Search · four archives
Search · four archives
18 papers · ranked by Valyu relevance
Robert Milletich, Justin Downes, Steve Goley, Newel Hirst
Conditional inference trees (CIT) and conditional inference forests (CIF) reduce split-selection bias by testing features before choosing split thresholds, but repeated permutation tests and threshold searches can make these methods computationally expensive. We study CIT and CIF as top-$k$ feature-ranking methods for…
Soham Bakshi, Snigdha Panigrahi
Decision trees are widely used for non-linear modeling, as they capture interactions between predictors while producing inherently interpretable models. Despite their popularity, performing inference on the non-linear fit remains largely unaddressed. This paper focuses on classification trees and makes two key…
Zijing Yang, Jonathan Klawitter, Remco Bouckaert, Alexei J. Drummond
Bayesian phylogenetic inference uses Markov chain Monte Carlo sampling to estimate the posterior distribution of phylogenetic trees. However, the complex geometry of treespace makes these distributions difficult to characterise. Traditional approaches often summarise posterior samples into a single point estimate…
Basu, Tathagata, Leisen, Fabrizio + 4 more
The study of dependence between random variables under external influences is a challenging problem in multivariate analysis. We address this by proposing a novel semi-parametric approach for conditional copula models using Bayesian additive regression trees (BART) models. BART is becoming a popular approach in…
Tianyu Xie, Yicong Mao, Cheng Zhang, Lun Hu
Probabilistic modeling over the combinatorially large space of tree topologies remains a central challenge in phylogenetic inference. Previous approaches often necessitate pre-sampled tree topologies, limiting their modeling capability to a subset of the entire tree space. A recent advancement is ARTree, a deep…
Polina V Polunina, Wolfgang Maier, Alan F Rubin
The evolutionary accessibility of a protein mutation depends on the sequence background in which it arises and its lineage history, yet most protein language models estimate sequence plausibility without explicitly considering the ordered sequence changes through which descendants arise. We developed evoPLM-Tree, a…
Lars Vogt
This manuscript introduces the Semantic Units Framework, a technology-agnostic representational approach to semantic modularization in which statements and compound meaning structures are treated as first-class semantic units with explicit boundaries, identity, and epistemic status. Motivated by recurring limitations…
Sungmin Kim, Youndo Do, Fan Zhang, Yuan Yao
In many industrial facilities, online monitoring systems have improved the reliability of key equipment, reducing the cost of operation and maintenance over recent decades. However, it often requires additional on-site inspection of target facilities due to limited information from installed sensors. To systematically…
Hwangbo, Junhyeong, Soo-Hyun Lee, Mathew Cheong + 2 more
InFerActive's backend architecture implements a scalable inference system designed for interactive token generation workflows. The system offers comprehensive management and optimization, complemented by efficient tree initialization and generation algorithms. Model Management and Resource Optimization: The backend…
Zelin Ding, Zhefei Fan, Yuanfeng Hao, Tao Wang + 3 more
To break through the efficiency and accuracy bottlenecks of manual mode in the compliance review of water conservancy project reports and promote the digital transformation of “Smart Water Conservancy”, this paper proposes a knowledge graph construction method for the compliance review of water conservancy project…
Zhenjiang Fan, Mengrui Zhang, Summer Han
Causal relationship identification is a fundamental and complex research challenge that spans multiple disciplines, including biology, epidemiology, economics, and philosophy. Various scoring techniques and independence tests, such as local scores (e.g., Degenerate Gaussian (DG) and Bayesian Information Criterion…
Flaminio, Tommaso, Godo, Lluis + 2 more
Methods for probability updating, of which Bayesian conditionalization is the most well-known and widely used, are modeling tools that aim to represent the process of modifying an initial epistemic state, typically represented by a prior probability function P, which is adjusted in light of new information. Notably…
Edo Dotan, Asaf Schers, Elya Wygoda, Tal Pupko + 1 more
Accurate inference of phylogenetic trees is fundamental to evolutionary biology, yet existing methods rely on complex pipelines involving multiple sequence alignment, explicit evolutionary models, and computationally intensive tree search procedures. Here, we present BetaInfer, a generative framework that reformulates…
Jesus Antonio Motta, Carolina Fernandez, Maria del Mar Motta
In this work, we present a machine learning model for identifying pathogenic DNA variants. The model was learned from the analysis of normal and pathogenic sequences extracted from the ClinVar database (supported by NCBI). This analysis was based on a conceptual semantic model of DNA sequences converted to peptide…
Jiansi Gao, Marius Brusselmans, Luiz M. Carvalho, Marc A. Suchard + 2 more
Title: Significance Bayesian phylodynamics is central to epidemiological studies, but exploring the complex tree space is computationally challenging. Phylodynamic datasets comprise many highly similar sequences, sampled through time, creating a uniquely structured landscape of optimal trees. Here, we show that…
Authors not listed
Quantitative Structure Activity Relationship (QSAR) remains an effective tool for early-stage chemical modelling and virtual screening in drug design. The advancements in this field are led by two core paradigms, 1) descriptor engineering, where complex fixed-length vectors of compounds are generated and conventional…
Jiaqi Wu
Many comparative analyses operate on rectangular matrices whose columns represent the same variables across observations. Phylogenomic measurements, however, are attached to tree branches. Converting locus-specific trees into a common locus-by-coordinate matrix is straightforward only when loci contain the same taxa…
Authors not listed
Phase equilibrium calculations are crucial in chemical engineering design and optimization processes. The PC-SAFT equation of state (EoS) can precisely calculate phase equilibrium, but is relatively complex and computationally intensive. Surrogate models are mathematically simple models that map or regress the…