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Sequence alignment is a memory bound computation whose performance in modern systems is limited by the memory bandwidth bottleneck. Processing-in-memory architectures alleviate this bottleneck by providing the memory with computing…
Sampling and budgeting training examples are two essential factors in tracking algorithms based on support vector machines (SVMs) as a trade-off between accuracy and efficiency. Recently, the circulant matrix formed by dense sampling of…
Many tasks in data mining and related fields can be formalized as matching between objects in two heterogeneous domains, including collaborative filtering, link prediction, image tagging, and web search. Machine learning techniques,…
We examine the Xeon Phi, which is based on Intel's Many Integrated Cores architecture, for its suitability to run the FDK algorithm--the most commonly used algorithm to perform the 3D image reconstruction in cone-beam computed tomography.…
Cartesian tree matching is the problem of finding all substrings of a given text which have the same Cartesian trees as that of a given pattern. So far there is one linear-time solution for Cartesian tree matching, which is based on the KMP…
This paper describes a new asynchronous algorithm and implementation for the problem of k-mer counting (KC), which concerns quantifying the frequency of length k substrings in a DNA sequence. This operation is common to many computational…
Given an array $X$ of $N+1$ strictly ordered floating point numbers and a floating point number $z$ in the interval $[X_0,X_N)$, a common problem is to find the index $i$ of the interval $[X_{i},X_{i+1})$ containing $z$. This problem arises…
Real-time decoding is crucial for fault-tolerant quantum computing but likely requires specialized hardware such as field-programmable gate arrays (FPGAs), whose parallelism can alter relative algorithmic performance. We analyze…
We present a novel algorithm attaining excessively fast, the sought solution of linear systems of equations. The algorithm is short in its basic formulation and, by definition, vectorized, while the memory allocation demands are trivial,…
To index the increasing volume of data, modern data indexes are typically stored on SSDs and cached in DRAM. However, searching such an index has resulted in significant I/O traffic due to limited access locality and inefficient cache…
Flow Matching (FM) is an effective framework for training a model to learn a vector field that transports samples from a source distribution to a target distribution. To train the model, early FM methods use random couplings, which often…
In this short note we present a comprehensive bibliography for the online exact string matching problem. The problem consists in finding all occurrences of a given pattern in a text. It is an extensively studied problem in computer science,…
Frame synchronization is the act of discerning the first bit of a valid data frame inside an incoming transmission. This is particularly important in high-noise environments where the communication channel significantly alters transmitted…
String sorting is an important part of tasks such as building index data structures. Unfortunately, current string sorting algorithms do not scale to massively parallel distributed-memory machines since they either have latency (at least)…
Computer vision technologies are very attractive for practical applications running on embedded systems. For such an application, it is desirable for the deployed algorithms to run in high-speed and require no offline training. To develop a…
Recent years have seen a surge of novel neural network architectures for the integration of multi-omics data for prediction. Most of the architectures include either encoders alone or encoders and decoders, i.e., autoencoders of various…
In this paper, we present a fast and strong neural approach for general purpose text matching applications. We explore what is sufficient to build a fast and well-performed text matching model and propose to keep three key features…
The problem of dictionary matching is a classical problem in string matching: given a set S of d strings of total length n characters over an (not necessarily constant) alphabet of size sigma, build a data structure so that we can match in…
We consider the problem of sampling $n$ numbers from the range $\{1,\ldots,N\}$ without replacement on modern architectures. The main result is a simple divide-and-conquer scheme that makes sequential algorithms more cache efficient and…
The two most common data-structures for genome indexing, FM-indices and hash-tables, exhibit a fundamental trade-off between memory footprint and performance. We present Ranger, a new indexing technique for nucleotide sequences that is both…