Deep Learning for Reference-Free Geolocation for Poplar Trees

Cai W. John; Owen Queen; Wellington Muchero; Scott J. Emrich

Home/Archive/arXiv

arXiv · 2301.13387

Deep Learning for Reference-Free Geolocation for Poplar Trees

Cai W. John·Owen Queen·Wellington Muchero·Scott J. Emrich

View original source ↗Read source document ↗Export metadata ↓

Abstract

A core task in precision agriculture is the identification of climatic and ecological conditions that are advantageous for a given crop. The most succinct approach is geolocation, which is concerned with locating the native region of a given sample based on its genetic makeup. Here, we investigate genomic geolocation of Populus trichocarpa, or poplar, which has been identified by the US Department of Energy as a fast-rotation biofuel crop to be harvested nationwide. In particular, we approach geolocation from a reference-free perspective, circumventing the need for compute-intensive processes such as variant calling and alignment. Our model, MashNet, predicts latitude and longitude for poplar trees from randomly-sampled, unaligned sequence fragments. We show that our model performs comparably to Locator, a state-of-the-art method based on aligned whole-genome sequence data. MashNet achieves an error of 34.0 km^2 compared to Locator's 22.1 km^2. MashNet allows growers to quickly and efficiently identify natural varieties that will be most productive in their growth environment based on genotype. This paper explores geolocation for precision agriculture while providing a framework and data source for further development by the machine learning community.

Explore related subjects

q-bio.GN cs.LG

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Cai W. John, Owen Queen, Wellington Muchero, Scott J. Emrich. 2023-01-31. Deep Learning for Reference-Free Geolocation for Poplar Trees. https://arxiv.org/abs/2301.13387

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

KEEP EXPLORING

Related papers

arXiv2026

Transcriptomic Models for Immunotherapy Response Prediction Show Limited Cross-cohort Generalisability

Immune checkpoint inhibitors (ICIs) have transformed cancer therapy; yet substantial proportion of patients exhibit intrinsic or acquired resistance, making accurate pre-treatment response prediction a critical unmet need. Transcriptomics-based biomarkers derived from bulk and single-cell RNA sequencing (scRNA-seq) offer a promising avenue for capturing tumour-immune interactions, yet the cross-cohort generalisability of existing prediction models remains unclear.We systematically benchmark nine state-of-the-art transcriptomic ICI response predictors, five bulk RNA-seq-based models (COMPASS, IRNet, NetBio, IKCScore, and TNBC-ICI) and four scRNA-seq-based models (PRECISE, DeepGeneX, Tres and scCURE), using publicly available independent datasets unseen during model development. Overall, predictive performance was modest: bulk RNA-seq models performed at or near chance level across most cohorts, while scRNA-seq models showed only marginal improvements. Pathway-level analyses revealed sparse and inconsistent biomarker signals across models. Although scRNA-seq-based predictors converged on immune-related programs such as allograft rejection, bulk RNA-seq-based models exhibited little reproducible overlap. PRECISE and NetBio identified the most coherent immune-related themes, whereas IRNet predominantly captured metabolic pathways weakly aligned with ICI biology. Together, these findings demonstrate the limited cross-cohort robustness and biological consistency of current transcriptomic ICI prediction models, underscoring the need for improved domain adaptation, standardised preprocessing, and biologically grounded model design.

q-bio.GN↗

arXiv2026

Large Language Model Agents for Evidence Based Genetic Disease Severity Classification

Disease severity classification for genetic conditions is subjective and labor-intensive, creating bottlenecks in genomic screening, where commercial panels vary widely in size and overlap. We developed an autonomous AI agent integrating Reasoning and Acting (ReAct) with Retrieval-Augmented Generation (RAG) to classify 10,211 Human Phenotype Ontology terms. It uses American College of Medical Genetics (ACMG)-endorsed severity guidelines and American College of Obstetricians and Gynecologists (ACOG) quality-of-life criteria to retrieve PubMed literature, generate interpretable reasoning chains, and independently verify claims. At the phenotype level, using expert-curated cohorts, the agent achieved 93.55% accuracy (MCC 0.9237) with 82.6% to 91.4% of claims supported by direct evidence or valid inferences. Gene-level severity was aggregated across 8,738 pairs, identifying 3,283 autosomal recessive pairs with severe or profound presentations. External validation showed 95.2% concordance with Mackenzie's Mission gene list. This system enables standardized panel design by providing reliable, automated classification supported by direct evidence.

q-bio.GN↗

arXiv2026

Harmonised benchmarking of foundation models for single-cell and spatial transcriptomics reveals context-dependent generalisation

Single-cell and spatial foundation models promise transferable biological representations, yet their generality remains largely untested across modalities, biological domains and analytical tasks. We benchmarked six representative models, Nicheformer, CellPLM, scGPT-spatial, GenePT, scELMo and Novae, using a harmonised framework spanning scRNA-seq, spatial transcriptomics and Perturb-seq. We evaluated zero-shot and continually pretrained clustering, supervised annotation, marker-gene concordance and perturbation prediction. Model performance was strongly conditional: expression-trained cell-level transformers best resolved many cell-identity tasks, spatial and graph-aware models better preserved tissue architecture, and language-derived gene embeddings were competitive for selected perturbation-response metrics. No model dominated across tasks, and rankings shifted with modality, preprocessing, tokenisation, biological prior, domain shift and metric choice. This benchmark provides practical guidance for model selection and argues that future models should be judged by biological generalisation, interpretability and perturbation-grounded validity, not by scale or leaderboard performance alone.

q-bio.GN↗