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Composite DNA is a recent novel method to increase the information capacity of DNA-based data storage above the theoretical limit of 2 bits/symbol. In this method, every composite symbol does not store a single DNA nucleotide but a mixture of the four nucleotides in a predetermined ratio. By using different mixtures and ratios, the alphabet can be extended to have much more than four symbols in the naive approach. While this method enables higher data content per synthesis cycle, potentially reducing the DNA synthesis cost, it also imposes significant challenges for accurate DNA sequencing since the base-level errors can easily change the mixture of bases and their ratio, resulting in changes to the composite symbols. With this motivation, we propose efficient constrained coding techniques to enforce the biological constraints, including the runlength-limited constraint and the GC-content constraint, into every DNA synthesized oligo, regardless of the mixture of bases in each composite letter and their corresponding ratio. Our goals include computing the capacity of the constrained channel, constructing efficient encoders/decoders, and providing the best options for the composite letters to obtain capacity-approaching codes. For certain codes' parameters, our methods incur only one redundant symbol.

We consider a dense assembly of repulsive particles whose fluctuating sizes are subject to a landscape that defines three species: particles with finite size, either of type $A$ or of type $B$, and point particles $\varnothing$. We show that the nonequilibrium synchronization of sizes systematically leads to a homogeneous configuration associated with the survival of a single species. Remarkably, the relaxation towards such a configuration features a transient phase separation. By delineating and analyzing the dominant kinetic factors at play during relaxation, we recapitulate the phase diagram of species survival in terms of the parameters of the size landscape. Finally, we obtain a hydrodynamic mapping to equilibrium by coarse-graining the microscopic dynamics, which leads to predicting the nature of the transitions between various regimes where distinct species survive., Comment: 17 pages, 7 figures

We study the dynamics of a family of replicator maps, depending on two parameters. Such studies are motivated by the analysis of the dynamics of evolutionary games under selections. From the dynamics viewpoint, we prove the existence of hyperbolic chaos for the considered map. Moreover, we also give a partial solution of an open problem formulated in \cite{Misiurewicz1}: to describe all the one-dimensional maps with all the periodic orbits having the same mean value., Comment: 19 pages, 2 figures

Bird's-eye-view (BEV) map layout estimation requires an accurate and full understanding of the semantics for the environmental elements around the ego car to make the results coherent and realistic. Due to the challenges posed by occlusion, unfavourable imaging conditions and low resolution, \emph{generating} the BEV semantic maps corresponding to corrupted or invalid areas in the perspective view (PV) is appealing very recently. \emph{The question is how to align the PV features with the generative models to facilitate the map estimation}. In this paper, we propose to utilize a generative model similar to the Vector Quantized-Variational AutoEncoder (VQ-VAE) to acquire prior knowledge for the high-level BEV semantics in the tokenized discrete space. Thanks to the obtained BEV tokens accompanied with a codebook embedding encapsulating the semantics for different BEV elements in the groundtruth maps, we are able to directly align the sparse backbone image features with the obtained BEV tokens from the discrete representation learning based on a specialized token decoder module, and finally generate high-quality BEV maps with the BEV codebook embedding serving as a bridge between PV and BEV. We evaluate the BEV map layout estimation performance of our model, termed VQ-Map, on both the nuScenes and Argoverse benchmarks, achieving 62.2/47.6 mean IoU for surround-view/monocular evaluation on nuScenes, as well as 73.4 IoU for monocular evaluation on Argoverse, which all set a new record for this map layout estimation task. The code and models are available on \url{https://github.com/Z1zyw/VQ-Map}.

In this paper, we study the topological entropy and the Hausdorff dimension of a shrinking target set. We give lower and upper bounds of topological entropy and Hausdorff dimension for dynamical systems with exponential specification property and Lipschitz continuity for maps and homeomorphisms. It generally applies to uniformly hyperbolic systems, expanding systems, and some symbolic dynamics. We show that lower and upper bounds coincide for both topological entropy and Hausdorff dimension when the systems are hyperbolic automorphisms of torus induced from a matrix with only two different eigenvalues, expanding endomorphism of the torus induced from a matrix with only one eigenvalue or some symbolic systems including one or two-sided shifts of finite type and sofic shifts., Comment: 34 pages

Bandt and Kravchenko \cite{BandtKravchenko2010} proved that if a self-similar set spans $\R^m$, then there is no tangent hyperplane at any point of the set. In particular, this indicates that a smooth planar curve is self-similar if and only if it is a straight line. When restricting curves to graphs of continuous functions, we can show that the graph of a continuous function is self-similar if and only if the graph is a straight line, i.e., the underlying function is affine., Comment: 4 Figures, 12 pages

Federated learning enables the collaborative learning of a global model on diverse data, preserving data locality and eliminating the need to transfer user data to a central server. However, data privacy remains vulnerable, as attacks can target user training data by exploiting the updates sent by users during each learning iteration. Secure aggregation protocols are designed to mask/encrypt user updates and enable a central server to aggregate the masked information. MicroSecAgg (PoPETS 2024) proposes a single server secure aggregation protocol that aims to mitigate the high communication complexity of the existing approaches by enabling a one-time setup of the secret to be re-used in multiple training iterations. In this paper, we identify a security flaw in the MicroSecAgg that undermines its privacy guarantees. We detail the security flaw and our attack, demonstrating how an adversary can exploit predictable masking values to compromise user privacy. Our findings highlight the critical need for enhanced security measures in secure aggregation protocols, particularly the implementation of dynamic and unpredictable masking strategies. We propose potential countermeasures to mitigate these vulnerabilities and ensure robust privacy protection in the secure aggregation frameworks.

In 1928, Jarn\'{\i}k \cite{Jar} obtained that the set of continued fractions with bounded coefficients has Hausdorff dimension one. Good \cite{Goo} observed a dimension drop phenomenon by proving that the Hausdorff dimension of the set of continued fractions whose coefficients tend to infinity is one-half. For the set of continued fractions whose coefficients tend to infinity rapidly, Luczak \cite{Luc} and Feng et al. \cite{FWLT} showed that its Hausdorff dimension decreases even further. Recently, Liao and Rams \cite{LR16} also observed an analogous dimension drop phenomenon when they studied the subexponential growth rate of the sum of coefficients. In this paper, we consolidate and considerably extend the studies of the abovementioned problem into a general dimension drop problem on the distribution of continued fractions with large coefficients. As applications, we use a different approach to reprove a result of Wang and Wu on the dimensions of the Borel-Bernstein sets \cite{WW}, fulfil the dimension gap proposed by Liao and Rams \cite{LR16}, and establish several new results concerning the dimension theory of liminf and limsup sets related to the maximum of coefficients., Comment: 5 Figures, 56 pages

Large language models have become increasingly prominent, also signaling a shift towards multimodality as the next frontier in artificial intelligence, where their embeddings are harnessed as prompts to generate textual content. Vision-language models (VLMs) stand at the forefront of this advancement, offering innovative ways to combine visual and textual data for enhanced understanding and interaction. However, this integration also enlarges the attack surface. Patch-based adversarial attack is considered the most realistic threat model in physical vision applications, as demonstrated in many existing literature. In this paper, we propose to address patched visual prompt injection, where adversaries exploit adversarial patches to generate target content in VLMs. Our investigation reveals that patched adversarial prompts exhibit sensitivity to pixel-wise randomization, a trait that remains robust even against adaptive attacks designed to counteract such defenses. Leveraging this insight, we introduce SmoothVLM, a defense mechanism rooted in smoothing techniques, specifically tailored to protect VLMs from the threat of patched visual prompt injectors. Our framework significantly lowers the attack success rate to a range between 0% and 5.0% on two leading VLMs, while achieving around 67.3% to 95.0% context recovery of the benign images, demonstrating a balance between security and usability., Comment: 15 pages

Let $A$ be an invertible $d\times d$ matrix with integer elements. Then $A$ determines a self-map $T$ of the $d$-dimensional torus $\mathbb{T}^d=\mathbb{R}^d/\mathbb{Z}^d$. Given a real number $\tau>0$, and a sequence $\{z_n\}$ of points in $\mathbb{T}^d$, let $W_\tau$ be the set of points $x\in\mathbb{T}^d$ such that $T^n(x)\in B(z_n,e^{-n\tau})$ for infinitely many $n\in\mathbb{N}$. The Hausdorff dimension of $W_\tau$ has previously been studied by Hill--Velani and Li--Liao--Velani--Zorin. We provide complete results on the Hausdorff dimension of $W_\tau$ for any expanding matrix. For hyperbolic matrices, we compute the dimension of $W_\tau$ only when $A$ is a $2 \times 2$ matrix. We give counterexamples to a natural candidate for a dimension formula for general dimension $d$., Comment: 24 pages, 3 figures

Motivated by DNA based data storage system, we investigate the errors that occur when synthesizing DNA strands in parallel, where each strand is appended one nucleotide at a time by the machine according to a template supersequence. If there is a cycle such that the machine fails, then the strands meant to be appended at this cycle will not be appended, and we refer to this as a synthesis defect. In this paper, we present two families of codes correcting synthesis defects, which are t-known-synthesis-defect correcting codes and t-synthesis-defect correcting codes. For the first one, it is assumed that the defective cycles are known, and each of the codeword is a quaternary sequence. We provide constructions for this family of codes for t = 1, 2, with redundancy log 4 and log n+18 log 3, respectively. For the second one, the codeword is a set of M ordered sequences, and we give constructions for t = 1, 2 to show a strategy for constructing this family of codes. Finally, we derive a lower bound on the redundancy for single-known-synthesis-defect correcting codes, which assures that our construction is almost optimal.

Batch codes are a type of codes specifically designed for coded distributed storage systems and private information retrieval protocols. These codes have got much attention in recent years due to their ability to enable efficient and secure storage in distributed systems. In this paper, we study an array code version of the batch codes, which is called the \emph{batch array code} (BAC). Under the setting of BAC, each node stores a bucket containing multiple code symbols and responds with a locally computed linear combination of the symbols in its bucket during the recovery of a requested symbol. We demonstrate that BACs can support the same type of requests as the original batch codes but with reduced redundancy. Specifically, we establish information theoretic lower bounds on the code lengths and provide several code constructions that confirm the tightness of the lower bounds for certain parameter regimes., Comment: 24 pages

Recently, codes for correcting a burst of errors have attracted significant attention. One of the most important reasons is that bursts of errors occur in certain emerging techniques, such as DNA storage. In this paper, we investigate a type of error, called a $(t,s)$-burst, which deletes $t$ consecutive symbols and inserts $s$ arbitrary symbols at the same coordinate. Note that a $(t,s)$-burst error can be seen as a generalization of a burst of insertions ($t=0$), a burst of deletions ($s=0$), and a burst of substitutions ($t=s$). Our main contribution is to give explicit constructions of $q$-ary $(t,s)$-burst correcting codes with $\log n + O(1)$ bits of redundancy for any given constant non-negative integers $t$, $s$, and $q \geq 2$. These codes have optimal redundancy up to an additive constant. Furthermore, we apply our $(t,s)$-burst correcting codes to combat other various types of errors and improve the corresponding results. In particular, one of our byproducts is a permutation code capable of correcting a burst of $t$ stable deletions with $\log n + O(1)$ bits of redundancy, which is optimal up to an additive constant., Comment: This paper is accepted for publication in IEEE Transactions on Information Theory

In this paper, we propose a new image-based visual place recognition (VPR) framework by exploiting the structural cues in bird's-eye view (BEV) from a single monocular camera. The motivation arises from two key observations about place recognition methods based on both appearance and structure: 1) For the methods relying on LiDAR sensors, the integration of LiDAR in robotic systems has led to increased expenses, while the alignment of data between different sensors is also a major challenge. 2) Other image-/camera-based methods, involving integrating RGB images and their derived variants (eg, pseudo depth images, pseudo 3D point clouds), exhibit several limitations, such as the failure to effectively exploit the explicit spatial relationships between different objects. To tackle the above issues, we design a new BEV-enhanced VPR framework, namely BEV$^2$PR, generating a composite descriptor with both visual cues and spatial awareness based on a single camera. The key points lie in: 1) We use BEV features as an explicit source of structural knowledge in constructing global features. 2) The lower layers of the pre-trained backbone from BEV generation are shared for visual and structural streams in VPR, facilitating the learning of fine-grained local features in the visual stream. 3) The complementary visual and structural features can jointly enhance VPR performance. Our BEV$^2$PR framework enables consistent performance improvements over several popular aggregation modules for RGB global features. The experiments on our collected VPR-NuScenes dataset demonstrate an absolute gain of 2.47% on Recall@1 for the strong Conv-AP baseline to achieve the best performance in our setting, and notably, a 18.06% gain on the hard set. The code and dataset will be available at https://github.com/FudongGe/BEV2PR., Comment: Accepted at IROS 2024 as Oral Presentation. Code available at https://github.com/FudongGe/BEV2PR

Expanding Thurston maps were introduced by M. Bonk and D. Meyer with motivation from complex dynamics and Cannon's conjecture from geometric group theory via Sullivan's dictionary. In this paper, we introduce subsystems of expanding Thurston maps motivated via Sullivan's dictionary as analogs of some subgroups of Kleinian groups. We use thermodynamic formalism to prove the Variational Principle and the existence of equilibrium states for strongly irreducible subsystems and real-valued H\"older continuous potentials. Here, the sphere $S^{2}$ is equipped with a natural metric, called a visual metric, introduced by M. Bonk and D. Meyer. As an application, we establish large deviation asymptotics for expanding Thurston maps., Comment: 67 pages, 4 figures. Minor polish, final published version

In this work, we investigate the Variational Principle and develop a thermodynamic formalism for correspondences. We define the measure-theoretic entropy for transition probability kernels and topological pressure for correspondences. Based on these two notions, we establish the following results: The Variational Principle holds and equilibrium states exist for continuous potential functions, provided that the correspondence satisfies some expansion property called forward expansiveness. If, in addition, the correspondence satisfies the specification property and the potential function is Bowen summable, then the equilibrium state is unique. On the other hand, for a distance-expanding, open, strongly transitive correspondence and a H\"{o}lder continuous potential function, there exists a unique equilibrium state, and the backward orbits are equidistributed. Furthermore, we investigate the Variational Principle for general correspondences. In conformal dynamics, we establish the Variational Principle for the Lee--Lyubich--Markorov--Mazor--Mukherjee anti-holomorphic correspondences, which are matings of some anti-holomorphic rational maps with anti-Hecke groups and not forward expansive. We also show a Ruelle--Perron--Frobenius Theorem for a family of hyperbolic holomorphic correspondences of the form $\boldsymbol{f}_c (z)= z^{q/p}+c$., Comment: 100 pages. Reformatted, polished, Index added, typos corrected

Equilibrium states are natural dynamical analogs of Gibbs states in thermodynamic formalism. This paper is devoted to the study of their computability in the sense of Computable Analysis. We show that the unique equilibrium state associated to a pair of a computable, topologically exact, distance-expanding, open map $T\colon X\rightarrow X$ and a computable H\"older continuous potential $\varphi\colon X\rightarrow\mathbb{R}$ is always computable. Furthermore, the Hausdorff dimension of the Julia set and the equilibrium state for the geometric potential of a computable hyperbolic rational map are computable. On the other hand, we introduce a mechanism to establish non-uniqueness of equilibrium states. We also present some computable dynamical systems whose equilibrium states are all non-computable., Comment: 41 pages. Reformatted, polished, typos corrected, Theorems D and E reformulated with Section 6 adjusted accordingly

In a DNA sequence, we have the celebrated Watson-Crick complement $\overline{T}=A$, $\overline{A}=T$, $\overline{C}=G$, and $\overline{G}=C$. Given an integer $m\ge 2$, a secondary structure in a DNA sequence refers to the existence of two non-overlapping reverse complement consecutive subsequences of length $m$, denoted as $\boldsymbol{x}=(x_1, \dots, x_m)$ and $\boldsymbol{y}=(y_1, \dots, y_m)$, such that $x_i=\overline{y_{m-i+1}}$ for $1\leq i \leq m$. The property of secondary structure avoidance (SSA) forbids a sequence to contain such reverse complement subsequences, and it is a key criterion in the design of single-stranded DNA sequences for DNA computing and storage. In this paper, we improve on a recent result of Nguyen et al., by introducing explicit constructions of secondary structure avoidance codes and analyzing the capacity for any given $m$. In particular, our constructions have optimal rate 1.1679bits/nt and 1.5515bits/nt when $m=2$ and $m=3$, respectively., Comment: Submitted to ISTC'23 (International Symposium on Topics in Coding)