the Attouch-Wets topology via empirical estimates of the moment generating function. This result may seem surprising as it is saying that for Cram\'er's theorem, one can quickly form non-parametric estimates of the function that governs the likelihood of rare events.

Information theory is rapidly approaching its 70th birthday. What are promising future directions for research in information theory? Where will information theory be having the most impact in 10-20 years? What new and emerging areas are ripe for the most impact, of the sort that information theory has had on the telecommunications industry over the last 60 years? How should the IEEE Information Theory Society promote high-risk new research directions and broaden the reach of information theory, while continuing to be true to its ideals and insisting on the intellectual rigor that makes its breakthroughs so powerful? These are some of the questions that an ad hoc committee (composed of the present authors) explored over the past two years. We have discussed and debated these questions, and solicited detailed inputs from experts in fields including genomics, biology, economics, and neuroscience. This report is the result of these discussions.

For proliferating cells subject to both division and death, how can one estimate the average generation number of the living population without continuous observation or a division-diluting dye? In this paper we provide a method for cell systems such that at each division there is an unlikely, heritable one-way label change that has no impact other than to serve as a distinguishing marker. If the probability of label change per cell generation can be determined and the proportion of labeled cells at a given time point can be measured, we establish that the average generation number of living cells can be estimated. Crucially, the estimator does not depend on knowledge of the statistics of cell cycle, death rates or total cell numbers. We validate the estimator and illustrate its features through comparison with published data and physiologically parameterized stochastic simulations, using it to suggest new experimental designs.

We present information-theoretic definitions and results for analyzing symmetric-key encryption schemes beyond the perfect secrecy regime, i.e. when perfect secrecy is not attained. We adopt two lines of analysis, one based on lossless source coding, and another akin to rate-distortion theory. We start by presenting a new information-theoretic metric for security, called symbol secrecy, and derive associated fundamental bounds. We then introduce list-source codes (LSCs), which are a general framework for mapping a key length (entropy) to a list size that an eavesdropper has to resolve in order to recover a secret message. We provide explicit constructions of LSCs, and demonstrate that, when the source is uniformly distributed, the highest level of symbol secrecy for a fixed key length can be achieved through a construction based on minimum-distance separable (MDS) codes. Using an analysis related to rate-distortion theory, we then show how symbol secrecy can be used to determine the probability that an eavesdropper correctly reconstructs functions of the original plaintext. We illustrate how these bounds can be applied to characterize security properties of symmetric-key encryption schemes, and, in particular, extend security claims based on symbol secrecy to a functional setting., Comment: Submitted to IEEE Transactions on Information Theory

For general connections, the problem of finding network codes and optimizing resources for those codes is intrinsically difficult and little is known about its complexity. Most of the existing solutions rely on very restricted classes of network codes in terms of the number of flows allowed to be coded together, and are not entirely distributed. In this paper, we consider a new method for constructing linear network codes for general connections of continuous flows to minimize the total cost of edge use based on mixing. We first formulate the minimumcost network coding design problem. To solve the optimization problem, we propose two equivalent alternative formulations with discrete mixing and continuous mixing, respectively, and develop distributed algorithms to solve them. Our approach allows fairly general coding across flows and guarantees no greater cost than any solution without network coding., Comment: 1 fig, technical report of ICC 2015

The problem of finding network codes for general connections is inherently difficult in capacity constrained networks. Resource minimization for general connections with network coding is further complicated. Existing methods for identifying solutions mainly rely on highly restricted classes of network codes, and are almost all centralized. In this paper, we introduce linear network mixing coefficients for code constructions of general connections that generalize random linear network coding (RLNC) for multicast connections. For such code constructions, we pose the problem of cost minimization for the subgraph involved in the coding solution and relate this minimization to a path-based Constraint Satisfaction Problem (CSP) and an edge-based CSP. While CSPs are NP-complete in general, we present a path-based probabilistic distributed algorithm and an edge-based probabilistic distributed algorithm with almost sure convergence in finite time by applying Communication Free Learning (CFL). Our approach allows fairly general coding across flows, guarantees no greater cost than routing, and shows a possible distributed implementation. Numerical results illustrate the performance improvement of our approach over existing methods., Comment: submitted to TON (conference version published at IEEE GLOBECOM 2015)

The Guesswork problem was originally motivated by a desire to quantify computational security for single user systems. Leveraging recent results from its analysis, we extend the remit and utility of the framework to the quantification of the computational security for multi-user systems. In particular, assume that $V$ users independently select strings stochastically from a finite, but potentially large, list. An inquisitor who does not know which strings have been selected wishes to identify $U$ of them. The inquisitor knows the selection probabilities of each user and is equipped with a method that enables the testing of each (user, string) pair, one at a time, for whether that string had been selected by that user. Here we establish that, unless $U=V$, there is no general strategy that minimizes the distribution of the number of guesses, but in the asymptote as the strings become long we prove the following: by construction, there is an asymptotically optimal class of strategies; the number of guesses required in an asymptotically optimal strategy satisfies a large deviation principle with a rate function, which is not necessarily convex, that can be determined from the rate functions of optimally guessing individual users' strings; if all user's selection statistics are identical, the exponential growth rate of the average guesswork as the string-length increases is determined by the specific R\'enyi entropy of the string-source with parameter $(V-U+1)/(V-U+2)$, generalizing the known $V=U=1$ case; and that the Shannon entropy of the source is a lower bound on the average guesswork growth rate for all $U$ and $V$, thus providing a bound on computational security for multi-user systems. Examples are presented to illustrate these results and their ramifications for systems design.

A string is sent over a noisy channel that erases some of its characters. Knowing the statistical properties of the string's source and which characters were erased, a listener that is equipped with an ability to test the veracity of a string, one string at a time, wishes to fill in the missing pieces. Here we characterize the influence of the stochastic properties of both the string's source and the noise on the channel on the distribution of the number of attempts required to identify the string, its guesswork. In particular, we establish that the average noise on the channel is not a determining factor for the average guesswork and illustrate simple settings where one recipient with, on average, a better channel than another recipient, has higher average guesswork. These results stand in contrast to those for the capacity of wiretap channels and suggest the use of techniques such as friendly jamming with pseudo-random sequences to exploit this guesswork behavior., Comment: Asilomar Conference on Signals, Systems & Computers, 2013

Lower bounds for the average probability of error of estimating a hidden variable X given an observation of a correlated random variable Y, and Fano's inequality in particular, play a central role in information theory. In this paper, we present a lower bound for the average estimation error based on the marginal distribution of X and the principal inertias of the joint distribution matrix of X and Y. Furthermore, we discuss an information measure based on the sum of the largest principal inertias, called k-correlation, which generalizes maximal correlation. We show that k-correlation satisfies the Data Processing Inequality and is convex in the conditional distribution of Y given X. Finally, we investigate how to answer a fundamental question in inference and privacy: given an observation Y, can we estimate a function f(X) of the hidden random variable X with an average error below a certain threshold? We provide a general method for answering this question using an approach based on rate-distortion theory., Comment: Allerton 2013 with extended proof, 10 pages

Consider the situation where a word is chosen probabilistically from a finite list. If an attacker knows the list and can inquire about each word in turn, then selecting the word via the uniform distribution maximizes the attacker's difficulty, its Guesswork, in identifying the chosen word. It is tempting to use this property in cryptanalysis of computationally secure ciphers by assuming coded words are drawn from a source's typical set and so, for all intents and purposes, uniformly distributed within it. By applying recent results on Guesswork, for i.i.d. sources it is this equipartition ansatz that we investigate here. In particular, we demonstrate that the expected Guesswork for a source conditioned to create words in the typical set grows, with word length, at a lower exponential rate than that of the uniform approximation, suggesting use of the approximation is ill-advised., Comment: ISIT 2013, with extended proof

We present a new information-theoretic definition and associated results, based on list decoding in a source coding setting. We begin by presenting list-source codes, which naturally map a key length (entropy) to list size. We then show that such codes can be analyzed in the context of a novel information-theoretic metric, \epsilon-symbol secrecy, that encompasses both the one-time pad and traditional rate-based asymptotic metrics, but, like most cryptographic constructs, can be applied in non-asymptotic settings. We derive fundamental bounds for \epsilon-symbol secrecy and demonstrate how these bounds can be achieved with MDS codes when the source is uniformly distributed. We discuss applications and implementation issues of our codes., Comment: Allerton 2012, 8 pages

How hard is it guess a password? Massey showed that that the Shannon entropy of the distribution from which the password is selected is a lower bound on the expected number of guesses, but one which is not tight in general. In a series of subsequent papers under ever less restrictive stochastic assumptions, an asymptotic relationship as password length grows between scaled moments of the guesswork and specific R\'{e}nyi entropy was identified. Here we show that, when appropriately scaled, as the password length grows the logarithm of the guesswork satisfies a Large Deviation Principle (LDP), providing direct estimates of the guesswork distribution when passwords are long. The rate function governing the LDP possess a specific, restrictive form that encapsulates underlying structure in the nature of guesswork. Returning to Massey's original observation, a corollary to the LDP shows that expectation of the logarithm of the guesswork is the specific Shannon entropy of the password selection process.

The busy period for a queue is cast as the area swept under the random walk until it first returns to zero, $B$. Encompassing non-i.i.d. increments, the large-deviations asymptotics of $B$ is addressed, under the assumption that the increments satisfy standard conditions, including a negative drift. The main conclusions provide insight on the probability of a large busy period, and the manner in which this occurs: I) The scaled probability of a large busy period has the asymptote, for any $b>0$, \lim_{n\to\infty} \frac{1}{\sqrt{n}} \log P(B\geq bn) = -K\sqrt{b}, \hbox{where} \quad K = 2 \sqrt{-\int_0^{\lambda^*} \Lambda(\theta) d\theta}, \quad \hbox{with $\lambda^*=\sup\{\theta:\Lambda(\theta)\leq0\}$,} and with $\Lambda$ denoting the scaled cumulant generating function of the increments process. II) The most likely path to a large swept area is found to be a simple rescaling of the path on $[0,1]$ given by, [\psi^*(t) = -\Lambda(\lambda^*(1-t))/\lambda^*.] In contrast to the piecewise linear most likely path leading the random walk to hit a high level, this is strictly concave in general. While these two most likely paths have very different forms, their derivatives coincide at the start of their trajectories, and at their first return to zero. These results partially answer an open problem of Kulick and Palmowski regarding the tail of the work done during a busy period at a single server queue. The paper concludes with applications of these results to the estimation of the busy period statistics $(\lambda^*, K)$ based on observations of the increments, offering the possibility of estimating the likelihood of a large busy period in advance of observing one., Comment: 15 pages, 5 figures

In this paper we establish the log-convexity of the rate region in 802.11 WLANs. This generalises previous results for Aloha networks and has immediate implications for optimisation based approaches to the analysis and design of 802.11 wireless networks.

By combining the features of CSMA and TDMA, fully decentralised WLAN MAC schemes have recently been proposed that converge to collision-free schedules. In this paper we describe a MAC with optimal long-run throughput that is almost decentralised. We then design two \changed{schemes} that are practically realisable, decentralised approximations of this optimal scheme and operate with different amounts of sensing information. We achieve this by (1) introducing learning algorithms that can substantially speed up convergence to collision free operation; (2) developing a decentralised schedule length adaptation scheme that provides long-run fair (uniform) access to the medium while maintaining collision-free access for arbitrary numbers of stations.

Loynes' distribution, which characterizes the one dimensional marginal of the stationary solution to Lindley's recursion, possesses an ultimately exponential tail for a large class of increment processes. If one can observe increments but does not know their probabilistic properties, what are the statistical limits of estimating the tail exponent of Loynes' distribution? We conjecture that in broad generality a consistent sequence of non-parametric estimators can be constructed that satisfies a large deviation principle. We present rigorous support for this conjecture under restrictive assumptions and simulation evidence indicating why we believe it to be true in greater generality., Comment: 7 pages, 2 figures

It is known that simulation of the mean position of a Reflected Random Walk (RRW) $\{W_n\}$ exhibits non-standard behavior, even for light-tailed increment distributions with negative drift. The Large Deviation Principle (LDP) holds for deviations below the mean, but for deviations at the usual speed above the mean the rate function is null. This paper takes a deeper look at this phenomenon. Conditional on a large sample mean, a complete sample path LDP analysis is obtained. Let $I$ denote the rate function for the one dimensional increment process. If $I$ is coercive, then given a large simulated mean position, under general conditions our results imply that the most likely asymptotic behavior, $\psi^*$, of the paths $n^{-1} W_{\lfloor tn\rfloor}$ is to be zero apart from on an interval $[T_0,T_1]\subset[0,1]$ and to satisfy the functional equation \begin{align*} \nabla I\left(\ddt\psi^*(t)\right)=\lambda^*(T_1-t) \quad \text{whenever } \psi(t)\neq 0. \end{align*} If $I$ is non-coercive, a similar, but slightly more involved, result holds. These results prove, in broad generality, that Monte Carlo estimates of the steady-state mean position of a RRW have a high likelihood of over-estimation. This has serious implications for the performance evaluation of queueing systems by simulation techniques where steady state expected queue-length and waiting time are key performance metrics. The results show that na\"ive estimates of these quantities from simulation are highly likely to be conservative., Comment: 23 pages, 8 figures