Atomic Depth Estimation From Noisy Electron Microscopy Data Via Deep Learning

We present a novel approach for extracting 3D atomic-level information from transmission electron microscopy (TEM) images affected by significant noise. The approach is based on formulating depth estimation as a semantic segmentation problem. We address the resulting segmentation problem by training a deep convolutional neural network to generate pixel-wise depth segmentation maps using simulated data corrupted by synthetic noise. The proposed method was applied to estimate the depth of atomic columns in CeO2 nanoparticles from simulated images and real-world TEM data. Our experiments show that the resulting depth estimates are accurate, calibrated and robust to noise.

Reg-TTR, Test-Time Refinement for Fast, Robust and Accurate Image Registration

Traditional image registration methods are robust but slow due to their iterative nature. While deep learning has accelerated inference, it often struggles with domain shifts. Emerging registration foundation models offer a balance of speed and robustness, yet typically cannot match the peak accuracy of specialized models trained on specific datasets. To mitigate this limitation, we propose Reg-TTR, a test-time refinement framework that synergizes the complementary strengths of both deep learning and conventional registration techniques. By refining the predictions of pre-trained models at inference, our method delivers significantly improved registration accuracy at a modest computational cost, requiring only 21% additional inference time (0.56s). We evaluate Reg-TTR on two distinct tasks and show that it achieves state-of-the-art (SOTA) performance while maintaining inference speeds close to previous deep learning methods. As foundation models continue to emerge, our framework offers an efficient strategy to narrow the performance gap between registration foundation models and SOTA methods trained on specialized datasets. The source code will be publicly available following the acceptance of this work.

GPCR-Filter: a deep learning framework for efficient and precise GPCR modulator discovery

G protein-coupled receptors (GPCRs) govern diverse physiological processes and are central to modern pharmacology. Yet discovering GPCR modulators remains challenging because receptor activation often arises from complex allosteric effects rather than direct binding affinity, and conventional assays are slow, costly, and not optimized for capturing these dynamics. Here we present GPCR-Filter, a deep learning framework specifically developed for GPCR modulator discovery. We assembled a high-quality dataset of over 90,000 experimentally validated GPCR-ligand pairs, providing a robust foundation for training and evaluation. GPCR-Filter integrates the ESM-3 protein language model for high-fidelity GPCR sequence representations with graph neural networks that encode ligand structures, coupled through an attention-based fusion mechanism that learns receptor-ligand functional relationships. Across multiple evaluation settings, GPCR-Filter consistently outperforms state-of-the-art compound-protein interaction models and exhibits strong generalization to unseen receptors and ligands. Notably, the model successfully identified micromolar-level agonists of the 5-HT\textsubscript{1A} receptor with distinct chemical frameworks. These results establish GPCR-Filter as a scalable and effective computational approach for GPCR modulator discovery, advancing AI-assisted drug development for complex signaling systems.

LaCoGSEA: Unsupervised deep learning for pathway analysis via latent correlation

Motivation: Pathway enrichment analysis is widely used to interpret gene expression data. Standard approaches, such as GSEA, rely on predefined phenotypic labels and pairwise comparisons, which limits their applicability in unsupervised settings. Existing unsupervised extensions, including single-sample methods, provide pathway-level summaries but primarily capture linear relationships and do not explicitly model gene-pathway associations. More recently, deep learning models have been explored to capture non-linear transcriptomic structure. However, their interpretation has typically relied on generic explainable AI (XAI) techniques designed for feature-level attribution. As these methods are not designed for pathway-level interpretation in unsupervised transcriptomic analyses, their effectiveness in this setting remains limited. Results: To bridge this gap, we introduce LaCoGSEA (Latent Correlation GSEA), an unsupervised framework that integrates deep representation learning with robust pathway statistics. LaCoGSEA employs an autoencoder to capture non-linear manifolds and proposes a global gene-latent correlation metric as a proxy for differential expression, generating dense gene rankings without prior labels. We demonstrate that LaCoGSEA offers three key advantages: (i) it achieves improved clustering performance in distinguishing cancer subtypes compared to existing unsupervised baselines; (ii) it recovers a broader range of biologically meaningful pathways at higher ranks compared with linear dimensionality reduction and gradient-based XAI methods; and (iii) it maintains high robustness and consistency across varying experimental protocols and dataset sizes. Overall, LaCoGSEA provides state-of-the-art performance in unsupervised pathway enrichment analysis. Availability and implementation: https://github.com/willyzzz/LaCoGSEA

Axe: A Simple Unified Layout Abstraction for Machine Learning Compilers

Scaling modern deep learning workloads demands coordinated placement of data and compute across device meshes, memory hierarchies, and heterogeneous accelerators. We present Axe Layout, a hardware-aware abstraction that maps logical tensor coordinates to a multi-axis physical space via named axes. Axe unifies tiling, sharding, replication, and offsets across inter-device distribution and on-device layouts, enabling collective primitives to be expressed consistently from device meshes to threads. Building on Axe, we design a multi-granularity, distribution-aware DSL and compiler that composes thread-local control with collective operators in a single kernel. Experiments show that our unified approach can bring performance close to hand-tuned kernels on across latest GPU devices and multi-device environments and accelerator backends.

Establishing dermatopathology encyclopedia DermpathNet with Artificial Intelligence-Based Workflow

Accessing high-quality, open-access dermatopathology image datasets for learning and cross-referencing is a common challenge for clinicians and dermatopathology trainees. To establish a comprehensive open-access dermatopathology dataset for educational, cross-referencing, and machine-learning purposes, we employed a hybrid workflow to curate and categorize images from the PubMed Central (PMC) repository. We used specific keywords to extract relevant images, and classified them using a novel hybrid method that combined deep learning-based image modality classification with figure caption analyses. Validation on 651 manually annotated images demonstrated the robustness of our workflow, with an F-score of 89.6\% for the deep learning approach, 61.0\% for the keyword-based retrieval method, and 90.4\% for the hybrid approach. We retrieved over 7,772 images across 166 diagnoses and released this fully annotated dataset, reviewed by board-certified dermatopathologists. Using our dataset as a challenging task, we found the current image analysis algorithm from OpenAI inadequate for analyzing dermatopathology images. In conclusion, we have developed a large, peer-reviewed, open-access dermatopathology image dataset, DermpathNet, which features a semi-automated curation workflow.

Scale-Consistent State-Space Dynamics via Fractal of Stationary Transformations

Recent deep learning models increasingly rely on depth without structural guarantees on the validity of intermediate representations, rendering early stopping and adaptive computation ill-posed. We address this limitation by formulating a structural requirement for state-space model's scale-consistent latent dynamics across iterative refinement, and derive Fractal of Stationary Transformations (FROST), which enforces a self-similar representation manifold through a fractal inductive bias. Under this geometry, intermediate states correspond to different resolutions of a shared representation, and we provide a geometric analysis establishing contraction and stable convergence across iterations. As a consequence of this scale-consistent structure, halting naturally admits a ranking-based formulation driven by intrinsic feature quality rather than extrinsic objectives. Controlled experiments on ImageNet-100 empirically verify the predicted scale-consistent behavior, showing that adaptive efficiency emerges from the aligned latent geometry.

High-quality data augmentation for code comment classification

Code comments serve a crucial role in software development for documenting functionality, clarifying design choices, and assisting with issue tracking. They capture developers' insights about the surrounding source code, serving as an essential resource for both human comprehension and automated analysis. Nevertheless, since comments are in natural language, they present challenges for machine-based code understanding. To address this, recent studies have applied natural language processing (NLP) and deep learning techniques to classify comments according to developers' intentions. However, existing datasets for this task suffer from size limitations and class imbalance, as they rely on manual annotations and may not accurately represent the distribution of comments in real-world codebases. To overcome this issue, we introduce new synthetic oversampling and augmentation techniques based on high-quality data generation to enhance the NLBSE'26 challenge datasets. Our Synthetic Quality Oversampling Technique and Augmentation Technique (Q-SYNTH) yield promising results, improving the base classifier by $2.56\%$.

How Do Transformers Learn to Associate Tokens: Gradient Leading Terms Bring Mechanistic Interpretability

Semantic associations such as the link between "bird" and "flew" are foundational for language modeling as they enable models to go beyond memorization and instead generalize and generate coherent text. Understanding how these associations are learned and represented in language models is essential for connecting deep learning with linguistic theory and developing a mechanistic foundation for large language models. In this work, we analyze how these associations emerge from natural language data in attention-based language models through the lens of training dynamics. By leveraging a leading-term approximation of the gradients, we develop closed-form expressions for the weights at early stages of training that explain how semantic associations first take shape. Through our analysis, we reveal that each set of weights of the transformer has closed-form expressions as simple compositions of three basis functions (bigram, token-interchangeability, and context mappings), reflecting the statistics of the text corpus and uncovering how each component of the transformer captures semantic associations based on these compositions. Experiments on real-world LLMs demonstrate that our theoretical weight characterizations closely match the learned weights, and qualitative analyses further show how our theorem shines light on interpreting the learned associations in transformers.

Grasynda: Graph-based Synthetic Time Series Generation

Data augmentation is a crucial tool in time series forecasting, especially for deep learning architectures that require a large training sample size to generalize effectively. However, extensive datasets are not always available in real-world scenarios. Although many data augmentation methods exist, their limitations include the use of transformations that do not adequately preserve data properties. This paper introduces Grasynda, a novel graph-based approach for synthetic time series generation that: (1) converts univariate time series into a network structure using a graph representation, where each state is a node and each transition is represented as a directed edge; and (2) encodes their temporal dynamics in a transition probability matrix. We performed an extensive evaluation of Grasynda as a data augmentation method for time series forecasting. We use three neural network variations on six benchmark datasets. The results indicate that Grasynda consistently outperforms other time series data augmentation methods, including ones used in state-of-the-art time series foundation models. The method and all experiments are publicly available.