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Integration and analysis of multi-omics data provide valuable insights for improving cancer subtype classification. However, such data are inherently heterogeneous, high-dimensional, and exhibit complex intra- and inter-modality dependencies. Graph neural networks (GNNs) offer a principled framework for modeling these structures, but existing approaches often rely on prior knowledge or predefined similarity networks that produce undirected or unweighted graphs and fail to capture task-specific directionality and interaction strength. Interpretability at both the modality and feature levels also remains limited. To address these challenges, we propose TF-DWGNet, a novel Graph Neural Network framework that combines tree-based Directed Weighted graph construction with Tensor Fusion for multiclass cancer subtype classification. TF-DWGNet introduces two key innovations: (i) a supervised tree-based strategy that constructs directed, weighted graphs tailored to each omics modality, and (ii) a tensor fusion mechanism that captures unimodal, bimodal, and trimodal interactions using low-rank decomposition for computational efficiency. Experiments on three real-world cancer datasets demonstrate that TF-DWGNet consistently outperforms state-of-the-art baselines across multiple metrics and statistical tests. In addition, the model provides biologically meaningful insights through modality-level contribution scores and ranked feature importance. These results highlight that TF-DWGNet is an effective and interpretable solution for multi-omics integration in cancer research.

Universal approximation theorems establish the expressive capacity of neural network architectures. For dynamical systems, existing results are limited to finite time horizons or systems with a globally stable equilibrium, leaving multistability and limit cycles unaddressed. We prove that Neural ODEs achieve $varepsilon$-$δ$ closeness -- trajectories within error $varepsilon$ except for initial conditions of measure $< δ$ -- over the emph{infinite} time horizon $[0,infty)$ for three target classes: (1) Morse-Smale systems (a structurally stable class) with hyperbolic fixed points, (2) Morse-Smale systems with hyperbolic limit cycles via exact period matching, and (3) systems with normally hyperbolic continuous attractors via discretization. We further establish a temporal generalization bound: $varepsilon$-$δ$ closeness implies $L^p$ error $leq varepsilon^p + δcdot D^p$ for all $t geq 0$, bridging topological guarantees to training metrics. These results provide the first universal approximation framework for multistable infinite-horizon dynamics.

Tabular datasets are commonly visualized as heatmaps, where data values are represented as color intensities in a matrix to reveal patterns and correlations. However, modern omics technologies increasingly generate matrices so large that existing visual exploration tools require downsampling or filtering, risking loss of biologically important patterns. Additional barriers arise from tools that require command-line expertise, or fragmented workflows for downstream biological interpretation. We present ClusterChirp, a web-based platform for real-time, interactive exploration of large-scale data matrices enabled by GPU-accelerated rendering and parallelized hierarchical clustering using multiple CPU cores. Built on deck.gl and multi-threaded clustering algorithms, ClusterChirp supports on-the-fly clustering, multi-metric sorting, feature search, and adjustable visualization parameters for interactive explorations. Uniquely, a natural language interface powered by a Large Language Model helps users perform complex operations and build reproducible workflows from conversational commands. Furthermore, users can select clusters to explore interactive within-cluster correlation networks in 2D or 3D, or perform functional enrichment through biological knowledge bases. Developed with iterative user feedback and adhering to FAIR4S principles, ClusterChirp empowers researchers to extract insights from high-dimensional omics data with unprecedented ease and speed. This website is freely available at clusterchirp.mssm.edu, with no login required.

Understanding how cells escape from embedded spheroids requires a mechanical framework linking stress generation within cells, across cells, and between cells and the surrounding extracellular matrix (ECM). We develop such a framework by coupling a 3D vertex model of a spheroid to a fibrous ECM network and deriving a 3D Cauchy stress tensor for deformable polyhedral cells, enabling direct cell-level stress quantification in three dimensions. We analyze maximum shear stress in solid-like and fluid-like spheroids: solid-like spheroids exhibit broader stress distributions and radial stress gradients, while fluid-like spheroids show lower stresses with weak spatial organization. Cell shape anisotropy is not generically aligned with principal stress directions, indicating that morphology alone is an unreliable proxy for mechanical state. We further demonstrate strain stiffening at the single-cell level, where elongation produces nonlinear increases in maximum shear stress, allowing boundary cells in otherwise low-stress, fluid-like spheroids to transiently generate forces sufficient to remodel the matrix. To connect strain-induced stress amplification to invasion modes, we introduce an extended 3D vertex model with explicit, tunable cell-cell adhesion springs. In this minimal mechanical framework, single-cell breakout results from strain stiffening combined with reduced adhesion, whereas multi-cell streaming additionally requires anisotropic adhesion strengthened along the elongation axis and weakened orthogonally. Together, these results identify distinct mechanical pathways coupling cell strain, stress amplification, and adhesion organization to spheroid invasion.

This study demonstrates the feasibility of a novel fabrication technique for high spatial resolution CsI: Tl scintillation detectors tailored for single photon emission computed tomography (SPECT) systems. Building upon our previously developed laser induced optical barrier (LIOB) method, which achieved high spatial resolution, excellent sensitivity, and 100% fabrication yield in CsI: Tl detectors, we extend this approach to a converging-pixel architecture. A CsI: Tl crystal array with converging pixels was designed and fabricated, featuring entrance-face pixels of 1.6x1.6 mm2 and photodetector side pixels of 2x2 mm2. To localize gamma-ray interactions, both the center of gravity (CoG) algorithm and a maximum-likelihood (ML) based decoding method were implemented. A custom built four axis motion platform was developed to deliver a finely collimated pencil beam at precisely controlled positions and angles across the array, enabling generation of a comprehensive dataset for prior knowledge and validation. The results demonstrate an energy resolution of 11.79+/-0.53% (collimated experiment) and a position localization accuracy of 1.00+/-0.42 mm (nearest neighbor interpolation), confirming that the proposed converging-pixel architecture, combined with statistical decoding algorithms, provides a promising path toward the development of high-performance SPECT detectors.

Positron range (PR) limits spatial resolution and quantitative accuracy in PET imaging, particularly for high-energy positron-emitting radionuclides like 68Ga. We propose a deep learning method using 3D residual encoder-decoder convolutional neural networks (3D RED-CNNs), incorporating tissue-dependent anatomical information through a u-map-dependent loss function. Models were trained with realistic simulations and, using initial PET and CT data, generated positron range corrected images. We validated the models in simulations and real acquisitions. Three 3D RED-CNN architectures, Single-channel, Two-channel, and DualEncoder, were trained on simulated PET datasets and evaluated on synthetic and real PET acquisitions from 68Ga-FH and 68Ga-PSMA-617 mouse studies. Performance was compared to a standard Richardson-Lucy-based positron range correction (RL-PRC) method using metrics such as mean absolute error (MAE), structural similarity index (SSIM), contrast recovery (CR), and contrast-to-noise ratio (CNR). CNN-based methods achieved up to 19 percent SSIM improvement and 13 percent MAE reduction compared to RL-PRC. The Two-Channel model achieved the highest CR and CNR, recovering lung activity with 97 percent agreement to ground truth versus 77 percent for RL-PRC. Noise levels remained stable for CNN models (approximately 5.9 percent), while RL-PRC increased noise by 5.8 percent. In preclinical acquisitions, the Two-Channel model achieved the highest CNR across tissues while maintaining the lowest noise level (9.6 percent). Although no ground truth was available for real data, tumor delineation and spillover artifacts improved with the Two-Channel model. These findings highlight the potential of CNN-based PRC to enhance quantitative PET imaging, particularly for 68Ga. Future work will improve model generalization through domain adaptation and hybrid training strategies.

A major goal of neuroscience is to understand brain computations during visual processing in naturalistic settings. A dominant approach is to use image-computable deep neural networks trained with different task objectives as a basis for linear encoding models. However, in addition to requiring estimation of a large number of linear encoding parameters, this approach ignores the structure of the feature maps both in the brain and the models. Recently proposed alternatives factor the linear mapping into separate sets of spatial and feature weights, thus finding static receptive fields for units, which is appropriate only for early visual areas. In this work, we employ the attention mechanism used in the transformer architecture to study how retinotopic visual features can be dynamically routed to category-selective areas in high-level visual processing. We show that this computational motif is significantly more powerful than alternative methods in predicting brain activity during natural scene viewing, across different feature basis models and modalities. We also show that this approach is inherently more interpretable as the attention-routing signals for different high-level categorical areas can be easily visualized for any input image. Given its high performance at predicting brain responses to novel images, the model deserves consideration as a candidate mechanistic model of how visual information from retinotopic maps is routed in the human brain based on the relevance of the input content to different category-selective regions.

Accurate simulations of electric fields (E-fields) in neural stimulation depend on tissue conductivity representations that link underlying microscopic tissue structure with macroscopic assumptions. Mesoscale conductivity variations can produce meaningful changes in E-fields and neural activation thresholds but remain largely absent from standard macroscopic models. Conductivity variations within the cortex are expected given the differences in cell density and volume fraction across layers. We review recent efforts modeling microscopic and mesoscopic E-fields and outline approaches that bridge micro- and macroscales to derive consistent mesoscale conductivity distributions. Using simplified microscopic models, effective tissue conductivity was estimated as a function of volume fraction of extracellular space, and the conductivities of different cortical layers were interpolated based on experimental volume fraction. The effective tissue conductivities were monotonically decreasing convex functions of the cell volume fraction. With decreasing cell volume fraction, the conductivity of cortical layers increased with depth from layer 2 to 6. Although the variation of conductivity within the cortex was small when compared to the conductivity of extracellular fluid (9% to 15%), the conductivity difference was considerably larger when compared between layers, e.g., with layer 3 and 6 being 20% and 50% more conductive than layer 2, respectively. The review and analysis provide a foundation for accurate multiscale models of E-fields and neural stimulation. Using layer-specific conductivity values within the cortex could improve the accuracy of estimations of thresholds and distributions of neural activation in E-field models of brain stimulation.

The function of biomolecules such as proteins depends on their ability to interconvert between a wide range of structures or "conformations." Researchers have endeavored for decades to develop computational methods to predict the distribution of conformations, which is far harder to determine experimentally than a static folded structure. We present ConforMix, an inference-time algorithm that enhances sampling of conformational distributions using a combination of classifier guidance, filtering, and free energy estimation. Our approach upgrades diffusion models-whether trained for static structure prediction or conformational generation-to enable more efficient discovery of conformational variability without requiring prior knowledge of major degrees of freedom. ConforMix is orthogonal to improvements in model pretraining and would benefit even a hypothetical model that perfectly reproduced the Boltzmann distribution. Remarkably, when applied to a diffusion model trained for static structure prediction, ConforMix captures structural changes including domain motion, cryptic pocket flexibility, and transporter cycling, while avoiding unphysical states. Case studies of biologically critical proteins demonstrate the scalability, accuracy, and utility of this method.

Many fields collect large-scale temporal data through repeated measurements ('trials'), where each trial is labeled with a set of metadata variables spanning several categories. For example, a trial in a neuroscience study may be linked to a value from category (a): task difficulty, and category (b): animal choice. A critical challenge in time-series analysis is to understand how these labels are encoded within the multi-trial observations, and disentangle the distinct effect of each label entry across categories. Here, we present MILCCI, a novel data-driven method that i) identifies the interpretable components underlying the data, ii) captures cross-trial variability, and iii) integrates label information to understand each category's representation within the data. MILCCI extends a sparse per-trial decomposition that leverages label similarities within each category to enable subtle, label-driven cross-trial adjustments in component compositions and to distinguish the contribution of each category. MILCCI also learns each component's corresponding temporal trace, which evolves over time within each trial and varies flexibly across trials. We demonstrate MILCCI's performance through both synthetic and real-world examples, including voting patterns, online page view trends, and neuronal recordings.