transitive inference

This article provides a step-by-step guideline for measuring and analyzing visual attention in 3D virtual reality (VR) environments based on eye-tracking data. We propose a solution to the challenges of obtaining relevant eye-tracking information in a dynamic 3D virtual environment and calculating interpretable indicators of learning and social behavior. With a method called "gaze-ray casting," we simulated 3D-gaze movements to obtain information about the gazed objects. This information was used to create graphical models of visual attention, establishing attention networks...

Brain-effective connectivity analysis quantifies directed influence of one neural element or region over another, and it is of great scientific interest to understand how effective connectivity pattern is affected by variations of subject conditions. Vector autoregression (VAR) is a useful tool for this type of problems. However, there is a paucity of solutions when there is measurement error, when there are multiple subjects, and when the focus is the inference of the transition matrix. In this article, we study the problem of transition matrix inference under the high-dimensional VAR model with measurement error and multiple subjects...

Cellular anatomy and signaling vary across niches, which can induce gradated gene expressions in subpopulations of cells. Such spatial transcriptomic gradient (STG) makes a significant source of intra-tumor heterogeneity and can influence tumor invasion, progression, and response to treatment. Here we report Local Spatial Gradient Inference (LSGI), a computational framework that systematically identifies spatial locations with prominent, interpretable STGs from spatial transcriptomic (ST) data. To achieve so, LSGI scrutinizes each sliding window employing non-negative matrix factorization (NMF) combined with linear regression...

Although heterogeneity of FAP+ Cancer-Associated Fibroblasts (CAF) has been described in breast cancer, their plasticity and spatial distribution remain poorly understood. Here, we analyze trajectory inference, deconvolute spatial transcriptomics at single-cell level and perform functional assays to generate a high-resolution integrated map of breast cancer (BC), with a focus on inflammatory and myofibroblastic (iCAF/myCAF) FAP+ CAF clusters. We identify 10 spatially-organized FAP+ CAF-related cellular niches, called EcoCellTypes, which are differentially localized within tumors...

Molecular surveillance of viral pathogens and inference of transmission networks from genomic data play an increasingly important role in public health efforts, especially for HIV-1. For many methods, the genetic distance threshold used to connect sequences in the transmission network is a key parameter informing the properties of inferred networks. Using a distance threshold that is too high can result in a network with many spurious links, making it difficult to interpret. Conversely, a distance threshold that is too low can result in a network with too few links, which may not capture key insights into clusters of public health concern...

In the field of medical diagnosis and patient monitoring, effective pattern recognition in neurological time-series data is essential. Traditional methods predominantly based on statistical or probabilistic learning and inference often struggle with multivariate, multi-source, state-varying, and noisy data while also posing privacy risks due to excessive information collection and modeling. Furthermore, these methods often overlook critical statistical information, such as the distribution of data points and inherent uncertainties...

The funneled energy landscape theory suggests that the folding pathway of homologous proteins should converge at the late stages of folding. In this respect, proteins displaying a broad energy landscape for folding are particularly instructive, allowing inferring both the early, intermediate and late stages of folding. In this paper we explore the folding mechanisms of human frataxin, an essential mitochondrial protein linked to the neurodegenerative disorder Friedreich's ataxia. Building upon previous studies on the yeast homologue, the folding pathway of human frataxin is thoroughly examined, revealing a mechanism implying the presence of a broad energy barrier, reminiscent of the yeast counterpart...

OBJECTIVE: The majority of tobacco users have had their first contact with nicotine at a young age. The aim of this study was to explore the association between the first tobacco or nicotine product tried and the transition to regular product use in 28 European countries. METHODS: A secondary analysis of participants aged 15-40 years (n=8884) from 28 countries was conducted (Eurobarometer wave 93.2; August-September 2020). Participants who reported having ever tried tobacco or nicotine products were asked which product they tried first...

The agent learns to organize decision behavior to achieve a behavioral goal, such as reward maximization, and reinforcement learning is often used for this optimization. Learning an optimal behavioral strategy is difficult under the uncertainty that events necessary for learning are only partially observable, called as Partially Observable Markov Decision Process (POMDP). However, the real-world environment also gives many events irrelevant to reward delivery and an optimal behavioral strategy. The conventional methods in POMDP, which attempt to infer transition rules among the entire observations, including irrelevant states, are ineffective in such an environment...

In this paper, we performed theoretical studies on the twelve D-A-π-A type organic dyes (G-1 ~ G-3, M-1 ~ M-3, J-1 ~ J-3, and S-1 ~ S-3) with 9-phenylcarbazole as the electron donor in anticipation of the application of these dyes in dye-sensitized solar cells (DSSCs). DFT and TD-DFT methods are applied to investigate in detail the molecular geometries, frontier molecular orbitals (FMOs), absorption spectra, charge density difference (CDD), and transition density matrix (TDM) of several dyes...

Secular change in the heights of adult men and women resident in ten rural communities in west-central Poland in four decennial surveys between 1986 and 2016 is considered. The adults were parents of children attending schools in rural communities in the province of Poznań. During each survey, parents of school children were asked to complete a questionnaire which requested their ages, heights and completed levels of education. Ages were reported in whole years. The self-reported heights were adjusted for the tendency of individuals to overestimate height...

This paper aims to elucidate the differentially coexpressed genes, their potential mechanisms, and possible drug targets in low-grade invasive serous ovarian carcinoma (LGSC) in terms of the biologic continuity of normal, borderline, and malignant LGSC. We performed a bioinformatics analysis, integrating datasets generated using the GPL570 platform from different studies from the GEO database to identify changes in this transition, gene expression, drug targets, and their relationships with tumor microenvironmental characteristics...

Among disabling post-traumatic stress symptoms (PTSS) are irritability, aggressive behavior, distressing memories and general impaired cognition and negative mood. Art therapy interventions, including mask-making, can potentially alleviate these symptoms. We tested the hypothesis that art conveys emotions and predicted that blinded viewers would be able to perceive changes in theoretically derived emotional profiles expressed in art made by military personnel with PTSS from the onset to the end of therapy. Five service members and veterans exhibiting PTSS were enrolled in an 8-session art therapy protocol, during which they artistically transformed papier-mâché masks at the beginning and end of the protocol...

This paper considers neural representation through the lens of active inference, a normative framework for understanding brain function. It delves into how living organisms employ generative models to minimize the discrepancy between predictions and observations (as scored with variational free energy). The ensuing analysis suggests that the brain learns generative models to navigate the world adaptively, not (or not solely) to understand it. Different living organisms may possess an array of generative models, spanning from those that support action-perception cycles to those that underwrite planning and imagination; namely, from explicit models that entail variables for predicting concurrent sensations, like objects, faces, or people-to action-oriented models that predict action outcomes...

Alkali metal potassium was beneficial to the electronic regulation and structural stability of transition metal oxides. Herein, K ions were introduced into manganese oxides by different methods to improve the degradation efficiency of toluene. The results of activity experiments indicated that KMnO4 -HT (HT: Hydrothermal method) exhibited outstanding low-temperature catalytic activity, and 90% conversion of toluene can be achieved at 243°C, which was 41°C and 43°C lower than that of KNO3 -HT and Mn-HT, respectively...

BACKGROUND AND AIMS: The geographic origin and evolutionary mechanisms underpinning the rich and distinctive New Caledonian flora remain poorly understood. This is due to the complex geological past of the island and to the scarcity of well-resolved species-level phylogenies. Here, we infer phylogenetic relationships and divergence times of New Caledonian palms, which comprise 40 species. We use this framework to elucidate the biogeography of New Caledonian palm lineages, and to explore how extant species may have formed...

We analyze time-averaged experimental data from in vitro activities of neuronal networks. Through a Pairwise Maximum-Entropy method, we identify through an inverse binary Ising-like model the local fields and interaction couplings which best reproduce the average activities of each neuron as well as the statistical correlations between the activities of each pair of neurons in the system. The specific information about the type of neurons is mainly stored in the local fields, while a symmetric distribution of interaction constants seems generic...

Density functional theory (DFT) is the workhorse of computational quantum chemistry. One of its main limitations is that choosing the right functional is a non-trivial task left for human experts. The choice is particularly hard for excited state calculations when using its time-dependent formulation (TD-DFT). This is due to the approximations of the method, but also because the photophysical properties of a molecule are defined by a manifold of states that all need to be properly described. This includes not only the relative energy of the states, but also capturing the correct character, order, and intensity of the transitions...

Understanding cell fate decision-making during complex biological processes is an open challenge that is now aided by high resolution single cell sequencing technologies. Specifically, it remains challenging to identify and characterize transition states corresponding to "tipping points" whereby cells commit to new cell states. Here, we present a computational method that takes advantage of single cell transcriptomics data to infer the stability and gene regulatory networks (GRN) along cell lineages. Our method uses the unspliced and spliced counts from single cell RNA sequencing (scRNA-seq) data and cell ordering along lineage trajectories to train an RNA splicing multivariate model, from which cell state stability along the lineage is inferred based on spectral analysis of the model's Jacobian matrix...

During cellular processes such as differentiation or response to external stimuli, cells exhibit dynamic changes in their gene expression profiles. Single-cell RNA sequencing (scRNA-seq) can be used to investigate these dynamic changes. To this end, cells are typically ordered along a pseudotemporal trajectory which recapitulates the progression of cells as they transition from one cell state to another. We infer transcriptional dynamics by modeling the gene expression profiles in pseudotemporally ordered cells using a Bayesian inference approach...