arXiv subjects

Cyrus Rashtchian

Publications and source records attributed to Cyrus Rashtchian.

34 records · Page 2Linked to original sources

arXiv2021

Batch Optimization for DNA Synthesis

Large pools of synthetic DNA molecules have been recently used to reliably store significant volumes of digital data. While DNA as a storage medium has enormous potential because of its high storage density, its practical use is currently severely limited because of the high cost and low throughput of available DNA synthesis technologies. We study the role of batch optimization in reducing the cost of large scale DNA synthesis, which translates to the following algorithmic task. Given a large pool $\mathcal{S}$ of random quaternary strings of fixed length, partition $\mathcal{S}$ into batches in a way that minimizes the sum of the lengths of the shortest common supersequences across batches. We introduce two ideas for batch optimization that both improve (in different ways) upon a naive baseline: (1) using both $(ACGT)^{*}$ and its reverse $(TGCA)^{*}$ as reference strands, and batching appropriately, and (2) batching via the quantiles of an appropriate ordering of the strands. We also prove asymptotically matching lower bounds on the cost of DNA synthesis, showing that one cannot improve upon these two ideas. Our results uncover a surprising separation between two cases that naturally arise in the context of DNA data storage: the asymptotic cost savings of batch optimization are significantly greater in the case where strings in $\mathcal{S}$ do not contain repeats of the same character (homopolymers), as compared to the case where strings in $\mathcal{S}$ are unconstrained.

cs.DS↗

arXiv2020

Approximate Trace Reconstruction

In the usual trace reconstruction problem, the goal is to exactly reconstruct an unknown string of length $n$ after it passes through a deletion channel many times independently, producing a set of traces (i.e., random subsequences of the string). We consider the relaxed problem of approximate reconstruction. Here, the goal is to output a string that is close to the original one in edit distance while using much fewer traces than is needed for exact reconstruction. We present several algorithms that can approximately reconstruct strings that belong to certain classes, where the estimate is within $n/\mathrm{polylog}(n)$ edit distance, and where we only use $\mathrm{polylog}(n)$ traces (or sometimes just a single trace). These classes contain strings that require a linear number of traces for exact reconstruction and which are quite different from a typical random string. From a technical point of view, our algorithms approximately reconstruct consecutive substrings of the unknown string by aligning dense regions of traces and using a run of a suitable length to approximate each region. To complement our algorithms, we present a general black-box lower bound for approximate reconstruction, building on a lower bound for distinguishing between two candidate input strings in the worst case. In particular, this shows that approximating to within $n^{1/3 - δ}$ edit distance requires $n^{1 + 3δ/2}/\mathrm{polylog}(n)$ traces for $0< δ< 1/3$ in the worst case.

cs.DS↗

arXiv2020

Unsupervised Embedding of Hierarchical Structure in Euclidean Space

Deep embedding methods have influenced many areas of unsupervised learning. However, the best methods for learning hierarchical structure use non-Euclidean representations, whereas Euclidean geometry underlies the theory behind many hierarchical clustering algorithms. To bridge the gap between these two areas, we consider learning a non-linear embedding of data into Euclidean space as a way to improve the hierarchical clustering produced by agglomerative algorithms. To learn the embedding, we revisit using a variational autoencoder with a Gaussian mixture prior, and we show that rescaling the latent space embedding and then applying Ward's linkage-based algorithm leads to improved results for both dendrogram purity and the Moseley-Wang cost function. Finally, we complement our empirical results with a theoretical explanation of the success of this approach. We study a synthetic model of the embedded vectors and prove that Ward's method exactly recovers the planted hierarchical clustering with high probability.

cs.LG↗

arXiv2020

Trace Reconstruction Problems in Computational Biology

The problem of reconstructing a string from its error-prone copies, the trace reconstruction problem, was introduced by Vladimir Levenshtein two decades ago. While there has been considerable theoretical work on trace reconstruction, practical solutions have only recently started to emerge in the context of two rapidly developing research areas: immunogenomics and DNA data storage. In immunogenomics, traces correspond to mutated copies of genes, with mutations generated naturally by the adaptive immune system. In DNA data storage, traces correspond to noisy copies of DNA molecules that encode digital data, with errors being artifacts of the data retrieval process. In this paper, we introduce several new trace generation models and open questions relevant to trace reconstruction for immunogenomics and DNA data storage, survey theoretical results on trace reconstruction, and highlight their connections to computational biology. Throughout, we discuss the applicability and shortcomings of known solutions and suggest future research directions.

cs.CC↗

arXiv2020

Explainable $k$-Means and $k$-Medians Clustering

Clustering is a popular form of unsupervised learning for geometric data. Unfortunately, many clustering algorithms lead to cluster assignments that are hard to explain, partially because they depend on all the features of the data in a complicated way. To improve interpretability, we consider using a small decision tree to partition a data set into clusters, so that clusters can be characterized in a straightforward manner. We study this problem from a theoretical viewpoint, measuring cluster quality by the $k$-means and $k$-medians objectives: Must there exist a tree-induced clustering whose cost is comparable to that of the best unconstrained clustering, and if so, how can it be found? In terms of negative results, we show, first, that popular top-down decision tree algorithms may lead to clusterings with arbitrarily large cost, and second, that any tree-induced clustering must in general incur an $Ω(\log k)$ approximation factor compared to the optimal clustering. On the positive side, we design an efficient algorithm that produces explainable clusters using a tree with $k$ leaves. For two means/medians, we show that a single threshold cut suffices to achieve a constant factor approximation, and we give nearly-matching lower bounds. For general $k \geq 2$, our algorithm is an $O(k)$ approximation to the optimal $k$-medians and an $O(k^2)$ approximation to the optimal $k$-means. Prior to our work, no algorithms were known with provable guarantees independent of dimension and input size.

cs.LG↗

arXiv2020

Reconstructing Trees from Traces

We study the problem of learning a node-labeled tree given independent traces from an appropriately defined deletion channel. This problem, tree trace reconstruction, generalizes string trace reconstruction, which corresponds to the tree being a path. For many classes of trees, including complete trees and spiders, we provide algorithms that reconstruct the labels using only a polynomial number of traces. This exhibits a stark contrast to known results on string trace reconstruction, which require exponentially many traces, and where a central open problem is to determine whether a polynomial number of traces suffice. Our techniques combine novel combinatorial and complex analytic methods.

cs.CC↗

arXiv2020

A Closer Look at Accuracy vs. Robustness

Current methods for training robust networks lead to a drop in test accuracy, which has led prior works to posit that a robustness-accuracy tradeoff may be inevitable in deep learning. We take a closer look at this phenomenon and first show that real image datasets are actually separated. With this property in mind, we then prove that robustness and accuracy should both be achievable for benchmark datasets through locally Lipschitz functions, and hence, there should be no inherent tradeoff between robustness and accuracy. Through extensive experiments with robustness methods, we argue that the gap between theory and practice arises from two limitations of current methods: either they fail to impose local Lipschitzness or they are insufficiently generalized. We explore combining dropout with robust training methods and obtain better generalization. We conclude that achieving robustness and accuracy in practice may require using methods that impose local Lipschitzness and augmenting them with deep learning generalization techniques. Code available at https://github.com/yangarbiter/robust-local-lipschitz

cs.LG↗

arXiv2020

ExKMC: Expanding Explainable $k$-Means Clustering

Despite the popularity of explainable AI, there is limited work on effective methods for unsupervised learning. We study algorithms for $k$-means clustering, focusing on a trade-off between explainability and accuracy. Following prior work, we use a small decision tree to partition a dataset into $k$ clusters. This enables us to explain each cluster assignment by a short sequence of single-feature thresholds. While larger trees produce more accurate clusterings, they also require more complex explanations. To allow flexibility, we develop a new explainable $k$-means clustering algorithm, ExKMC, that takes an additional parameter $k' \geq k$ and outputs a decision tree with $k'$ leaves. We use a new surrogate cost to efficiently expand the tree and to label the leaves with one of $k$ clusters. We prove that as $k'$ increases, the surrogate cost is non-increasing, and hence, we trade explainability for accuracy. Empirically, we validate that ExKMC produces a low cost clustering, outperforming both standard decision tree methods and other algorithms for explainable clustering. Implementation of ExKMC available at https://github.com/navefr/ExKMC.

cs.LG↗

arXiv2020

Vector-Matrix-Vector Queries for Solving Linear Algebra, Statistics, and Graph Problems

We consider the general problem of learning about a matrix through vector-matrix-vector queries. These queries provide the value of $\boldsymbol{u}^{\mathrm{T}}\boldsymbol{M}\boldsymbol{v}$ over a fixed field $\mathbb{F}$ for a specified pair of vectors $\boldsymbol{u},\boldsymbol{v} \in \mathbb{F}^n$. To motivate these queries, we observe that they generalize many previously studied models, such as independent set queries, cut queries, and standard graph queries. They also specialize the recently studied matrix-vector query model. Our work is exploratory and broad, and we provide new upper and lower bounds for a wide variety of problems, spanning linear algebra, statistics, and graphs. Many of our results are nearly tight, and we use diverse techniques from linear algebra, randomized algorithms, and communication complexity.

cs.DS↗

arXiv2020

Covering Codes using Insertions or Deletions

A covering code is a set of codewords with the property that the union of balls, suitably defined, around these codewords covers an entire space. Generally, the goal is to find the covering code with the minimum size codebook. While most prior work on covering codes has focused on the Hamming metric, we consider the problem of designing covering codes defined in terms of either insertions or deletions. First, we provide new sphere-covering lower bounds on the minimum possible size of such codes. Then, we provide new existential upper bounds on the size of optimal covering codes for a single insertion or a single deletion that are tight up to a constant factor. Finally, we derive improved upper bounds for covering codes using $R\geq 2$ insertions or deletions. We prove that codes exist with density that is only a factor $O(R \log R)$ larger than the lower bounds for all fixed~$R$. In particular, our upper bounds have an optimal dependence on the word length, and we achieve asymptotic density matching the best known bounds for Hamming distance covering codes.

cs.IT↗

arXiv2020

Shattered Sets and the Hilbert Function

We study complexity measures on subsets of the boolean hypercube and exhibit connections between algebra (the Hilbert function) and combinatorics (VC theory). These connections yield results in both directions. Our main complexity-theoretic result proves that most linear program feasibility problems cannot be computed by polynomial-sized constant-depth circuits. Moreover, our result applies to a stronger regime in which the hyperplanes are fixed and only the directions of the inequalities are given as input to the circuit. We derive this result by proving that a rich class of extremal functions in VC theory cannot be approximated by low-degree polynomials. We also present applications of algebra to combinatorics. We provide a new algebraic proof of the Sandwich Theorem, which is a generalization of the well-known Sauer-Perles-Shelah Lemma. Finally, we prove a structural result about downward-closed sets, related to the Chvátal conjecture in extremal combinatorics.

math.CO↗

arXiv2020

Edge Estimation with Independent Set Oracles

We study the task of estimating the number of edges in a graph with access to only an independent set oracle. Independent set queries draw motivation from group testing and have applications to the complexity of decision versus counting problems. We give two algorithms to estimate the number of edges in an $n$-vertex graph, using (i) $\mathrm{polylog}(n)$ bipartite independent set queries, or (ii) ${n}^{2/3} \cdot\mathrm{polylog}(n)$ independent set queries.

cs.DS↗

arXiv2020

LSF-Join: Locality Sensitive Filtering for Distributed All-Pairs Set Similarity Under Skew

All-pairs set similarity is a widely used data mining task, even for large and high-dimensional datasets. Traditionally, similarity search has focused on discovering very similar pairs, for which a variety of efficient algorithms are known. However, recent work highlights the importance of finding pairs of sets with relatively small intersection sizes. For example, in a recommender system, two users may be alike even though their interests only overlap on a small percentage of items. In such systems, some dimensions are often highly skewed because they are very popular. Together these two properties render previous approaches infeasible for large input sizes. To address this problem, we present a new distributed algorithm, LSF-Join, for approximate all-pairs set similarity. The core of our algorithm is a randomized selection procedure based on Locality Sensitive Filtering. Our method deviates from prior approximate algorithms, which are based on Locality Sensitive Hashing. Theoretically, we show that LSF-Join efficiently finds most close pairs, even for small similarity thresholds and for skewed input sets. We prove guarantees on the communication, work, and maximum load of LSF-Join, and we also experimentally demonstrate its accuracy on multiple graphs.

cs.DS↗

arXiv2020

Robustness for Non-Parametric Classification: A Generic Attack and Defense

Adversarially robust machine learning has received much recent attention. However, prior attacks and defenses for non-parametric classifiers have been developed in an ad-hoc or classifier-specific basis. In this work, we take a holistic look at adversarial examples for non-parametric classifiers, including nearest neighbors, decision trees, and random forests. We provide a general defense method, adversarial pruning, that works by preprocessing the dataset to become well-separated. To test our defense, we provide a novel attack that applies to a wide range of non-parametric classifiers. Theoretically, we derive an optimally robust classifier, which is analogous to the Bayes Optimal. We show that adversarial pruning can be viewed as a finite sample approximation to this optimal classifier. We empirically show that our defense and attack are either better than or competitive with prior work on non-parametric classifiers. Overall, our results provide a strong and broadly-applicable baseline for future work on robust non-parametrics. Code available at https://github.com/yangarbiter/adversarial-nonparametrics/ .

cs.LG↗

arXiv2019

Equivalence of Systematic Linear Data Structures and Matrix Rigidity

Recently, Dvir, Golovnev, and Weinstein have shown that sufficiently strong lower bounds for linear data structures would imply new bounds for rigid matrices. However, their result utilizes an algorithm that requires an $NP$ oracle, and hence, the rigid matrices are not explicit. In this work, we derive an equivalence between rigidity and the systematic linear model of data structures. For the $n$-dimensional inner product problem with $m$ queries, we prove that lower bounds on the query time imply rigidity lower bounds for the query set itself. In particular, an explicit lower bound of $ω\left(\frac{n}{r}\log m\right)$ for $r$ redundant storage bits would yield better rigidity parameters than the best bounds due to Alon, Panigrahy, and Yekhanin. We also prove a converse result, showing that rigid matrices directly correspond to hard query sets for the systematic linear model. As an application, we prove that the set of vectors obtained from rank one binary matrices is rigid with parameters matching the known results for explicit sets. This implies that the vector-matrix-vector problem requires query time $Ω(n^{3/2}/r)$ for redundancy $r \geq \sqrt{n}$ in the systematic linear model, improving a result of Chakraborty, Kamma, and Larsen. Finally, we prove a cell probe lower bound for the vector-matrix-vector problem in the high error regime, improving a result of Chattopadhyay, Koucký, Loff, and Mukhopadhyay.

cs.CC↗

arXiv2016

Massively-Parallel Similarity Join, Edge-Isoperimetry, and Distance Correlations on the Hypercube

We study distributed protocols for finding all pairs of similar vectors in a large dataset. Our results pertain to a variety of discrete metrics, and we give concrete instantiations for Hamming distance. In particular, we give improved upper bounds on the overhead required for similarity defined by Hamming distance $r>1$ and prove a lower bound showing qualitative optimality of the overhead required for similarity over any Hamming distance $r$. Our main conceptual contribution is a connection between similarity search algorithms and certain graph-theoretic quantities. For our upper bounds, we exhibit a general method for designing one-round protocols using edge-isoperimetric shapes in similarity graphs. For our lower bounds, we define a new combinatorial optimization problem, which can be stated in purely graph-theoretic terms yet also captures the core of the analysis in previous theoretical work on distributed similarity joins. As one of our main technical results, we prove new bounds on distance correlations in subsets of the Hamming cube.

cs.DS↗