bioRxiv Science⌕ Search

Biology subjects

Alberdi Escudero, A.

Publications and source records attributed to Alberdi Escudero, A..

2 recordsLinked to original sources

Testing diffusion-derived orientation priors for streamline modelling of the MRI-visible glioblastoma core: the BRIAN framework

Glioblastoma spreads diffusely beyond the abnormality visible on conventional magnetic resonance imaging, and because tumour cells migrate preferentially along white-matter pathways, growth models that assume isotropic spread may misrepresent the geometry of invasion relevant to radiotherapy planning. This work introduces and evaluates BRIAN, a diffusion-informed simulator that biases tumour propagation along directions derived from diffusion MRI. Patient tumour masks from the UPENN-GBM cohort are transferred onto healthy host brains from the Human Connectome Project through the MNI152 template as a proxy, diffusion orientation distribution functions (dODFs) are reconstructed on each host, and stochastic streamline propagation with the MRtrix3 iFOD2 algorithm yields volumetric occupancy maps. Propagation parameters are fitted per tumour under a three-stage curriculum that tightens a constrained five-metric objective. Across 30 unifocal tumours, each propagated onto 65 validation hosts (1 950 tumour-host pairings), the simulator reached a per-tumour median Dice coefficient of 0.748 (0.745 pooled across all pairings) and a median bounded Hausdorff agreement of 0.776. Because parameters are calibrated against each tumours own reference mask and the train/validation split is over hosts, these figures quantify reproduction and host-transfer of a known lesion; prediction of unseen tumours is outside their scope. On a purposively selected ten-tumour subset, controlled comparisons tested both the contribution of directional information and whether a richer angular reconstruction improved performance. Relative to a direction-blind isotropic null, orientation-informed tracking improved all five evaluated metrics (dz = 0.4-1.2), although only surface Dice remained significant after Holm correction. A second comparison replaced the multi-shell SHORE dODF with a single-tensor dODF while keeping the tracking framework unchanged. No statistically detectable differences were observed between the two directional models on this subset, providing no evidence that resolving crossing fibres improved agreement with the visible tumour envelope. Directional sampling improved agreement with the MRI-visible tumour core, but the selected subset provided no evidence that the SHORE dODF outperformed the tensor dODF.

neuroscience↗

Agentomics: An Agentic System that Autonomously Develops Novel State-of-the-art Solutions for Biomedical Machine Learning Tasks

MotivationExtracting knowledge from biomedical data is crucial for advancing our understanding of biological systems and developing novel therapeutics. The quantity, quality, and resolution of biomedical data constantly evolves, requiring the automation of biomedical machine learning (ML). Existing Automated ML tools lack flexibility, while Large Language Models (LLMs) struggle to consistently deliver reproducible machine learning codebases, and existing LLM Agent-powered solutions lag behind human-engineered ML models. ResultsHere, we introduce Agentomics, an autonomous LLM-powered agentic system for end-to-end ML experimentation. Given a biomedical dataset, Agentomics implements various ML modeling strategies, and produces a ready-to-use ML model. Agentomics introduces strict validation checkpoints for standard ML development steps, allowing gradual development on top of working code with defined interfaces and validated artifacts. Further, it offers native support for biomedical foundation models that can be leveraged during experimentation. The generic nature of Agentomics allows the user to create ML solutions for a large variety of datasets and use various LLMs. We evaluate Agentomics across 20 datasets from the domains of Protein Engineering, Drug Discovery, and Regulatory Genomics. When benchmarked against other agentic systems, Agentomics outperformed them in all tested domains. When benchmarked against human expert solutions, Agentomics generated novel state-of-the-art models for 11/20 established benchmark datasets. Availability and ImplementationAgentomics is implemented in Python. Source code and documentation are freely available at: https://github.com/BioGeMT/Agentomics-ML. Contactpanagiotis.alexiou@um.edu.mt

bioinformatics↗