Search arXiv⌕ Search

arXiv · q-bio/0510031

Statistical Predictive Models in Ecology: Comparison of Performances and Assessment of Applicability

Abstract

Ecological systems are governed by complex interactions which are mainly nonlinear. In order to capture this complexity and nonlinearity, statistical models recently gained popularity. However, although these models are commonly applied in ecology, there are no studies to date aiming to assess the applicability and performance. We provide an overview for nature of the wide range of the data sets and predictive variables, from both aquatic and terrestrial ecosystems with different scales of time-dependent dynamics, and the applicability and robustness of predictive modeling methods on such data sets by comparing different statistical modeling approaches. The methods considered k-NN, LDA, QDA, generalized linear models (GLM) feedforward multilayer backpropagation networks and pseudo-supervised network ARTMAP. For ecosystems involving time-dependent dynamics and periodicities whose frequency are possibly less than the time scale of the data considered, GLM and connectionist neural network models appear to be most suitable and robust, provided that a predictive variable reflecting these time-dependent dynamics included in the model either implicitly or explicitly. For spatial data, which does not include any time-dependence comparable to the time scale covered by the data, on the other hand, neighborhood based methods such as k-NN and ARTMAP proved to be more robust than other methods considered in this study. In addition, for predictive modeling purposes, first a suitable, computationally inexpensive method should be applied to the problem at hand a good predictive performance of which would render the computational cost and efforts associated with complex variants unnecessary.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Can Ozan Tan, Uygar Ozesmi, Meryem Beklioglu, Esra Per, Bahtiyar Kurt. 2005-10-16. Statistical Predictive Models in Ecology: Comparison of Performances and Assessment of Applicability. https://doi.org/10.1016/j.ecoinf.2006.03.002

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

Multimodal AI predicts clinical outcomes of drug combinations from preclinical data

Predicting clinical outcomes from preclinical data is essential for selecting safe and effective drug combinations and for reducing late-stage failures. AI models use molecular structure and target annotations, and do not leverage the perturbation readouts that report how a compound acts in a cellular context. Here we introduce Madrigal, a multimodal AI model that learns from structural, pathway, cell-viability, and transcriptomic data. Madrigal aligns these modalities across 21,842 compounds into a shared latent space and predicts combination outcomes even for drugs observed in only a subset of the data modalities. Trained on 158 expert-curated and 795 patient-reported combination outcomes, Madrigal outperforms single-modality and state-of-the-art multimodal methods. Ablations show that modality alignment and multimodal input each improve predictive performance. Madrigal predicts elevated risk for combinations that share membrane transporters. In head-to-head trials that compare two combination arms,the arm with the higher observed incidence of neutropenia, anemia, alopecia, or hypoglycemia receives the higher predicted risk in 25 of 28 comparisons. In MASH, Madrigal ranks resmetirom among the candidates with favorable predicted safety when paired with type 2 diabetes drugs. Madrigal also improves adverse-event prediction in a longitudinal patient cohort and an independent oncology cohort and predicts efficacy in primary acute myeloid leukemia samples and patient-derived xenografts.

q-bio.QM↗

ProteoEM: probabilistic protein abundance estimation from iterative affinity traces

Single-molecule affinity mapping enables molecular-level measurement of proteins and proteoforms, but imperfect and nonspecific probe binding makes individual affinity traces compatible with multiple molecular identities. Accurate abundance estimation therefore requires apportionment of ambiguous traces by weight rather than assignment to a single candidate. We developed ProteoEM, an expectation-maximization framework for weighted proteoform quantification, inspired by transcript abundance estimation methods for RNA sequencing and released as an open-source Python package. ProteoEM evaluates each molecule against every candidate using fixed, pre-calibrated probe-response rates held separate from the abundance estimate, while retaining the full likelihood of the observed affinity features. The framework estimates proteoform abundances, reports indistinguishable proteoforms as groups when measurements cannot separate them, and accounts for differential observation yields to distinguish the composition of observed molecules from that of the source sample. In simulations, ProteoEM accurately recovered the underlying molecular composition where approaches that reduce each trace to a hard yes/no call introduced substantial errors. ProteoEM's performance was insensitive to a moderate, uniform calibration error but was biased by informative missing data and by proteoforms absent from the reference. When observation yields were known, it also recovered source-sample composition from observed molecular counts. ProteoEM provides an open-source, reproducible framework for quantitative analysis of single-molecule affinity measurements, and these results motivate validation on experimental molecule-level data.

q-bio.QM↗

PRAXIS-VirtualCell: A Programmable and Trustworthy Framework for Agentic Virtual Cell Experiments

Virtual cells are evolving from single-task predictive models toward programmable biological simulation systems, yet heterogeneous data, models, and validation evidence still lack a unified organizational framework. Here, we present PRAXIS-VirtualCell, a modular framework that organizes biological data, predictive models, perturbations, adapters, execution environments, and validation evidence to enable reproducible and auditable virtual experiments. The system supports cross-species tasks spanning Escherichia coli, Saccharomyces cerevisiae, and human K562 cells, while using biological contracts and evidence-aware execution to distinguish supported predictions from extrapolation and abstention. By further integrating agentic orchestration, PRAXIS-VirtualCell automatically translates natural-language questions into traceable virtual experiments, providing a unified runtime foundation for trustworthy and scalable Virtual Cell systems.

q-bio.QM↗