Input-output HMMs for sequence processing.

IEEE Trans Neural Netw

Dept. of Comput. Sci. and Oper. Res., Montreal Univ., Que.

Published: October 2012

AI Article Synopsis

  • The text discusses a new approach to sequence processing using a discrete-state model, called the input-output hidden Markov model (IOHMM), which incorporates past context.
  • This model features a recurrent architecture with modular subnetworks for each state and can be trained with estimation-maximization algorithms that treat state trajectories as missing data.
  • Experimental results indicate that IOHMMs outperform traditional hidden Markov models in grammatical inference tasks, demonstrating strong generalization capabilities on benchmark tests.

Article Abstract

We consider problems of sequence processing and propose a solution based on a discrete-state model in order to represent past context. We introduce a recurrent connectionist architecture having a modular structure that associates a subnetwork to each state. The model has a statistical interpretation we call input-output hidden Markov model (IOHMM). It can be trained by the estimation-maximization (EM) or generalized EM (GEM) algorithms, considering state trajectories as missing data, which decouples temporal credit assignment and actual parameter estimation. The model presents similarities to hidden Markov models (HMMs), but allows us to map input sequences to output sequences, using the same processing style as recurrent neural networks. IOHMMs are trained using a more discriminant learning paradigm than HMMs, while potentially taking advantage of the EM algorithm. We demonstrate that IOHMMs are well suited for solving grammatical inference problems on a benchmark problem. Experimental results are presented for the seven Tomita grammars, showing that these adaptive models can attain excellent generalization.

Download full-text PDF

Source
http://dx.doi.org/10.1109/72.536317DOI Listing

Publication Analysis

Top Keywords

sequence processing
8
hidden markov
8
input-output hmms
4
hmms sequence
4
processing consider
4
consider problems
4
problems sequence
4
processing propose
4
propose solution
4
solution based
4

Similar Publications

In 2021, a year before ChatGPT took the world by storm amid the excitement about generative artificial intelligence (AI), AlphaFold 2 cracked the 50-year-old protein-folding problem, predicting three-dimensional (3D) structures for more than 200 million proteins from their amino acid sequences. This accomplishment was a precursor to an unprecedented burgeoning of large language models (LLMs) in the life sciences. That was just the beginning.

View Article and Find Full Text PDF

Entity-enhanced BERT for medical specialty prediction based on clinical questionnaire data.

PLoS One

January 2025

School of Industrial and Management Engineering, Korea University, Seongbuk-gu, Seoul, Republic of Korea.

A medical specialty prediction system for remote diagnosis can reduce the unexpected costs incurred by first-visit patients who visit the wrong hospital department for their symptoms. To develop medical specialty prediction systems, several researchers have explored clinical predictive models using real medical text data. Medical text data include large amounts of information regarding patients, which increases the sequence length.

View Article and Find Full Text PDF

Mechanisms underlying the interactions and adaptability of nitrogen removal microorganisms in freshwater sediments.

Adv Biotechnol (Singap)

June 2024

Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Environmental Science and Engineering/Life Sciences/Ecology, Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, State Key Laboratory for Biocontrol, Sun Yat-Sen University, Zhuhai, 519082, China.

Microorganisms in eutrophic water play a vital role in nitrogen (N) removal, which contributes significantly to the nutrient cycling and sustainability of eutrophic ecosystems. However, the mechanisms underlying the interactions and adaptation strategies of the N removal microorganisms in eutrophic ecosystems remain unclear. We thus analyzed field sediments collected from a eutrophic freshwater ecosystem, enriched the N removal microorganisms, examined their function and adaptability through amplicon, metagenome and metatranscriptome sequencing.

View Article and Find Full Text PDF

Advances in biotechnology and breeding innovations in China's marine aquaculture.

Adv Biotechnol (Singap)

October 2024

State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, Shandong, China.

Biotechnology is the key driving force behind the sustainable development of aquaculture, as biological innovation would significantly improve the capabilities of aquatic breeding and achieve independent and controllable seeding sources to ensure food safety. In this article, we have analyzed the current status and existing problems of marine aquaculture in China. Based on these data, we have summarized the recent (especially the last 10 years) biotechnological innovation and breeding progress of marine aquaculture in China, including whole genome sequencing, sex-related marker screening, genomic selection, and genome editing, as well as progress of improved marine fish varieties in China.

View Article and Find Full Text PDF

Gonadal miRNomes and transcriptomes in infected fish reveal sexually dimorphic patterns of the immune response.

Funct Integr Genomics

January 2025

Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (ICM-CSIC), Barcelona, 08003, Spain.

Fish disease outbreaks caused by bacterial burdens are responsible for decreasing productivity in aquaculture. Unraveling the molecular mechanisms activated in the gonads after infections is pivotal for enhancing husbandry techniques in fish farms, ensuring disease management, and selecting the most resilience phenotype. The present study, with an important commercial species the European sea bass (Dicentrarchus labrax), an important commercial species in Europe, examined changes in the miRNome and transcriptome 48 h after an intraperitoneal infection with Vibrio anguillarum.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!