Property Prediction of Stacked Bilayer Materials: A Multimodal Learning Approach

AI for materials science is a critical topic within AI for science, aiming to accelerate materials discovery and produce accurate property predictions. Bilayer 2D material stacking is essential for exploring new materials with novel functions and inherent phenomena, enabling the creation of new 2D bilayers for diverse real-world applications. Research on bilayer vdWs materials has made significant progress from experimental and computational perspectives. Various bilayer materials have been successfully synthe sized experimentally and the increasing utilization of high-throughput computing technology has con structed several computational two-dimensional materials databases. However, the use of AI to model bilayer stacking and predict new properties remains underexplored, necessitating further research studies. In this work, we propose a novel multimodal learning approach to study the interfaces between dissimilar materials that jointly enable new or multiple functions, and to predict new properties arising from the vertical integration (stacking) of different functional material layers under given configurations. Comprehensive experiments demonstrate the effectiveness and efficiency of our approach compared to baseline methods. Our code is available at https://github.com/AnVuong123/bimat ml.

SDM-Q: Cost-Aware Staged Decision-Making for Multi-Omics Classification with Deep Q-Learning

Multi-omics data provide complementary molecular characterizations of disease phenotypes and play an important role in disease diagnosis and subtype classification in precision medicine. However, acquiring complete multi-omics profiles is expensive and time-consuming, while most existing deep learning methods assume full modality availability during inference, resulting in substantial redundancy and limited practicality in clinical settings. To address this issue, we propose SDM-Q, a reinforcement learning framework for adaptive and cost-aware multi-omics classification. Specifically, multi-omics diagnosis is reformulated as a finite-horizon sequential decision problem, where the currently acquired omics modalities define the diagnostic state at each stage. An action--value function determines whether to acquire an additional modality or terminate the decision process and output the final prediction. To balance diagnostic utility and acquisition cost, the reward is defined only at the terminal stage and jointly determined by classification correctness and cumulative modality acquisition cost. A backward stage-wise optimization strategy is introduced to improve policy consistency and training stability. Experiments on four public multi-omics datasets, including ROSMAP, LGG, BRCA, and KIPAN, demonstrate that SDM-Q effectively reduces redundant modality acquisition while maintaining competitive classification performance compared with methods using complete multi-omics inputs. In the BRCA and KIPAN datasets, more than 99\% and 95\% of subjects, respectively, achieve accurate classification using only a single omics modality, while the average number of acquired modalities remains below two for ROSMAP and LGG. These results suggest that cost-aware sequential decision-making provides an effective paradigm for improving the efficiency of precision medicine workflows.

From "Weak" Signals to Strong Models: Preference Delta Aggregation with LoRA Merging

Training strong large language models (LLMs) requires high-quality supervision, which is often scarce. Recent work shows that paired preference data from weak-weaker model pairs (e.g., Qwen3 4B over 1.7B), despite the limited quality of individual responses, can provide an effective supervision signal through relative quality deltas, which we term a "weak" signal. This motivates a key research question: can multiple "weak" signals be constructively aggregated for improving strong models (e.g., Qwen3 8B)? To this end, we propose Preference Delta Aggregation (PDA), the first framework that derives a preference delta from each weak-weaker model pair, instantiates it as a LoRA adapter learned through preference optimization, and aggregates the resulting deltas via LoRA merging. To further mitigate directional interference during LoRA merging, we introduce Geometric Alignment Merging (GAM), a geometry-aware merging method that aligns adapter subspaces before aggregation, enabling more robust composition of diverse deltas. Evaluations on knowledge reasoning and agentic search benchmarks show that aggregating multiple "weak" signals pushes performance beyond any single signal, with further gains as additional signals are incorporated. Correspondingly, PDA with GAM improves the strong model by 6.8 and 7.3 points on average for knowledge reasoning and agentic search, respectively. It outperforms all single-delta and multi-delta baselines, exceeding the best single-delta baseline by 2.1 and 4.3 points. Further analysis attributes these gains to the effective composition of complementary capabilities encoded across distinct preference deltas.

Uncertainty-Guided Conservative Propagation for Structured Inference in Vessel Segmentation

Accurate vessel segmentation is essential for medical image analysis, yet remains challenging due to complex vascular patterns and imaging ambiguity. Most deep models rely on single-pass prediction, limiting their ability to refine uncertain or disconnected regions during inference. To address this limitation, we propose Uncertainty-Guided Conservative Propagation (UGCP), a general plug-in module for vessel segmentation. Instead of directly using a one-shot output as the final prediction, UGCP performs a small number of logit-space update steps to refine the segmentation through local predictions interaction. Predictive uncertainty guides reliable regions to support ambiguous regions, while structure-aware modulation and source-based stabilization reduce unreliable propagation and excessive drift. The module is differentiable and can be trained end-to-end with different segmentation networks. We evaluate UGCP on four public vessel segmentation datasets covering 2D and 3D tasks, including retinal vessel, coronary artery, and cerebral vessel segmentation. Experiments with convolutional neural network-based and Transformer-based backbones show consistent improvements in Dice similarity coefficient, centerline Dice, and 95th percentile Hausdorff distance. Further analysis demonstrates that UGCP reduces vessel disconnections and improves structural consistency with limited additional computation. The code will be made available at https://github.com/chenzhao2023/UGC_PR.

Correct Code, Vulnerable Dependencies: A Large Scale Measurement Study of LLM-Specified Library Versions

Large language models (LLMs) are now largely involved in software development workflows, and the code they generate routinely includes third-party library (TPL) imports annotated with specific version identifiers. These version choices can carry security and compatibility risks, yet they have not been systematically studied. We present the first large-scale measurement study of version-level risk in LLM-generated Python code, evaluating 10 LLMs on PinTrace, a curated benchmark of 1,000 Stack Overflow programming tasks. LLMs tend to specify version identifiers when directly prompted at 26.83%-95.18%, while down to 6.45%-59.19% in creating a manifest file directly. Among the specified versions, 36.70%-55.70% of tasks contain at least one known CVE, and 62.75%-74.51% of them carry Critical or High severity ratings. In 72.27%-91.37% of cases, the associated CVEs were publicly disclosed before the model's knowledge cutoff. The statistics show all models converge on the same small set of risky release versions, indicating a systemic bias rather than isolated model error. Static compatibility rates range from 19.70% to 63.20%, with installation failure as the dominant cause. The dynamic test cases confirm the pattern by 6.49%-48.62% pass rates. Further experiments confirm that these failures are attributable to version selection rather than code quality, and that externally anchored version constraints substantially reduce both vulnerability exposure and compatibility failures. Our findings reveal LLM version selection as a first-class, previously overlooked risk surface in LLM-based development. We disclosed these findings to the community of the evaluated models, and several confirmed the issue. All the code and dataset have been released for open science at https://github.com/dw763j/PinTrace.

Rethinking Reasoning-Intensive Retrieval: Evaluating and Advancing Retrievers in Agentic Search Systems

Reasoning-intensive retrieval aims to surface evidence that supports downstream reasoning rather than merely matching topical similarity. This capability is increasingly important for agentic search systems, where retrievers must provide complementary evidence across iterative search and synthesis. However, existing work remains limited on both evaluation and training: benchmarks such as BRIGHT provide narrow gold sets and evaluate retrievers in isolation, while synthetic training corpora often optimize single-passage relevance rather than evidence portfolio construction. We introduce BRIGHT-Pro, an expert-annotated benchmark that expands each query with multi-aspect gold evidence and evaluates retrievers under both static and agentic search protocols. We further construct RTriever-Synth, an aspect-decomposed synthetic corpus that generates complementary positives and positive-conditioned hard negatives, and use it to LoRA fine-tune RTriever-4B from Qwen3-Embedding-4B. Experiments across lexical, general-purpose, and reasoning-intensive retrievers show that aspect-aware and agentic evaluation expose behaviors hidden by standard metrics, while RTriever-4B substantially improves over its base model.

Point Cloud Registration for Fusion between SPECT MPI and CTA Images

Clinical fusion of Single Photon Emission Computed Tomography Myocardial Perfusion Imaging (SPECT MPI) and Computed Tomography Angiography (CTA) remains limited by cross-modality misregistration and reliance on manual landmarks, which can hinder accurate ischemia localization and lesion-level functional assessment. To address this issue, we propose a registration and fusion framework for SPECT MPI and CTA that integrates functional and structural information for comprehensive cardiac evaluation. The proposed pipeline performs U-Net-based segmentation on both modalities. On SPECT MPI, only the left ventricle (LV) is extracted, and anatomical landmarks are automatically derived from characteristic LV structures. On CTA, both ventricles are segmented, and their spatial relationship is used to automatically define landmarks at the interventricular septal junction. Scale-space consistency preprocessing and landmark-driven coarse registration are applied to mitigate initial misalignment. Based on this initialization, multiple fine registration methods are evaluated on LV epicardial surface point clouds, including ICP, SICP, CPD, CluReg, FFD, and BCPD-plus-plus. The resulting transformations are then propagated to voxel-level resampling for high-precision SPECT-CTA fusion. In a retrospective cohort of 60 patients, the proposed framework preserved sub-millimeter coronary detail from CTA while accurately overlaying quantitative SPECT perfusion. Among the evaluated methods, BCPD-plus-plus achieved the highest accuracy with a mean point cloud distance of 1.7 mm. By combining robust initialization, comparative fine registration, and voxel-level fusion, the proposed approach provides a practical solution for myocardial ischemia localization and functional evaluation of coronary lesions, while remaining independent of any specific fine registration algorithm.

Search, Do not Guess: Teaching Small Language Models to Be Effective Search Agents

Agents equipped with search tools have emerged as effective solutions for knowledge-intensive tasks. While Large Language Models (LLMs) exhibit strong reasoning capabilities, their high computational cost limits practical deployment for search agents. Consequently, recent work has focused on distilling agentic behaviors from LLMs into Small Language Models (SLMs). Through comprehensive evaluation on complex multi-hop reasoning tasks, we find that despite possessing less parametric knowledge, SLMs invoke search tools less frequently and are more prone to hallucinations. To address this issue, we propose \policy, a lightweight fine-tuning approach that explicitly trains SLMs to reliably retrieve and generate answers grounded in retrieved evidence. Compared to agent distillation from LLMs, our approach improves performance by 17.3 scores on Bamboogle and 15.3 scores on HotpotQA, achieving LLM-level results across benchmarks. Our further analysis reveals that adaptive search strategies in SLMs often degrade performance, highlighting the necessity of consistent search behavior for reliable reasoning.

Hierarchical Awareness Adapters with Hybrid Pyramid Feature Fusion for Dense Depth Prediction

Monocular depth estimation from a single RGB image remains a fundamental challenge in computer vision due to inherent scale ambiguity and the absence of explicit geometric cues. Existing approaches typically rely on increasingly complex network architectures to regress depth maps, which escalates training costs and computational overhead without fully exploiting inter-pixel spatial dependencies. We propose a multilevel perceptual conditional random field (CRF) model built upon the Swin Transformer backbone that addresses these limitations through three synergistic innovations: (1) an adaptive hybrid pyramid feature fusion (HPF) strategy that captures both short-range and long-range dependencies by combining multi-scale spatial pyramid pooling with biaxial feature aggregation, enabling effective integration of global and local contextual information; (2) a hierarchical awareness adapter (HA) that enriches cross-level feature interactions within the encoder through lightweight broadcast modules with learnable dimensional scaling, reducing computational complexity while enhancing representational capacity; and (3) a fully-connected CRF decoder with dynamic scaling attention that models fine-grained pixel-level spatial relationships, incorporating a bias learning unit to prevent extreme-value collapse and ensure stable training. Extensive experiments on NYU Depth v2, KITTI, and MatterPort3D datasets demonstrate that our method achieves state-of-the-art performance, reducing Abs Rel to 0.088 ($-$7.4\%) and RMSE to 0.316 ($-$5.4\%) on NYU Depth v2, while attaining near-perfect threshold accuracy ($δ< 1.25^3 \approx 99.8\%$) on KITTI with only 194M parameters and 21ms inference time.

GenoBERT: A Language Model for Accurate Genotype Imputation

Genotype imputation enables dense variant coverage for genome-wide association and risk-prediction studies, yet conventional reference-panel methods remain limited by ancestry bias and reduced rare-variant accuracy. We present Genotype Bidirectional Encoder Representations from Transformers (GenoBERT), a transformer-based, reference-free framework that tokenizes phased genotypes and uses a self-attention mechanism to capture both short- and long-range linkage disequilibrium (LD) dependencies. Benchmarking on two independent datasets including the Louisiana Osteoporosis Study (LOS) and the 1000 Genomes Project (1KGP) across ancestry groups and multiple genotype missingness levels (5-50%) shows that GenoBERT achieves the highest overall accuracy compared to four baseline methods (Beagle5.4, SCDA, BiU-Net, and STICI). At practical sparsity levels (up to 25% missing), GenoBERT attains high overall imputation accuracy ($r^2 approx 0.98$) across datasets, and maintains robust performance ($r^2 > 0.90$) even at 50% missingness. Experimental results across different ancestries confirm consistent gains across datasets, with resilience to small sample sizes and weak LD. A 128-SNP (single-nucleotide polymorphism) context window (approximately 100 Kb) is validated through LD-decay analyses as sufficient to capture local correlation structures. By eliminating reference-panel dependence while preserving high accuracy, GenoBERT provides a scalable and robust solution for genotype imputation and a foundation for downstream genomic modeling.