Gregory Schwing | Search arXiv

arXiv2026

CTSpinoPelvic1K: spine, pelvis, ribs and femora in one coordinate frame, annotated for lumbosacral transitional anatomy

Purpose: A vertebra at the lumbosacral junction is named by counting caudally from C2 on whole-spine imaging, but a lumbar case is planned on lumbar-only imaging (T12 to S1), without C2. Abdominopelvic CT holds that span plus the lowest ribs and pelvis. Where a lumbosacral transitional vertebra (LSTV) alters the count, the local anatomy is ambiguous: four rib-free vertebrae may be an L1 with a lumbar rib or an L5 assimilated to the sacrum, and six may be a sixth lumbar vertebra, a T12 with aplastic ribs, or a lumbarized S1. CTSpinoPelvic1K asks whether local morphology resolves it without the count. CTSpine1K's vertebrae and CTPelvic1K's pelvis covered these patients but were never joined; this release joins them on one series and adds the bones neither had. It provides 802 CT records with per-level ribs and femora, levels anchored on the lowest rib-bearing vertebra and S1, and classes for L6, T13, a separate S1 and lumbar ribs, so anomalies are recorded as such. Acquisition and Validation Methods: Records pair CTSpine1K and CTPelvic1K labels on each patient's bone-richest series under a VerSe-native scheme. Validation covered geometric invariants (802/802 pass), rib-vertebra incidence across 5,749 ribs (0.035% offset), and spinopelvic measures matching published values. Data Format and Usage Notes: NIfTI image/label pairs with patient-grouped LSTV-stratified five-fold splits and a loader; archived at https://doi.org/10.5281/zenodo.22139642. Potential Applications: Classifying a vertebra from local features; updating cadaveric morphometry; spinopelvic assessment; opportunistic screening; and, absent a public preoperative lumbar cohort, surgical planning research (377 records prone). Limitations: thoracic ground truth is field-of-view limited; postural angles supine; no held-out test set; ribs are triaged-review pseudolabels; Castellvi grades two-reader consensus on 33 records.

cs.AI↗

arXiv2022

Molecular dynamics without molecules: searching the conformational space of proteins with generative neural networks

All-atom and coarse-grained molecular dynamics are two widely used computational tools to study the conformational states of proteins. Yet, these two simulation methods suffer from the fact that without access to supercomputing resources, the time and length scales at which these states become detectable are difficult to achieve. One alternative to such methods is based on encoding the atomistic trajectory of molecular dynamics as a shorthand version devoid of physical particles, and then learning to propagate the encoded trajectory through the use of artificial intelligence. Here we show that a simple textual representation of the frames of molecular dynamics trajectories as vectors of Ramachandran basin classes retains most of the structural information of the full atomistic representation of a protein in each frame, and can be used to generate equivalent atom-less trajectories suitable to train different types of generative neural networks. In turn, the trained generative models can be used to extend indefinitely the atom-less dynamics or to sample the conformational space of proteins from their representation in the models latent space. We define intuitively this methodology as molecular dynamics without molecules, and show that it enables to cover physically relevant states of proteins that are difficult to access with traditional molecular dynamics.

q-bio.QM↗