Learning Consistent Taxonomic Classification through Hierarchical Reasoning

While Vision-Language Models (VLMs) excel at visual understanding, they often fail to grasp hierarchical knowledge. This leads to common errors where VLMs misclassify coarser taxonomic levels even when correctly identifying the most specific level (leaf level). Existing approaches largely overlook this issue by failing to model hierarchical reasoning. To address this gap, we propose VL-Taxon, a two-stage, hierarchy-based reasoning framework designed to improve both leaf-level accuracy and hierarchical consistency in taxonomic classification. The first stage employs a top-down process to enhance leaf-level classification accuracy. The second stage then leverages this accurate leaf-level output to ensure consistency throughout the entire taxonomic hierarchy. Each stage is initially trained with supervised fine-tuning to instill taxonomy knowledge, followed by reinforcement learning to refine the model's reasoning and generalization capabilities. Extensive experiments reveal a remarkable result: our VL-Taxon framework, implemented on the Qwen2.5-VL-7B model, outperforms its original 72B counterpart by over 10% in both leaf-level and hierarchical consistency accuracy on average on the iNaturalist-2021 dataset. Notably, this significant gain was achieved by fine-tuning on just a small subset of data, without relying on any examples generated by other VLMs.

ASBA: A-line State Space Model and B-line Attention for Sparse Optical Doppler Tomography Reconstruction

Optical Doppler Tomography (ODT) is an emerging blood flow analysis technique. A 2D ODT image (B-scan) is generated by sequentially acquiring 1D depth-resolved raw A-scans (A-line) along the lateral axis (B-line), followed by Doppler phase-subtraction analysis. To ensure high-fidelity B-scan images, current practices rely on dense sampling, which prolongs scanning time, increases storage demands, and limits the capture of rapid blood flow dynamics. Recent studies have explored sparse sampling of raw A-scans to alleviate these limitations, but their effectiveness is hindered by the conservative sampling rates and the uniform modeling of flow and background signals. In this study, we introduce a novel blood flow-aware network, named ASBA (A-line ROI State space model and B-line phase Attention), to reconstruct ODT images from highly sparsely sampled raw A-scans. Specifically, we propose an A-line ROI state space model to extract sparsely distributed flow features along the A-line, and a B-line phase attention to capture long-range flow signals along each B-line based on phase difference. Moreover, we introduce a flow-aware weighted loss function that encourages the network to prioritize the accurate reconstruction of flow signals. Extensive experiments on real animal data demonstrate that the proposed approach clearly outperforms existing state-of-the-art reconstruction methods.

How well can off-the-shelf LLMs elucidate molecular structures from mass spectra using chain-of-thought reasoning?

Mass spectrometry (MS) is a powerful analytical technique for identifying small molecules, yet determining complete molecular structures directly from tandem mass spectra (MS/MS) remains a long-standing challenge due to complex fragmentation patterns and the vast diversity of chemical space. Recent progress in large language models (LLMs) has shown promise for reasoning-intensive scientific tasks, but their capability for chemical interpretation is still unclear. In this work, we introduce a Chain-of-Thought (CoT) prompting framework and benchmark that evaluate how LLMs reason about mass spectral data to predict molecular structures. We formalize expert chemists' reasoning steps-such as double bond equivalent (DBE) analysis, neutral loss identification, and fragment assembly-into structured prompts and assess multiple state-of-the-art LLMs (Claude-3.5-Sonnet, GPT-4o-mini, and Llama-3 series) in a zero-shot setting using the MassSpecGym dataset. Our evaluation across metrics of SMILES validity, formula consistency, and structural similarity reveals that while LLMs can produce syntactically valid and partially plausible structures, they fail to achieve chemical accuracy or link reasoning to correct molecular predictions. These findings highlight both the interpretive potential and the current limitations of LLM-based reasoning for molecular elucidation, providing a foundation for future work that combines domain knowledge and reinforcement learning to achieve chemically grounded AI reasoning.

TARG: Training-Free Adaptive Retrieval Gating for Efficient RAG

Retrieval-Augmented Generation (RAG) improves factuality but retrieving for every query often hurts quality while inflating tokens and latency. We propose Training-free Adaptive Retrieval Gating (TARG), a single-shot policy that decides when to retrieve using only a short, no-context draft from the base model. From the draft's prefix logits, TARG computes lightweight uncertainty scores: mean token entropy, a margin signal derived from the top-1/top-2 logit gap via a monotone link, or small-N variance across a handful of stochastic prefixes, and triggers retrieval only when the score exceeds a threshold. The gate is model agnostic, adds only tens to hundreds of draft tokens, and requires no additional training or auxiliary heads. On NQ-Open, TriviaQA, and PopQA, TARG consistently shifts the accuracy-efficiency frontier: compared with Always-RAG, TARG matches or improves EM/F1 while reducing retrieval by 70-90% and cutting end-to-end latency, and it remains close to Never-RAG in overhead. A central empirical finding is that under modern instruction-tuned LLMs the margin signal is a robust default (entropy compresses as backbones sharpen), with small-N variance offering a conservative, budget-first alternative. We provide ablations over gate type and prefix length and use a delta-latency view to make budget trade-offs explicit.

CryoGS: Gaussian Splatting for Cryo-EM Homogeneous Reconstruction

As a critical modality for structural biology, cryogenic electron microscopy (cryo-EM) facilitates the determination of macromolecular structures at near-atomic resolution. The core computational task in single-particle cryo-EM is to reconstruct the 3D electrostatic potential of a molecule from a large collection of noisy 2D projections acquired at unknown orientations. Gaussian mixture models (GMMs) provide a continuous, compact, and physically interpretable representation for molecular density and have recently gained interest in cryo-EM reconstruction. However, existing methods rely on external consensus maps or atomic models for initialization, limiting their use in self-contained pipelines. Addressing this issue, we introduce cryoGS, a GMM-based method that integrates Gaussian splatting with the physics of cryo-EM image formation. In particular, we develop an orthogonal projection-aware Gaussian splatting, with adaptations such as a normalization term and FFT-aligned coordinate system tailored for cryo-EM imaging. All these innovations enable stable and efficient homogeneous reconstruction directly from raw cryo-EM particle images using random initialization. Experimental results on real datasets validate the effectiveness and robustness of cryoGS over representative baselines. The code will be released upon publication.

OTSurv: A Novel Multiple Instance Learning Framework for Survival Prediction with Heterogeneity-aware Optimal Transport

Survival prediction using whole slide images (WSIs) can be formulated as a multiple instance learning (MIL) problem. However, existing MIL methods often fail to explicitly capture pathological heterogeneity within WSIs, both globally -- through long-tailed morphological distributions, and locally through -- tile-level prediction uncertainty. Optimal transport (OT) provides a principled way of modeling such heterogeneity by incorporating marginal distribution constraints. Building on this insight, we propose OTSurv, a novel MIL framework from an optimal transport perspective. Specifically, OTSurv formulates survival predictions as a heterogeneity-aware OT problem with two constraints: (1) global long-tail constraint that models prior morphological distributions to avert both mode collapse and excessive uniformity by regulating transport mass allocation, and (2) local uncertainty-aware constraint that prioritizes high-confidence patches while suppressing noise by progressively raising the total transport mass. We then recast the initial OT problem, augmented by these constraints, into an unbalanced OT formulation that can be solved with an efficient, hardware-friendly matrix scaling algorithm. Empirically, OTSurv sets new state-of-the-art results across six popular benchmarks, achieving an absolute 3.6% improvement in average C-index. In addition, OTSurv achieves statistical significance in log-rank tests and offers high interpretability, making it a powerful tool for survival prediction in digital pathology. Our codes are available at https://github.com/Y-Research-SBU/OTSurv.

Spectra-to-Structure and Structure-to-Spectra Inference Across the Periodic Table

X-ray Absorption Spectroscopy (XAS) is a powerful technique for probing local atomic environments, yet its interpretation remains limited by the need for expert-driven analysis, computationally expensive simulations, and element-specific heuristics. Recent advances in machine learning have shown promise for accelerating XAS interpretation, but many existing models are narrowly focused on specific elements, edge types, or spectral regimes. In this work, we present XAStruct, a learning framework capable of both predicting XAS spectra from crystal structures and inferring local structural descriptors from XAS input. XAStruct is trained on a large-scale dataset spanning over 70 elements across the periodic table, enabling generalization to a wide variety of chemistries and bonding environments. The model includes the first machine learning approach for predicting neighbor atom types directly from XAS spectra, as well as a unified regression model for mean nearest-neighbor distance that requires no element-specific tuning. While we explored integrating the two pipelines into a single end-to-end model, empirical results showed performance degradation. As a result, the two tasks were trained independently to ensure optimal accuracy and task-specific performance. By combining deep neural networks for complex structure-property mappings with efficient baseline models for simpler tasks, XAStruct offers a scalable and extensible solution for data-driven XAS analysis and local structure inference. The source code will be released upon paper acceptance.

RISE: Radius of Influence based Subgraph Extraction for 3D Molecular Graph Explanation

3D Geometric Graph Neural Networks (GNNs) have emerged as transformative tools for modeling molecular data. Despite their predictive power, these models often suffer from limited interpretability, raising concerns for scientific applications that require reliable and transparent insights. While existing methods have primarily focused on explaining molecular substructures in 2D GNNs, the transition to 3D GNNs introduces unique challenges, such as handling the implicit dense edge structures created by a cut-off radius. To tackle this, we introduce a novel explanation method specifically designed for 3D GNNs, which localizes the explanation to the immediate neighborhood of each node within the 3D space. Each node is assigned an radius of influence, defining the localized region within which message passing captures spatial and structural interactions crucial for the model's predictions. This method leverages the spatial and geometric characteristics inherent in 3D graphs. By constraining the subgraph to a localized radius of influence, the approach not only enhances interpretability but also aligns with the physical and structural dependencies typical of 3D graph applications, such as molecular learning.

LAPIG: Language Guided Projector Image Generation with Surface Adaptation and Stylization

We propose LAPIG, a language guided projector image generation method with surface adaptation and stylization. LAPIG consists of a projector-camera system and a target textured projection surface. LAPIG takes the user text prompt as input and aims to transform the surface style using the projector. LAPIG's key challenge is that due to the projector's physical brightness limitation and the surface texture, the viewer's perceived projection may suffer from color saturation and artifacts in both dark and bright regions, such that even with the state-of-the-art projector compensation techniques, the viewer may see clear surface texture-related artifacts. Therefore, how to generate a projector image that follows the user's instruction while also displaying minimum surface artifacts is an open problem. To address this issue, we propose projection surface adaptation (PSA) that can generate compensable surface stylization. We first train two networks to simulate the projector compensation and project-and-capture processes, this allows us to find a satisfactory projector image without real project-and-capture and utilize gradient descent for fast convergence. Then, we design content and saturation losses to guide the projector image generation, such that the generated image shows no clearly perceivable artifacts when projected. Finally, the generated image is projected for visually pleasing surface style morphing effects. The source code and video are available on the project page: https://Yu-chen-Deng.github.io/LAPIG/.

DPCS: Path Tracing-Based Differentiable Projector-Camera Systems

Projector-camera systems (ProCams) simulation aims to model the physical project-and-capture process and associated scene parameters of a ProCams, and is crucial for spatial augmented reality (SAR) applications such as ProCams relighting and projector compensation. Recent advances use an end-to-end neural network to learn the project-and-capture process. However, these neural network-based methods often implicitly encapsulate scene parameters, such as surface material, gamma, and white balance in the network parameters, and are less interpretable and hard for novel scene simulation. Moreover, neural networks usually learn the indirect illumination implicitly in an image-to-image translation way which leads to poor performance in simulating complex projection effects such as soft-shadow and interreflection. In this paper, we introduce a novel path tracing-based differentiable projector-camera systems (DPCS), offering a differentiable ProCams simulation method that explicitly integrates multi-bounce path tracing. Our DPCS models the physical project-and-capture process using differentiable physically-based rendering (PBR), enabling the scene parameters to be explicitly decoupled and learned using much fewer samples. Moreover, our physically-based method not only enables high-quality downstream ProCams tasks, such as ProCams relighting and projector compensation, but also allows novel scene simulation using the learned scene parameters. In experiments, DPCS demonstrates clear advantages over previous approaches in ProCams simulation, offering better interpretability, more efficient handling of complex interreflection and shadow, and requiring fewer training samples.