K-mer counting is a requisite process for DNA assembly because it speeds up its overall process. The frequency of K-mers is used for estimating the parameters of DNA assembly, error correction, etc. The process also provides a list of district K-mers which assist in searching large databases and reducing the size of de Bruijn graphs. Nonetheless, K-mer counting is a data and compute-intensive process. Hence, it is crucial to implement a lightweight data structure that occupies low memory but does fast processing of K-mers. We proposed a lightweight K-mer counting technique, called KmerCo that implements a potent counting Bloom Filter variant, called countBF. KmerCo has two phases: insertion and classification. The insertion phase inserts all K-mers into countBF and determines distinct K-mers. The classification phase is responsible for the classification of distinct K-mers into trustworthy and erroneous K-mers based on a user-provided threshold value. We also proposed a novel benchmark performance metric. We used the Hadoop MapReduce program to determine the frequency of K-mers. We have conducted rigorous experiments to prove the dominion of KmerCo compared to state-of-the-art K-mer counting techniques. The experiments are conducted using DNA sequences of four organisms. The datasets are pruned to generate four different size datasets. KmerCo is compared with Squeakr, BFCounter, and Jellyfish. KmerCo took the lowest memory, highest number of insertions per second, and a positive trustworthy rate as compared with the three above-mentioned methods.
Ferrers diagram rank-metric codes were introduced by Etzion and Silberstein in 2009. In their work, they proposed a conjecture on the largest dimension of a space of matrices over a finite field whose nonzero elements are supported on a given Ferrers diagram and all have rank lower bounded by a fixed positive integer $d$. Since stated, the Etzion-Silberstein conjecture has been verified in a number of cases, often requiring additional constraints on the field size or on the minimum rank $d$ in dependence of the corresponding Ferrers diagram. As of today, this conjecture still remains widely open. Using modular methods, we give a constructive proof of the Etzion-Silberstein conjecture for the class of strictly monotone Ferrers diagrams, which does not depend on the minimum rank $d$ and holds over every finite field. In addition, we leverage on the last result to also prove the conjecture for the class of MDS-constructible Ferrers diagrams, without requiring any restriction on the field size.
Lightweight data compression is a key technique that allows column stores to exhibit superior performance for analytical queries. Despite a comprehensive study on dictionary-based encodings to approach Shannon's entropy, few prior works have systematically exploited the serial correlation in a column for compression. In this paper, we propose LeCo (i.e., Learned Compression), a framework that uses machine learning to remove the serial redundancy in a value sequence automatically to achieve an outstanding compression ratio and decompression performance simultaneously. LeCo presents a general approach to this end, making existing (ad-hoc) algorithms such as Frame-of-Reference (FOR), Delta Encoding, and Run-Length Encoding (RLE) special cases under our framework. Our microbenchmark with three synthetic and six real-world data sets shows that a prototype of LeCo achieves a Pareto improvement on both compression ratio and random access speed over the existing solutions. When integrating LeCo into widely-used applications, we observe up to 3.9x speed up in filter-scanning a Parquet file and a 16% increase in Rocksdb's throughput.
For many applications involving a sequence of linear systems with slowly changing system matrices, subspace recycling, which exploits relationships among systems and reuses search space information, can achieve huge gains in iterations across the total number of linear system solves in the sequence. However, for general (i.e., non-identity) shifted systems with the shift value varying over a wide range, the properties of the linear systems vary widely as well, which makes recycling less effective. If such a sequence of systems is embedded in a nonlinear iteration, the problem is compounded, and special approaches are needed to use recycling effectively. In this paper, we develop new, more efficient, Krylov subspace recycling approaches for large-scale image reconstruction and restoration techniques that employ a nonlinear iteration to compute a suitable regularization matrix. For each new regularization matrix, we need to solve regularized linear systems, ${\bf A} + \gamma_\ell {\bf E}_k$, for a sequence of regularization parameters, $\gamma_\ell$, to find the optimally regularized solution that, in turn, will be used to update the regularization matrix. In this paper, we analyze system and solution characteristics to choose appropriate techniques to solve each system rapidly. Specifically, we use an inner-outer recycling approach with a larger, principal recycle space for each nonlinear step and smaller recycle spaces for each shift. We propose an efficient way to obtain good initial guesses from the principle recycle space and smaller shift-specific recycle spaces that lead to fast convergence. Our method is substantially reduces the total number of matrix-vector products that would arise in a naive approach. Our approach is more generally applicable to sequences of shifted systems where the matrices in the sum are positive semi-definite.
Cumulative memory -- the sum of space used per step over the duration of a computation -- is a fine-grained measure of time-space complexity that was introduced to analyze cryptographic applications like password hashing. It is a more accurate cost measure for algorithms that have infrequent spikes in memory usage and are run in environments such as cloud computing that allow dynamic allocation and de-allocation of resources during execution, or when many multiple instances of an algorithm are interleaved in parallel. We prove the first lower bounds on cumulative memory complexity for both sequential classical computation and quantum circuits. Moreover, we develop general paradigms for bounding cumulative memory complexity inspired by the standard paradigms for proving time-space tradeoff lower bounds that can only lower bound the maximum space used during an execution. The resulting lower bounds on cumulative memory that we obtain are just as strong as the best time-space tradeoff lower bounds, which are very often known to be tight. Although previous results for pebbling and random oracle models have yielded time-space tradeoff lower bounds larger than the cumulative memory complexity, our results show that in general computational models such separations cannot follow from known lower bound techniques and are not true for many functions. Among many possible applications of our general methods, we show that any classical sorting algorithm with success probability at least $1/\text{poly}(n)$ requires cumulative memory $\tilde \Omega(n^2)$, any classical matrix multiplication algorithm requires cumulative memory $\Omega(n^6/T)$, any quantum sorting circuit requires cumulative memory $\Omega(n^3/T)$, and any quantum circuit that finds $k$ disjoint collisions in a random function requires cumulative memory $\Omega(k^3n/T^2)$.
In this paper we investigate the problem of quantifying the contribution of each variable to the satisfying assignments of a Boolean function based on the Shapley value. Our main result is a polynomial-time equivalence between computing Shapley values and model counting for any class of Boolean functions that are closed under substitutions of variables with disjunctions of fresh variables. This result settles an open problem raised in prior work, which sought to connect the Shapley value computation to probabilistic query evaluation. We show two applications of our result. First, the Shapley values can be computed in polynomial time over deterministic and decomposable circuits, since they are closed under OR-substitutions. Second, there is a polynomial-time equivalence between computing the Shapley value for the tuples contributing to the answer of a Boolean conjunctive query and counting the models in the lineage of the query. This equivalence allows us to immediately recover the dichotomy for Shapley value computation in case of self-join-free Boolean conjunctive queries; in particular, the hardness for non-hierarchical queries can now be shown using a simple reduction from the #P-hard problem of model counting for lineage in positive bipartite disjunctive normal form.
In many practical applications of differential privacy, practitioners seek to provide the best privacy guarantees subject to a target level of accuracy. A recent line of work by \cite{LigettNeRoWaWu17, WhitehouseWuRaRo22} has developed such accuracy-first mechanisms by leveraging the idea of \emph{noise reduction} that adds correlated noise to the sufficient statistic in a private computation and produces a sequence of increasingly accurate answers. A major advantage of noise reduction mechanisms is that the analysts only pay the privacy cost of the least noisy or most accurate answer released. Despite this appealing property in isolation, there has not been a systematic study on how to use them in conjunction with other differentially private mechanisms. A fundamental challenge is that the privacy guarantee for noise reduction mechanisms is (necessarily) formulated as \emph{ex-post privacy} that bounds the privacy loss as a function of the released outcome. Furthermore, there has yet to be any study on how ex-post private mechanisms compose, which allows us to track the accumulated privacy over several mechanisms. We develop privacy filters \citep{RogersRoUlVa16, FeldmanZr21, WhitehouseRaRoWu22} that allow an analyst to adaptively switch between differentially private and ex-post private mechanisms subject to an overall privacy guarantee.
In this article we propose two finite element schemes for the Navier-Stokes equations, based on a reformulation that involves differential operators from the de Rham sequence and an advection operator with explicit skew-symmetry in weak form. Our first scheme is obtained by discretizing this formulation with conforming FEEC (Finite Element Exterior Calculus) spaces: it preserves the pointwise divergence free constraint of the velocity, its total momentum and its energy, in addition to being pressure robust. Following the broken-FEEC approach, our second scheme uses fully discontinuous spaces and local conforming projections to define the discrete differential operators. It preserves the same invariants up to a dissipation of energy to stabilize numerical discontinuities. For both schemes we use a middle point time discretization which preserve these invariants at the fully discrete level and we analyse its well-posedness in terms of a CFL condition. Numerical test cases performed with spline finite elements allow us to verify the high order accuracy of the resulting numerical methods, as well as their ability to handle general boundary conditions.
Computer-assisted treatment has emerged as a viable application of medical imaging, owing to the efficacy of deep learning models. Real-time inference speed remains a key requirement for such applications to help medical personnel. Even though there generally exists a trade-off between performance and model size, impressive efforts have been made to retain near-original performance by compromising model size. Neural network pruning has emerged as an exciting area that aims to eliminate redundant parameters to make the inference faster. In this study, we show an application of neural network pruning in polyp segmentation. We compute the importance score of convolutional filters and remove the filters having the least scores, which to some value of pruning does not degrade the performance. For computing the importance score, we use the Taylor First Order (TaylorFO) approximation of the change in network output for the removal of certain filters. Specifically, we employ a gradient-normalized backpropagation for the computation of the importance score. Through experiments in the polyp datasets, we validate that our approach can significantly reduce the parameter count and FLOPs retaining similar performance.
Spatio-temporal forecasting is challenging attributing to the high nonlinearity in temporal dynamics as well as complex location-characterized patterns in spatial domains, especially in fields like weather forecasting. Graph convolutions are usually used for modeling the spatial dependency in meteorology to handle the irregular distribution of sensors' spatial location. In this work, a novel graph-based convolution for imitating the meteorological flows is proposed to capture the local spatial patterns. Based on the assumption of smoothness of location-characterized patterns, we propose conditional local convolution whose shared kernel on nodes' local space is approximated by feedforward networks, with local representations of coordinate obtained by horizon maps into cylindrical-tangent space as its input. The established united standard of local coordinate system preserves the orientation on geography. We further propose the distance and orientation scaling terms to reduce the impacts of irregular spatial distribution. The convolution is embedded in a Recurrent Neural Network architecture to model the temporal dynamics, leading to the Conditional Local Convolution Recurrent Network (CLCRN). Our model is evaluated on real-world weather benchmark datasets, achieving state-of-the-art performance with obvious improvements. We conduct further analysis on local pattern visualization, model's framework choice, advantages of horizon maps and etc.
Multivariate time series forecasting is extensively studied throughout the years with ubiquitous applications in areas such as finance, traffic, environment, etc. Still, concerns have been raised on traditional methods for incapable of modeling complex patterns or dependencies lying in real word data. To address such concerns, various deep learning models, mainly Recurrent Neural Network (RNN) based methods, are proposed. Nevertheless, capturing extremely long-term patterns while effectively incorporating information from other variables remains a challenge for time-series forecasting. Furthermore, lack-of-explainability remains one serious drawback for deep neural network models. Inspired by Memory Network proposed for solving the question-answering task, we propose a deep learning based model named Memory Time-series network (MTNet) for time series forecasting. MTNet consists of a large memory component, three separate encoders, and an autoregressive component to train jointly. Additionally, the attention mechanism designed enable MTNet to be highly interpretable. We can easily tell which part of the historic data is referenced the most.