Browse
Submit Data
Databases
API
Help

Dataset Information

27 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Beyond the topics: how deep learning can improve the discriminability of probabilistic topic modelling.

ABSTRACT: The article presents a discriminative approach to complement the unsupervised probabilistic nature of topic modelling. The framework transforms the probabilities of the topics per document into class-dependent deep learning models that extract highly discriminatory features suitable for classification. The framework is then used for sentiment analysis with minimum feature engineering. The approach transforms the sentiment analysis problem from the word/document domain to the topics domain making it more robust to noise and incorporating complex contextual information that are not represented otherwise. A stacked denoising autoencoder (SDA) is then used to model the complex relationship among the topics per sentiment with minimum assumptions. To achieve this, a distinct topic model and SDA per sentiment polarity is built with an additional decision layer for classification. The framework is tested on a comprehensive collection of benchmark datasets that vary in sample size, class bias and classification task. A significant improvement to the state of the art is achieved without the need for a sentiment lexica or over-engineered features. A further analysis is carried out to explain the observed improvement in accuracy.

SUBMITTER: Al Moubayed N

PROVIDER: S-EPMC7924555 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Stimulus discriminability may bias value-based probabilistic learning.

Project description:Reinforcement learning tasks are often used to assess participants' tendency to learn more from the positive or more from the negative consequences of one's action. However, this assessment often requires comparison in learning performance across different task conditions, which may differ in the relative salience or discriminability of the stimuli associated with more and less rewarding outcomes, respectively. To address this issue, in a first set of studies, participants were subjected to two versions of a common probabilistic learning task. The two versions differed with respect to the stimulus (Hiragana) characters associated with reward probability. The assignment of character to reward probability was fixed within version but reversed between versions. We found that performance was highly influenced by task version, which could be explained by the relative perceptual discriminability of characters assigned to high or low reward probabilities, as assessed by a separate discrimination experiment. Participants were more reliable in selecting rewarding characters that were more discriminable, leading to differences in learning curves and their sensitivity to reward probability. This difference in experienced reinforcement history was accompanied by performance biases in a test phase assessing ability to learn from positive vs. negative outcomes. In a subsequent large-scale web-based experiment, this impact of task version on learning and test measures was replicated and extended. Collectively, these findings imply a key role for perceptual factors in guiding reward learning and underscore the need to control stimulus discriminability when making inferences about individual differences in reinforcement learning.

| S-EPMC5421749 | biostudies-literature

Deep learning for COVID-19 topic modelling via Twitter: Alpha, Delta and Omicron.

Project description:Topic modelling with innovative deep learning methods has gained interest for a wide range of applications that includes COVID-19. It can provide, psychological, social and cultural insights for understanding human behaviour in extreme events such as the COVID-19 pandemic. In this paper, we use prominent deep learning-based language models for COVID-19 topic modelling taking into account data from the emergence (Alpha) to the Omicron variant in India. Our results show that the topics extracted for the subsequent waves had certain overlapping themes such as governance, vaccination, and pandemic management while novel issues aroused in political, social and economic situations during the COVID-19 pandemic. We also find a strong correlation between the major topics with news media prevalent during the respective time period. Hence, our framework has the potential to capture major issues arising during different phases of the COVID-19 pandemic which can be extended to other countries and regions.

| S-EPMC10393149 | biostudies-literature

Beyond K-complex binary scoring during sleep: probabilistic classification using deep learning.

Project description:K-complexes (KCs) are a recognized electroencephalography marker of sensory processing and a defining feature of sleep stage 2. KC frequency and morphology may also be reflective of sleep quality, aging, and a range of sleep and sensory processing deficits. However, manual scoring of K-complexes is impractical, time-consuming, and thus costly and currently not well-standardized. Although automated KC detection methods have been developed, performance and uptake remain limited. The proposed algorithm is based on a deep neural network and Gaussian process, which gives the input waveform a probability of being a KC ranging from 0% to 100%. The algorithm was trained on half a million synthetic KCs derived from manually scored sleep stage 2 KCs from the Montreal Archive of Sleep Study containing 19 healthy young participants. Algorithm performance was subsequently assessed on 700 independent recordings from the Cleveland Family Study using sleep stages 2 and 3 data. The developed algorithm showed an F1 score (a measure of binary classification accuracy) of 0.78 and thus outperforms currently available KC scoring algorithms with F1 = 0.2-0.6. The probabilistic approach also captured expected variability in KC shape and amplitude within individuals and across age groups. An automated probabilistic KC classification is well suited and effective for systematic KC detection for a more in-depth exploration of potential relationships between KCs during sleep and clinical outcomes such as health impacts and daytime symptomatology.

| S-EPMC7751135 | biostudies-literature

Mapping topics and topic bursts in PNAS.

Project description:Scientific research is highly dynamic. New areas of science continually evolve; others gain or lose importance, merge, or split. Due to the steady increase in the number of scientific publications, it is hard to keep an overview of the structure and dynamic development of one's own field of science, much less all scientific domains. However, knowledge of "hot" topics, emergent research frontiers, or change of focus in certain areas is a critical component of resource allocation decisions in research laboratories, governmental institutions, and corporations. This paper demonstrates the utilization of Kleinberg's burst detection algorithm, co-word occurrence analysis, and graph layout techniques to generate maps that support the identification of major research topics and trends. The approach was applied to analyze and map the complete set of papers published in PNAS in the years 1982-2001. Six domain experts examined and commented on the resulting maps in an attempt to reconstruct the evolution of major research areas covered by PNAS.

| S-EPMC387309 | biostudies-other

Seasonal Arctic sea ice forecasting with probabilistic deep learning.

Project description:Anthropogenic warming has led to an unprecedented year-round reduction in Arctic sea ice extent. This has far-reaching consequences for indigenous and local communities, polar ecosystems, and global climate, motivating the need for accurate seasonal sea ice forecasts. While physics-based dynamical models can successfully forecast sea ice concentration several weeks ahead, they struggle to outperform simple statistical benchmarks at longer lead times. We present a probabilistic, deep learning sea ice forecasting system, IceNet. The system has been trained on climate simulations and observational data to forecast the next 6 months of monthly-averaged sea ice concentration maps. We show that IceNet advances the range of accurate sea ice forecasts, outperforming a state-of-the-art dynamical model in seasonal forecasts of summer sea ice, particularly for extreme sea ice events. This step-change in sea ice forecasting ability brings us closer to conservation tools that mitigate risks associated with rapid sea ice loss.

| S-EPMC8390499 | biostudies-literature

Deep learning models incorporating endogenous factors beyond DNA sequences improve the prediction accuracy of base editing outcomes.

Project description:Adenine base editors (ABEs) and cytosine base editors (CBEs) enable the single nucleotide editing of targeted DNA sites avoiding generation of double strand breaks, however, the genomic features that influence the outcomes of base editing in vivo still remain to be characterized. High-throughput datasets from lentiviral integrated libraries were used to investigate the sequence features affecting base editing outcomes, but the effects of endogenous factors beyond the DNA sequences are still largely unknown. Here the base editing outcomes of ABE and CBE were evaluated in mammalian cells for 5012 endogenous genomic sites and 11,868 genome-integrated target sequences, with 4654 genomic sites sharing the same target sequences. The comparative analyses revealed that the editing outcomes of ABE and CBE at endogenous sites were substantially different from those obtained using genome-integrated sequences. We found that the base editing efficiency at endogenous target sites of both ABE and CBE was influenced by endogenous factors, including epigenetic modifications and transcriptional activity. A deep-learning algorithm referred as BE_Endo, was developed based on the endogenous factors and sequence information from our genomic datasets, and it yielded unprecedented accuracy in predicting the base editing outcomes. These findings along with the developed computational algorithms may facilitate future application of BEs for scientific research and clinical gene therapy.

| S-EPMC10879117 | biostudies-literature

Topic classification of electric vehicle consumer experiences with transformer-based deep learning.

Project description:The transportation sector is a major contributor to greenhouse gas (GHG) emissions and is a driver of adverse health effects globally. Increasingly, government policies have promoted the adoption of electric vehicles (EVs) as a solution to mitigate GHG emissions. However, government analysts have failed to fully utilize consumer data in decisions related to charging infrastructure. This is because a large share of EV data is unstructured text, which presents challenges for data discovery. In this article, we deploy advances in transformer-based deep learning to discover topics of attention in a nationally representative sample of user reviews. We report classification accuracies greater than 91% (F1 scores of 0.83), outperforming previously leading algorithms in this domain. We describe applications of these deep learning models for public policy analysis and large-scale implementation. This capability can boost intelligence for the EV charging market, which is expected to grow to US$27.6 billion by 2027.

| S-EPMC7892356 | biostudies-literature

Deep Probabilistic Learning Model for Prediction of Ionic Liquids Toxicity.

Project description:Identification of ionic liquids with low toxicity is paramount for applications in various domains. Traditional approaches used for determining the toxicity of ionic liquids are often expensive, and can be labor intensive and time consuming. In order to mitigate these limitations, researchers have resorted to using computational models. This work presents a probabilistic model built from deep kernel learning with the aim of predicting the toxicity of ionic liquids in the leukemia rat cell line (IPC-81). Only open source tools, namely, RDKit and Mol2vec, are required to generate predictors for this model; as such, its predictions are solely based on chemical structure of the ionic liquids and no manual extraction of features is needed. The model recorded an RMSE of 0.228 and R2 of 0.943. These results indicate that the model is both reliable and accurate. Furthermore, this model provides an accompanying uncertainty level for every prediction it makes. This is important because discrepancies in experimental measurements that generated the dataset used herein are inevitable, and ought to be modeled. A user-friendly web server was developed as well, enabling researchers and practitioners ti make predictions using this model.

| S-EPMC9104997 | biostudies-literature

cisTopic: cis-regulatory topic modelling on single-cell ATAC-seq data

Project description:We present cisTopic, a probabilistic framework to simultaneously discover co-accessible enhancers and stable cell states from sparse single-cell epigenomics data (http://github.com/aertslab/cistopic). On a compendium of single-cell ATAC-seq datasets from differentiating hematopoietic cells, brain, and transcription-factor perturbation dynamics, we demonstrate that topic modelling can be exploited for a robust identification of cell types, enhancers, and relevant transcription factors. cisTopic provides insight into the mechanisms underlying regulatory heterogeneity within cell populations.

2019-02-18 | GSE114557 | GEO

Topic-driven toxicity: Exploring the relationship between online toxicity and news topics.

Project description:Hateful commenting, also known as 'toxicity', frequently takes place within news stories in social media. Yet, the relationship between toxicity and news topics is poorly understood. To analyze how news topics relate to the toxicity of user comments, we classify topics of 63,886 online news videos of a large news channel using a neural network and topical tags used by journalists to label content. We score 320,246 user comments from those videos for toxicity and compare how the average toxicity of comments varies by topic. Findings show that topics like Racism, Israel-Palestine, and War & Conflict have more toxicity in the comments, and topics such as Science & Technology, Environment & Weather, and Arts & Culture have less toxic commenting. Qualitative analysis reveals five themes: Graphic videos, Humanistic stories, History and historical facts, Media as a manipulator, and Religion. We also observe cases where a typically more toxic topic becomes non-toxic and where a typically less toxic topic becomes "toxicified" when it involves sensitive elements, such as politics and religion. Findings suggest that news comment toxicity can be characterized as topic-driven toxicity that targets topics rather than as vindictive toxicity that targets users or groups. Practical implications suggest that humanistic framing of the news story (i.e., reporting stories through real everyday people) can reduce toxicity in the comments of an otherwise toxic topic.

| S-EPMC7034861 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data