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We propose a simple tractable pair hidden Markov model for pairwise sequence alignment that accounts for the presence of short tandem repeats. Using the framework of gain functions, we design several optimization criteria for decoding this…

Quantitative Methods · Quantitative Biology 2013-07-31 Michal Nánási , Tomáš Vinař , Broňa Brejová

In this article, we review the literature on design and analysis of recursive algorithms for reconstructing a time sequence of sparse signals from compressive measurements. The signals are assumed to be sparse in some transform domain or in…

Information Theory · Computer Science 2016-06-29 Namrata Vaswani , Jinchun Zhan

Effective image and sentence matching depends on how to well measure their global visual-semantic similarity. Based on the observation that such a global similarity arises from a complex aggregation of multiple local similarities between…

Computer Vision and Pattern Recognition · Computer Science 2017-12-07 Yan Huang , Wei Wang , Liang Wang

Retrieving homologous protein sequences is essential for a broad range of protein modeling tasks such as fitness prediction, protein design, structure modeling, and protein-protein interactions. Traditional workflows have relied on a…

Quantitative Methods · Quantitative Biology 2025-06-11 Ruben Weitzman , Peter Mørch Groth , Lood Van Niekerk , Aoi Otani , Yarin Gal , Debora Marks , Pascal Notin

In partial multi-label learning (PML), each instance is associated with a set of candidate labels containing both ground-truth and noisy labels. The presence of noisy labels disrupts the correspondence between features and labels, degrading…

Machine Learning · Computer Science 2026-04-13 Yu Chen , Weijun Lv , Yue Huang , Xiaozhao Fang , Jie Wen , Yong Xu , Guanbin Li

In this work, we propose a purely geometrical approach for the robust matching of line segments for challenging stereo streams with severe illumination changes or High Dynamic Range (HDR) environments. To that purpose, we exploit the…

Computer Vision and Pattern Recognition · Computer Science 2018-09-26 Ruben Gomez-Ojeda , Javier Gonzalez-Jimenez

Semblance velocity analysis is a crucial step in seismic data processing. To avoid the huge time-cost when performed manually, some deep learning methods are proposed for automatic semblance velocity picking. However, the application of…

Geophysics · Physics 2022-07-04 Chenyu Qiu , Bangyu Wu , Meng Li , Hui Yang , Xu Zhu

Long Short-Term Memory (LSTM) neural network models have become the cornerstone for sequential data modeling in numerous applications, ranging from natural language processing to time series forecasting. Despite their success, the problem…

Machine Learning · Statistics 2026-05-26 Fahad Mostafa

In recent years, specific evaluation metrics for time series anomaly detection algorithms have been developed to handle the limitations of the classical precision and recall. However, such metrics are heuristically built as an aggregate of…

Machine Learning · Computer Science 2022-10-13 Alexis Huet , Jose Manuel Navarro , Dario Rossi

Phase retrieval is in general a non-convex and non-linear task and the corresponding algorithms struggle with the issue of local minima. We consider the case where the measurement samples within typically very small and disconnected subsets…

Signal Processing · Electrical Eng. & Systems 2022-06-28 Jonas Kornprobst , Alexander Paulus , Josef Knapp , Thomas F. Eibert

This paper presents an unsupervised approach that leverages raw aerial videos to learn to estimate planar homographic transformation between consecutive video frames. Previous learning-based estimators work on pairs of images to estimate…

Computer Vision and Pattern Recognition · Computer Science 2023-04-07 Pu Li , Xiaobai Liu

A novel hierarchical search technique is presented for all-sky surveys for continuous gravitational-wave sources, such as rapidly spinning nonaxisymmetric neutron stars. Analyzing yearlong detector data sets over realistic ranges of…

General Relativity and Quantum Cosmology · Physics 2015-03-18 Holger J. Pletsch

Large language models require continuous adaptation to new tasks while preserving safety alignment. However, fine-tuning on even benign data often compromises safety behaviors, including refusal of harmful requests, truthfulness, and…

Machine Learning · Computer Science 2026-04-21 Thong Bach , Dung Nguyen , Thao Minh Le , Truyen Tran

A time series is a sequence of data items; typical examples are videos, stock ticker data, or streams of temperature measurements. Quite some research has been devoted to comparing and indexing simple time series, i.e., time series where…

Computational Complexity · Computer Science 2018-06-04 Jörg P. Bachmann , Johann-Christoph Freytag , Benjamin Hauskeller , Nicole Schweikardt

Ensemble modeling has been widely used to solve complex problems as it helps to improve overall performance and generalization. In this paper, we propose a novel TemporalAugmenter approach based on ensemble modeling for augmenting the…

Machine Learning · Computer Science 2024-01-17 Nelly Elsayed , Constantinos L. Zekios , Navid Asadizanjani , Zag ElSayed

Embedding-based retrieval aims to learn a shared semantic representation space for both queries and items, enabling efficient and effective item retrieval through approximate nearest neighbor (ANN) algorithms. In current industrial…

Information Retrieval · Computer Science 2025-10-14 Han Zhang , Yunjiang Jiang , Mingming Li , Haowei Yuan , Yiming Qiu , Wen-Yun Yang

The use of Hirschberg algorithm reduces the spatial cost of recovering the Longest Common Subsequence to linear space. The same technique can be applied to similar problems like Sequence Alignment. However, the price to pay is a duplication…

Data Structures and Algorithms · Computer Science 2022-04-28 David Llorens , Juan Miguel Vilar

Advances in bio-technology have made available massive amounts of functional, structural and genomic data for many biological sequences. This increased availability of heterogeneous biological data has resulted in biological applications…

Computational Engineering, Finance, and Science · Computer Science 2013-02-26 Srikrishnan Divakaran , Arpit Mithal , Namit Jain

Hidden Markov Models (HMMs) can be accurately approximated using co-occurrence frequencies of pairs and triples of observations by using a fast spectral method in contrast to the usual slow methods like EM or Gibbs sampling. We provide a…

Machine Learning · Statistics 2012-03-29 Dean P. Foster , Jordan Rodu , Lyle H. Ungar

Human motion prediction (HMP) has emerged as a popular research topic due to its diverse applications, but it remains a challenging task due to the stochastic and aperiodic nature of future poses. Traditional methods rely on hand-crafted…

Computer Vision and Pattern Recognition · Computer Science 2024-07-18 Jiexin Wang , Yujie Zhou , Wenwen Qiang , Ying Ba , Bing Su , Ji-Rong Wen
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