Cluster2Former: Semisupervised Clustering Transformers for Video Instance Segmentation.

A novel approach for video instance segmentation is presented using semisupervised learning. Our Cluster2Former model leverages scribble-based annotations for training, significantly reducing the need for comprehensive pixel-level masks. We augment a video instance segmenter, for example, the Mask2Former architecture, with similarity-based constraint loss to handle partial annotations efficiently. We demonstrate that despite using lightweight annotations (using only 0.5% of the annotated pixels), Cluster2Former achieves competitive performance on standard benchmarks. The approach offers a cost-effective and computationally efficient solution for video instance segmentation, especially in scenarios with limited annotation resources.

Design of a Machine Learning System to Predict the Thickness of a Melanoma Lesion in a Non-Invasive Way from Dermoscopic Images.

OBJECTIVES: Melanoma is the deadliest form of skin cancer, but it can be fully cured through early detection and treatment in 99% of cases. Our aim was to develop a non-invasive machine learning system that can predict the thickness of a melanoma lesion, which is a proxy for tumor progression, through dermoscopic images. This method can serve as a valuable tool in identifying urgent cases for treatment. METHODS: A modern convolutional neural network architecture (EfficientNet) was used to construct a model capable of classifying dermoscopic images of melanoma lesions into three distinct categories based on thickness. We incorporated techniques to reduce the impact of an imbalanced training dataset, enhanced the generalization capacity of the model through image augmentation, and utilized five-fold cross-validation to produce more reliable metrics. RESULTS: Our method achieved 71% balanced accuracy for three-way classification when trained on a small public dataset of 247 melanoma images. We also presented performance projections for larger training datasets. CONCLUSIONS: Our model represents a new state-of-the-art method for classifying melanoma thicknesses. Performance can be further optimized by expanding training datasets and utilizing model ensembles. We have shown that earlier claims of higher performance were mistaken due to data leakage during the evaluation process.

Interacting jammed granular systems.

More than 30 years ago Edwards and co-authors proposed a model to describe the statistics of granular packings by an ensemble of equiprobable jammed states. Experimental tests of this model remained scarce so far. We introduce a simple system to analyze statistical properties of jammed granular ensembles to test Edwards theory. Identical spheres packed in a nearly two-dimensional geometrical confinement were studied in experiments and numerical simulations. When tapped, the system evolves toward a ground state, but due to incompatible domain structures it gets trapped. Analytical calculations reproduce relatively well our simulation results, which allows us to test Edwards theory on a coupled system of two subsystems with different properties. We find that the joint system can only be described by the Edwards theory if considered as a single system due to the constraints in the stresses. The results show counterintuitive effects as in the coupled system the change in the order parameter is opposite to what is expected from the change in the compactivity.

Orientational order in dense suspensions of elliptical particles in the non-Stokesian regime.

Suspensions of neutrally buoyant elliptic particles are modeled in 2D using fully resolved simulations that provide two-way interaction between the particle and the fluid medium. Forces due to particle collisions are represented by a diffuse interface approach that allows the investigation of dense suspensions (up to 47% packing fraction). We focus on the role inertial forces play at low and high particle Reynolds numbers termed low Reynolds number and inertial regimes, respectively. The suspensions are characterized by the orientation distribution function (ODF) that reflects shear induced rotation of the particles at low Reynolds numbers, and nearly stationary (swaying) particles at high Reynolds numbers. In both cases, orientational ordering differs qualitatively from the behavior observed in the Stokesian-regime. The ODF becomes flatter with increasing packing fraction, as opposed to the sharpening previous work predicted in the Stokesian regime. The ODF at low particle concentrations differs significantly for the low Reynolds number and inertial regimes, whereas with increasing packing fraction convergence is observed. For dense suspensions, the particle-particle interactions dominate the particle motion.

Soluble VEGFR1 signaling guides vascular patterns into dense branching morphologies.

Vascular patterning is a key process during development and disease. The diffusive decoy receptor sVEGFR1 (sFlt1) is a known regulator of endothelial cell behavior, yet the mechanism by which it controls vascular structure is little understood. We propose computational models to shed light on how vascular patterning is guided by self-organized gradients of the VEGF/sVEGFR1 factors. We demonstrate that a diffusive inhibitor can generate structures with a dense branching morphology in models where the activator elicits directed growth. Inadequate presence of the inhibitor leads to compact growth, while excessive production of the inhibitor blocks expansion and stabilizes existing structures. Model predictions were compared with time-resolved experimental data obtained from endothelial sprout kinetics in fibrin gels. In the presence of inhibitory antibodies against VEGFR1 vascular sprout density increases while the speed of sprout expansion remains unchanged. Thus, the rate of secretion and stability of extracellular sVEGFR1 can modulate vascular sprout density.

Softening and yielding of soft glassy materials.

Solids deform and fluids flow, but soft glassy materials, such as emulsions, foams, suspensions, and pastes, exhibit an intricate mix of solid- and liquid-like behavior. While much progress has been made to understand their elastic (small strain) and flow (infinite strain) properties, such understanding is lacking for the softening and yielding phenomena that connect these asymptotic regimes. Here we present a comprehensive framework for softening and yielding of soft glassy materials, based on extensive numerical simulations of oscillatory rheological tests, and show that two distinct scenarios unfold depending on the material's packing density. For dense systems, there is a single, pressure-independent strain where the elastic modulus drops and the particle motion becomes diffusive. In contrast, for weakly jammed systems, a two-step process arises: at an intermediate softening strain, the elastic and loss moduli both drop down and then reach a new plateau value, whereas the particle motion becomes diffusive at the distinctly larger yield strain. We show that softening is associated with an extensive number of microscopic contact changes leading to a non-analytic rheological signature. Moreover, the scaling of the softening strain with pressure suggest the existence of a novel pressure scale above which softening and yielding coincide, and we verify the existence of this crossover scale numerically. Our findings thus evidence the existence of two distinct classes of soft glassy materials - jamming dominated and dense - and show how these can be distinguished by their rheological fingerprint.

Stress relaxation in viscous soft spheres.

We report the results of molecular dynamics simulations of stress relaxation tests in athermal viscous soft sphere packings close to their unjamming transition. By systematically and simultaneously varying both the amplitude of the applied strain step and the pressure of the initial condition, we access both linear and nonlinear response regimes and control the distance to jamming. Stress relaxation in viscoelastic solids is characterized by a relaxation time τ* that separates short time scales, where viscous loss is substantial, from long time scales, where elastic storage dominates and the response is essentially quasistatic. We identify two distinct plateaus in the strain dependence of the relaxation time, one each in the linear and nonlinear regimes. The height of both plateaus scales as an inverse power law with the distance to jamming. By probing the time evolution of particle velocities during relaxation, we further identify a correlation between mechanical relaxation in the bulk and the degree of non-affinity in the particle velocities on the micro scale.

Rheology of dense granular flows for elongated particles.

We study the rheology of dense granular flows for frictionless spherocylinders by means of 3D numerical simulations. As in the case of spherical particles, the effective friction µ is an increasing function of the inertial number I, and we systematically investigate the dependence of µ on the particle aspect ratio Q, as well as that of the normal stress differences, the volume fraction, and the coordination number. We show in particular that the quasistatic friction coefficient is nonmonotonic with Q: from the spherical case Q=1, it first sharply increases, reaches a maximum around Q≃1.05, and then gently decreases until Q=3, passing its initial value at Q≃2. We provide a microscopic interpretation for this unexpected behavior through the analysis of the distribution of dissipative contacts around the particles: as compared to spheres, slightly elongated grains enhance contacts in their central cylindrical band, whereas at larger aspect ratios particles tend to align and dissipate by preferential contacts at their hemispherical caps.

Shear-driven segregation of dry granular materials with different friction coefficients.

We report the first experimental demonstration of bulk segregation in a shear-driven dry granular mixture, where the particles only differ in their surface friction coefficients. We found that the smoother particles tend to sink to the bottom of the shear zone, while rough particles migrate to the top of the sample. This phenomenon is similar to the well known kinetic sieving in particle mixtures with size heterogeneity. In the present case the smooth particles have a higher probability to penetrate into voids created by the shearing than the rough ones. Discrete element simulations were carried out and reproduced the experimentally observed segregation patterns. Moreover, simulations performed in the absence of gravity revealed that rough particles tend to remain in the shear zone, while the smooth particles are being expelled from it. We propose a mechanism in which the smooth particles are driven towards regions of lower shear rate.

Beyond linear elasticity: jammed solids at finite shear strain and rate.

The shear response of soft solids can be modeled with linear elasticity, provided the forcing is slow and weak. Both of these approximations must break down when the material loses rigidity, such as in foams and emulsions at their (un)jamming point - suggesting that the window of linear elastic response near jamming is exceedingly narrow. Yet precisely when and how this breakdown occurs remains unclear. To answer these questions, we perform computer simulations of stress relaxation and shear start-up tests in athermal soft sphere packings, the canonical model for jamming. By systematically varying the strain amplitude, strain rate, distance to jamming, and system size, we identify characteristic strain and time scales that quantify how and when the window of linear elasticity closes, and relate these scales to changes in the microscopic contact network.

Heaping, secondary flows and broken symmetry in flows of elongated granular particles.

In this paper we report experiments where we shear granular rods in split-bottom geometries, and find that a significant heap of height of least 40% of the filling height can form at the particle surface. We show that heaping is caused by a significant secondary flow, absent for spherical particles. Flow reversal transiently reverses the secondary flow, leading to a quick collapse and slower regeneration of the heap. We present a symmetry argument and experimental data that show that the generation of the secondary flow is driven by a misalignment of the mean particle orientation with the streamlines of the flow. This general mechanism is expected to be important in all flows of sufficiently anisometric grains.

Evolution of shear zones in granular materials.

The evolution of wide shear zones or shear bands was investigated experimentally and numerically for quasistatic dry granular flows in split bottom shear cells. We compare the behavior of materials consisting of beads, irregular grains, such as sand, and elongated particles. Shearing an initially random sample, the zone width was found to significantly decrease in the first stage of the process. The characteristic shear strain associated with this decrease is about unity and it is systematically increasing with shape anisotropy, i.e., when the grain shape changes from spherical to irregular (e.g., sand) and becomes elongated (pegs). The strongly decreasing tendency of the zone width is followed by a slight increase which is more pronounced for rodlike particles than for grains with smaller shape anisotropy (beads or irregular particles). The evolution of the zone width is connected to shear-induced packing density change and for nonspherical particles it also involves grain reorientation effects. The final zone width is significantly smaller for irregular grains than for spherical beads.

Effects of grain shape on packing and dilatancy of sheared granular materials.

A granular material exposed to shear shows a variety of unique phenomena: Reynolds dilatancy, positional order and orientational order effects may compete in the shear zone. We study granular packing consisting of macroscopic prolate, oblate and spherical grains and compare their behaviour. X-ray tomography is used to determine the particle positions and orientations in a cylindrical split bottom shear cell. Packing densities and the arrangements of individual particles in the shear zone are evaluated. For anisometric particles, we observe the competition of two opposite effects. On the one hand, the sheared granules are dilated, on the other hand the particles reorient and align with respect to the streamlines. Even though aligned cylinders in principle may achieve higher packing densities, this alignment compensates for the effect of dilatancy only partially. The complex rearrangements lead to a depression of the surface above the well oriented region while neighbouring parts still show the effect of dilation in the form of heaps. For grains with isotropic shapes, the surface remains rather flat. Perfect monodisperse spheres crystallize in the shear zone, whereby positional order partially overcompensates dilatancy effects. However, even slight deviations from the ideal monodisperse sphere shape inhibit crystallization.

Scale-invariant growth processes in expanding space.

Many growth processes lead to intriguing stochastic patterns and complex fractal structures which exhibit local scale invariance properties. Such structures can often be described effectively by space-time trajectories of interacting particles, and their large scale behavior depends on the overall growth geometry. We establish an exact relation between statistical properties of structures in uniformly expanding and fixed geometries, which preserves the local scale invariance and is independent of other properties such as the dimensionality. This relation generalizes standard conformal transformations as the natural symmetry of self-affine growth processes. We illustrate our main result numerically for various structures of coalescing Lévy flights and fractional Brownian motions, including also branching and finite particle sizes. One of the main benefits of this approach is a full, explicit description of the asymptotic statistics in expanding domains, which are often nontrivial and random due to amplification of initial fluctuations.

Shear-induced alignment and dynamics of elongated granular particles.

The alignment, ordering, and rotation of elongated granular particles was studied in shear flow. The time evolution of the orientation of a large number of particles was monitored in laboratory experiments by particle tracking using optical imaging and x-ray computed tomography. The experiments were complemented by discrete element simulations. The particles develop an orientational order. In the steady state the time- and ensemble-averaged direction of the main axis of the particles encloses a small angle with the streamlines. This shear alignment angle is independent of the applied shear rate, and it decreases with increasing grain aspect ratio. At the grain level the steady state is characterized by a net rotation of the particles, as dictated by the shear flow. The distribution of particle rotational velocities was measured both in the steady state and also during the initial transients. The average rotation speed of particles with their long axis perpendicular to the shear alignment angle is larger, while shear aligned particles rotate slower. The ratio of this fast/slow rotation increases with particle aspect ratio. During the initial transient starting from an unaligned initial condition, particles having an orientation just beyond the shear alignment angle rotate opposite to the direction dictated by the shear flow.

Orientational order and alignment of elongated particles induced by shear.

Shear induced alignment of elongated particles is studied experimentally and numerically. We show that shear alignment of ensembles of macroscopic particles is comparable even on a quantitative level to simple molecular systems, despite the completely different types of particle interactions. We demonstrate that for dry elongated grains the preferred orientation forms a small angle with the streamlines, independent of shear rate across three decades. For a given particle shape, this angle decreases with increasing aspect ratio of the particles. The shear-induced alignment results in a considerable reduction of the effective friction of the granular material.

Reproduction-time statistics and segregation patterns in growing populations.

Pattern formation in microbial colonies of competing strains under purely space-limited population growth has recently attracted considerable research interest. We show that the reproduction time statistics of individuals has a significant impact on the sectoring patterns. Generalizing the standard Eden growth model, we introduce a simple one-parameter family of reproduction time distributions indexed by the variation coefficient δ∈[0,1], which includes deterministic (δ=0) and memory-less exponential distribution (δ=1) as extreme cases. We present convincing numerical evidence and heuristic arguments that the generalized model is still in the Kardar-Parisi-Zhang (KPZ) universality class, and the changes in patterns are due to changing prefactors in the scaling relations, which we are able to predict quantitatively. With the example of Saccharomyces cerevisiae, we show that our approach using the variation coefficient also works for more realistic reproduction time distributions.

Coherent structures in dissipative particle dynamics simulations of the transition to turbulence in compressible shear flows.

We present simulations of coherent structures in compressible flows near the transition to turbulence using the dissipative particle dynamics method. The structures we find are remarkably consistent with experimental observations and direct numerical simulations (DNS) simulations of incompressible flows, despite a difference in Mach number of several orders of magnitude. The bifurcation from the laminar flow is bistable and shifts to higher Reynolds numbers when the fluid becomes more compressible. This work underlines the robustness of coherent structures in the transition to turbulence and illustrates the ability of particle-based methods to reproduce complex nonlinear instabilities.

Critical and noncritical jamming of frictional grains.

We probe the nature of the jamming transition of frictional granular media by studying their vibrational properties as a function of the applied pressure p and friction coefficient mu. The density of vibrational states exhibits a crossover from a plateau at frequencies omega > or similar to omega*(p,mu) to a linear growth for omega < or similar to omega*(p,mu). We show that omega* is proportional to Deltaz, the excess number of contacts per grain relative to the minimally allowed, isostatic value. For zero and infinitely large friction, typical packings at the jamming threshold have Deltaz-->0, and then exhibit critical scaling. We study the nature of the soft modes in these two limits, and find that the ratio of elastic moduli is governed by the distance from isostaticity.

Scale invariance and universality of force networks in static granular matter.

Force networks form the skeleton of static granular matter. They are the key factor that determines mechanical properties such as stability, elasticity and sound transmission, which are important for civil engineering and industrial processing. Previous studies have focused on investigations of the global structure of external forces (the boundary condition) and on the probability distribution of individual contact forces. So far, however, precise knowledge of the disordered spatial structure of the force network has remained elusive. Here we report that molecular dynamics simulations of realistic granular packings reveal scale invariance of clusters of particles interacting by means of relatively strong forces. Despite visual variation, force networks for various values of the confining pressure and other parameters have identical scaling exponents and scaling function, thereby determining a universality class. Unexpectedly, the flat ensemble of force configurations (a simple generalization of equilibrium statistical mechanics) belongs to this universality class, whereas some widely studied simplified models do not. This implies that the elasticity of the grains and their geometrical disorder do not affect the universal mechanical properties.