bioRxiv Science⌕ Search

bioRxiv · 10.64898/2026.07.06.736692

VESTA: Machine Learning-Enabled Estimation of ViscoElastic Ratios from On-Axis Spatio-Temporal ARFI Features

Abstract

Viscoelastic characterization of tissue has significant diagnostic value in oncology, as tumor progression alters both elasticity and viscosity in ways that neither property alone can fully capture. Existing acoustic radiation force (ARF)-based methods such as Viscoelastic Response (VisR) ultrasound estimate relative elasticity and viscosity through per-A-line nonlinear model fitting, which is computationally intensive and requires auxiliary simulations to correct elasticity-dependent bias. This work presents VESTA (Machine Learning-Enabled Estimation of ViscoElastic Ratios from On-Axis Spatio-Temporal ARFI Features), a two-stage data-driven pipeline that predicts elasticity ratio (ER) and viscosity ratio (VR) directly from seven normalized ARFI displacement features at the A-line level, without model fitting or compensation. Stage 1 is an MLP classifier that detects inclusion boundaries from normalized peak displacement and negative peak velocity ratios; Stage 2 is a dilated Conv1D regression model that estimates ER and VR along the full axial sequence using the predicted mask alongside displacement features. The pipeline was trained on 500 simulated inclusion scenarios spanning three geometries, five focal depths, two F-numbers, and a broad range of material contrasts. In silico, mean predicted ER and VR were within 12% of ground truth across all geometries, with performance best when ER and VR were moderate or decoupled. Experimental validation on a chicken breast phantom demonstrated plausible generalization to real tissue heterogeneity. Applied to an in vivo murine 4T1 breast cancer model, the pipeline tracked treatment-related attenuation of mechanical contrast in paclitaxel-treated tumors relative to controls over a 36-day imaging period, supporting its relevance for tumor monitoring.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Trisha, S. M., Rahman, M. A., Hassan, M. W., Gi, Y. J., Lee, J., Hossain, M. M.. 2026-07-07. VESTA: Machine Learning-Enabled Estimation of ViscoElastic Ratios from On-Axis Spatio-Temporal ARFI Features. https://doi.org/10.64898/2026.07.06.736692

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

KEEP EXPLORING

Related preprints

Selected for the surface: adaptive laboratory evolution for accelerated cathodic biofilm development in Cupriavidus necator

Cupriavidus necator is a metabolically versatile facultative chemolithoautotroph and a promising chassis for sustainable bioproduction from CO2. Efficient coupling of its metabolism to renewable electricity through microbial electrosynthesis (MES) requires the organism to form stable, electroactive biofilms on cathodes. This step is hindered under oxic conditions (oxic MES, oMES) by electrochemically generated reactive oxygen species (ROS), mass-transfer limitations and poor biofilm stability. Systematic strategies to improve C. necator biofilm formation on cathodes have been lacking. Here we used adaptive laboratory evolution (ALE) to address this gap. The progenitor strain colonised graphite cathodes only after an initial heterotrophic phase and formed spatially uneven biofilms whose distribution mirrored the local flow field, as resolved by micro-particle tracking velocimetry. Populations were then selected over five passages under controlled, oxygen-limited cathodic conditions. Resequencing revealed that the recovered population was genetically heterogeneous, and its dominant isolate, strain 890, was characterised in a microfluidic oMES platform. Strain 890 reached the target electrode coverage in about one day instead of six and maintained a robust biofilm at the progenitor's steady-state biovolume, whereas the multi-strain pool peaked higher but proved unstable. Relative to the progenitor, the accelerated biofilm phenotype of strain 890 is driven by a single novel mutation in a bifunctional diguanylate cyclase/phosphodiesterase locus, which likely encodes a central regulator of the planktonic-to-biofilm transition. The steady-state biovolume itself remained bounded, most probably due to a mass-transfer ceiling set by the counter-directional supply of H2 and O2. This work shows that ALE renders the initial-attachment barrier of cathodic biofilm formation genetically tractable, providing strain 890 as a robust chassis and a well-defined starting point for oMES-based CO2 valorisation.

bioengineering↗

Engineering a High-Fidelity CRISPR-Cas13d System for Targeted RNA Depletion in Plasmodium falciparum

Functional genomics in Plasmodium falciparum is severely constrained by the evolutionary absence of an endogenous RNA interference pathway and the requirement for time-consuming direct target locus modification by conventional conditional genetic engineering systems. To overcome these limitations, we established a programmable post-transcriptional gene silencing system in P. falciparum using High-Fidelity RfxCas13d (HF-RfxCas13d), an RNA-guided RNA nuclease that has been previously tested in several eukaryotic hosts. Using CRISPR-SpyCas9 we integrated a HF-RfxCas13d expression cassette at the dispensable pfs47 locus and generated a stable marker-free transgenic line capable of constitutive HF-RfxCas13d cytosolic expression without impairing intraerythrocytic asexual growth. Episomal delivery of single or dual guide RNAs (gRNAs) achieved significant target mRNA depletion (41%-76%) across three endogenous loci atp4, ap2-exp, ap2-g genes. Applying this system to the master transcriptional regulator of gametocytogenesis (ap2-g) resulted in transcript depletion that functionally impaired sexual differentiation in committed parasites, reducing significantly the Sexual Conversion Rate a 70%. Overall, our novel HF-Cas13d line provides a flexible, scalable, and non-locus-modifying addition to the P. falciparum genetic toolbox to accelerate functional genomics and malaria drug target identification.

bioengineering↗

DECODE: DEcomposition of COupled and DEcoupled Brain States: Separating Structure-Coupled and Structure-Decoupled Functional Organization in Alzheimers Disease

Brain functional activity emerges within an underlying structural scaffold. While structural network connectivity provides a relatively stable anatomical backbone for large-scale communication, functional interactions are high-dimensional and temporally dynamic, forming recurrent patterns that can be represented in a latent space of transient functional states. Yet, how these transient functional states are organized and the extent to which they remain constrained by structural network connectivity or become relatively decoupled from structural organization over time remain poorly understood. To address this gap, we introduce DECODE (DEcomposition of COupled and DEcoupled Brain States), a data-driven latent-space framework that uses independent component analysis (ICA) and multimodal data to decompose resting-state dynamic functional network connectivity into a lower-dimensional representation of transient functional states. These states capture temporally varying structure-coupled and structure-decoupled patterns using diffusion MRI-derived structural network connectivity priors. Structure-coupled states reflect functional configurations more strongly anchored to major structural motifs, whereas structure-decoupled states represent configurations less constrained by the identified structural organization, while potentially remaining within structurally defined dynamical bounds. DECODE identifies reproducible structure-coupled and structure-decoupled states, with mean squared error reconstruction of dynamic information < 0.1 and adjusted R-squared = 0.4. Applied to Alzheimers disease (AD), DECODE revealed stronger group differences (FDR-corrected p-value 0.05) in both connectivity organization and temporal dynamics for decoupled states. These findings suggest that functional states less constrained by identified structural organization may be more vulnerable to AD-related disruption, whereas structure-coupled states may be relatively preserved. More broadly, DECODE provides a reproducible and generalizable framework for quantifying how functional dynamics are shaped by, or diverge from, structural organization by incorporating a latent representation of the structural connectome as an informative prior. Our findings established structural and functional alignment variation by distinguishing dynamic functional patterns closely coupled with structure from those that deviate from it.

bioengineering↗