Related papers: Optimal Seed Solver: Optimizing Seed Selection in …
The notion of the cover is a generalization of a period of a string, and there are linear time algorithms for finding the shortest cover. The seed is a more complicated generalization of periodicity, it is a cover of a superstring of a…
The advent of high-throughput sequencing technologies constituted a major advance in genomic studies, offering new prospects in a wide range of applications. We propose a rigorous and flexible algorithmic solution to mapping SOLiD…
Most current sampling algorithms for high-dimensional distributions are based on MCMC techniques and are approximate in the sense that they are valid only asymptotically. Rejection sampling, on the other hand, produces valid samples, but is…
We study a ranking and selection (R&S) problem when all solutions share common parametric Bayesian input models updated with the data collected from multiple independent data-generating sources. Our objective is to identify the best system…
In the last twenty-five years (1990-2014), algorithmic advances in integer optimization combined with hardware improvements have resulted in an astonishing 200 billion factor speedup in solving Mixed Integer Optimization (MIO) problems. We…
The Adaptive Seeding problem is an algorithmic challenge motivated by influence maximization in social networks: One seeks to select among certain accessible nodes in a network, and then select, adaptively, among neighbors of those nodes as…
Motivation: Seed filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. Read mappers 1) quickly…
Autonomous robots rely on geometric maps to inform a diverse set of perception and decision-making algorithms. As autonomy requires reasoning and planning on multiple scales, each algorithm may require a different map for optimal…
In this paper, we re-evaluate the basic strategies for label correcting algorithms for the multiobjective shortest path (MOSP) problem, i.e., node and label selection. In contrast to common believe, we show that---when carefully…
Background: Identifying all possible mapping locations of next-generation sequencing (NGS) reads is highly essential in several applications such as prediction of genomic variants or protein binding motifs located in repeat regions, isoform…
Sizing a residential microgrid efficiently requires solving a coupled design-and-operation problem: photovoltaic (PV) and battery capacities should be chosen in a way that reflects how the system will actually be dispatched over time. This…
We formulate selecting the best optimizing system (SBOS) problems and provide solutions for those problems. In an SBOS problem, a finite number of systems are contenders. Inside each system, a continuous decision variable affects the…
Speculative sampling reduces the latency of autoregressive decoding for target model LLMs without sacrificing inference quality, by using a cheap draft model to suggest a candidate token and a verification criterion to accept or resample…
Optimal contribution selection (OCS) is a mathematical optimization problem that aims to maximize the total benefit from selecting a group of individuals under a constraint on genetic diversity. We are specifically focused on OCS as applied…
Decision tree optimization is fundamental to interpretable machine learning. The most popular approach is to greedily search for the best feature at every decision point, which is fast but provably suboptimal. Recent approaches find the…
We present a novel, general, optimally fast, incremental way of searching for a universal algorithm that solves each task in a sequence of tasks. The Optimal Ordered Problem Solver (OOPS) continually organizes and exploits previously found…
Motivation: Seed location filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. State-of-the-art read…
When nodes can repeatedly update their behavior (as in agent-based models from computational social science or repeated-game play settings) the problem of optimal network seeding becomes very complex. For a popular spreading-phenomena model…
Timer-based mechanisms are often used to help a given (sink) node select the best helper node among many available nodes. Specifically, a node transmits a packet when its timer expires, and the timer value is a monotone non-increasing…
A recently proposed exact algorithm for the maximum independent set problem is analyzed. The typical running time is improved exponentially in some parameter regions compared to simple binary search. The algorithm also overcomes the core…