Related papers: ApHMM: Accelerating Profile Hidden Markov Models f…
In this paper, we explore the effectiveness of dynamic analysis techniques for identifying malware, using Hidden Markov Models (HMMs) and Profile Hidden Markov Models (PHMMs), both trained on sequences of API calls. We contrast our results…
Hidden Markov models (HMMs) are commonly used for disease progression modeling when the true patient health state is not fully known. Since HMMs typically have multiple local optima, incorporating additional patient covariates can improve…
We derive the Baum-Welch algorithm for hidden Markov models (HMMs) through an information-theoretical approach using cross-entropy instead of the Lagrange multiplier approach which is universal in machine learning literature. The proposed…
Hidden Markov models (HMMs) are popular models to identify a finite number of latent states from sequential data. However, fitting them to large data sets can be computationally demanding because most likelihood maximization techniques…
This report describes a new technique for inducing the structure of Hidden Markov Models from data which is based on the general `model merging' strategy (Omohundro 1992). The process begins with a maximum likelihood HMM that directly…
Fully Homomorphic Encryption (FHE) is a technique that allows arbitrary computations to be performed on encrypted data without the need for decryption, making it ideal for securing many emerging applications. However, FHE computation is…
A Hidden Markov Model (HMM) is a common statistical model which is widely used for analysis of biological sequence data and other sequential phenomena. In the present paper we show how HMMs can be extended with side-constraints and present…
Sparse Matrix-Matrix Multiplication (SpMM) is a fundamental operation in graph computing and analytics. However, the irregularity of real-world graphs poses significant challenges to achieving efficient SpMM operation for graph data on…
Hidden semi-Markov models (HSMMs) are latent variable models which allow latent state persistence and can be viewed as a generalization of the popular hidden Markov models (HMMs). In this paper, we introduce a novel spectral algorithm to…
Actigraphy is widely used in sleep studies but lacks a universal unsupervised algorithm for sleep/wake identification. In this study, we proposed a Hidden Markov Model (HMM) based unsupervised algorithm that can automatically and…
We propose a new method for the estimation of parameters of hidden diffusion processes. Based on parametrization of the transition matrix, the Baum-Welch algorithm is improved. The algorithm is compared to the particle filter in application…
Serving Large Language Models (LLMs) often requires choosing between stronger reasoning and lower inference cost. Model merging offers a practical way to build several models between a reasoning-oriented model and a cheaper base model, but…
Linear mixed models (LMM) are widely adopted in genome-wide association studies (GWAS) to account for population stratification and cryptic relatedness. However, the parameter estimation of LMMs imposes substantial computational burdens due…
The hidden Markov model (HMM) is a fundamental tool for sequence modeling that cleanly separates the hidden state from the emission structure. However, this separation makes it difficult to fit HMMs to large datasets in modern NLP, and they…
Standard practice in Hidden Markov Model (HMM) selection favors the candidate with the highest full-sequence likelihood, although this is equivalent to making a decision based on a single realization. We introduce a \emph{fragment-based}…
We present a lightweight approach to sequence classification using Ensemble Methods for Hidden Markov Models (HMMs). HMMs offer significant advantages in scenarios with imbalanced or smaller datasets due to their simplicity,…
Genome sequence analysis has enabled significant advancements in medical and scientific areas such as personalized medicine, outbreak tracing, and the understanding of evolution. Unfortunately, it is currently bottlenecked by the…
The hidden Markov model (HMM) has been a workhorse of single molecule data analysis and is now commonly used as a standalone tool in time series analysis or in conjunction with other analyses methods such as tracking. Here we provide a…
Fully Homomorphic Encryption (FHE) allows for computation directly on encrypted data and enables privacy-preserving neural inference in the cloud. Prior work has focused on models with dense inputs (e.g., CNNs), with less attention given to…
Computing on encrypted data is a promising approach to reduce data security and privacy risks, with homomorphic encryption serving as a facilitator in achieving this goal. In this work, we accelerate homomorphic operations using the…