Do Papers Match Code? A Benchmark and Framework for Paper-Code Consistency Detection in Bioinformatics Software

Ensuring consistency between research papers and their corresponding software implementations is fundamental to software reliability and scientific reproducibility. However, this problem remains underexplored, particularly in the domain of bioinformatics, where discrepancies between methodological descriptions in papers and their actual code implementations are prevalent. To address this gap, this paper introduces a new task, namely paper-code consistency detection, and curates a collection of 48 bioinformatics software projects along with their associated publications. We systematically align sentence-level algorithmic descriptions from papers with function-level code snippets. Combined with expert annotations and a hybrid negative sampling strategy, we construct the first benchmark dataset in the bioinformatics domain tailored to this task, termed BioCon. Based on this benchmark, we further propose a cross-modal consistency detection framework designed to model the semantic relationships between natural language descriptions and code implementations. The framework adopts a unified input representation and leverages pre-trained models to capture deep semantic alignment between papers and code. To mitigate the effects of class imbalance and hard samples, we incorporate a weighted focal loss to enhance model robustness. Experimental results demonstrate that our framework effectively identifies consistency between papers and code in bioinformatics, achieving an accuracy of 0.9056 and an F1 score of 0.8011. Overall, this study opens a new research direction for paper-code consistency analysis and lays the foundation for automated reproducibility assessment and cross-modal understanding in scientific software.

SR3R: Rethinking Super-Resolution 3D Reconstruction With Feed-Forward Gaussian Splatting

3D super-resolution (3DSR) aims to reconstruct high-resolution (HR) 3D scenes from low-resolution (LR) multi-view images. Existing methods rely on dense LR inputs and per-scene optimization, which restricts the high-frequency priors for constructing HR 3D Gaussian Splatting (3DGS) to those inherited from pretrained 2D super-resolution (2DSR) models. This severely limits reconstruction fidelity, cross-scene generalization, and real-time usability. We propose to reformulate 3DSR as a direct feed-forward mapping from sparse LR views to HR 3DGS representations, enabling the model to autonomously learn 3D-specific high-frequency geometry and appearance from large-scale, multi-scene data. This fundamentally changes how 3DSR acquires high-frequency knowledge and enables robust generalization to unseen scenes. Specifically, we introduce SR3R, a feed-forward framework that directly predicts HR 3DGS representations from sparse LR views via the learned mapping network. To further enhance reconstruction fidelity, we introduce Gaussian offset learning and feature refinement, which stabilize reconstruction and sharpen high-frequency details. SR3R is plug-and-play and can be paired with any feed-forward 3DGS reconstruction backbone: the backbone provides an LR 3DGS scaffold, and SR3R upscales it to an HR 3DGS. Extensive experiments across three 3D benchmarks demonstrate that SR3R surpasses state-of-the-art (SOTA) 3DSR methods and achieves strong zero-shot generalization, even outperforming SOTA per-scene optimization methods on unseen scenes.

Quark Medical Alignment: A Holistic Multi-Dimensional Alignment and Collaborative Optimization Paradigm

While reinforcement learning for large language model alignment has progressed rapidly in recent years, transferring these paradigms to high-stakes medical question answering reveals a fundamental paradigm mismatch. Reinforcement Learning from Human Feedback relies on preference annotations that are prohibitively expensive and often fail to reflect the absolute correctness of medical facts. Reinforcement Learning from Verifiable Rewards lacks effective automatic verifiers and struggles to handle complex clinical contexts. Meanwhile, medical alignment requires the simultaneous optimization of correctness, safety, and compliance, yet multi-objective heterogeneous reward signals are prone to scale mismatch and optimization conflicts.To address these challenges, we propose a robust medical alignment paradigm. We first construct a holistic multi-dimensional medical alignment matrix that decomposes alignment objectives into four categories: fundamental capabilities, expert knowledge, online feedback, and format specifications. Within each category, we establish a closed loop of where observable metrics inform attributable diagnosis, which in turn drives optimizable rewards, thereby providing fine-grained, high-resolution supervision signals for subsequent iterative optimization. To resolve gradient domination and optimization instability problem caused by heterogeneous signals, we further propose a unified optimization mechanism. This mechanism employs Reference-Frozen Normalization to align reward scales and implements a Tri-Factor Adaptive Dynamic Weighting strategy to achieve collaborative optimization that is weakness-oriented, risk-prioritized, and redundancy-reducing. Experimental results demonstrate the effectiveness of our proposed paradigm in real-world medical scenario evaluations, establishing a new paradigm for complex alignment in vertical domains.

Tighnari v2: Mitigating Label Noise and Distribution Shift in Multimodal Plant Distribution Prediction via Mixture of Experts and Weakly Supervised Learning

Large-scale, cross-species plant distribution prediction plays a crucial role in biodiversity conservation, yet modeling efforts in this area still face significant challenges due to the sparsity and bias of observational data. Presence-Absence (PA) data provide accurate and noise-free labels, but are costly to obtain and limited in quantity; Presence-Only (PO) data, by contrast, offer broad spatial coverage and rich spatiotemporal distribution, but suffer from severe label noise in negative samples. To address these real-world constraints, this paper proposes a multimodal fusion framework that fully leverages the strengths of both PA and PO data. We introduce an innovative pseudo-label aggregation strategy for PO data based on the geographic coverage of satellite imagery, enabling geographic alignment between the label space and remote sensing feature space. In terms of model architecture, we adopt Swin Transformer Base as the backbone for satellite imagery, utilize the TabM network for tabular feature extraction, retain the Temporal Swin Transformer for time-series modeling, and employ a stackable serial tri-modal cross-attention mechanism to optimize the fusion of heterogeneous modalities. Furthermore, empirical analysis reveals significant geographic distribution shifts between PA training and test samples, and models trained by directly mixing PO and PA data tend to experience performance degradation due to label noise in PO data. To address this, we draw on the mixture-of-experts paradigm: test samples are partitioned according to their spatial proximity to PA samples, and different models trained on distinct datasets are used for inference and post-processing within each partition. Experiments on the GeoLifeCLEF 2025 dataset demonstrate that our approach achieves superior predictive performance in scenarios with limited PA coverage and pronounced distribution shifts.

Weak to Strong: VLM-Based Pseudo-Labeling as a Weakly Supervised Training Strategy in Multimodal Video-based Hidden Emotion Understanding Tasks

To tackle the automatic recognition of "concealed emotions" in videos, this paper proposes a multimodal weak-supervision framework and achieves state-of-the-art results on the iMiGUE tennis-interview dataset. First, YOLO 11x detects and crops human portraits frame-by-frame, and DINOv2-Base extracts visual features from the cropped regions. Next, by integrating Chain-of-Thought and Reflection prompting (CoT + Reflection), Gemini 2.5 Pro automatically generates pseudo-labels and reasoning texts that serve as weak supervision for downstream models. Subsequently, OpenPose produces 137-dimensional key-point sequences, augmented with inter-frame offset features; the usual graph neural network backbone is simplified to an MLP to efficiently model the spatiotemporal relationships of the three key-point streams. An ultra-long-sequence Transformer independently encodes both the image and key-point sequences, and their representations are concatenated with BERT-encoded interview transcripts. Each modality is first pre-trained in isolation, then fine-tuned jointly, with pseudo-labeled samples merged into the training set for further gains. Experiments demonstrate that, despite severe class imbalance, the proposed approach lifts accuracy from under 0.6 in prior work to over 0.69, establishing a new public benchmark. The study also validates that an "MLP-ified" key-point backbone can match - or even surpass - GCN-based counterparts in this task.

PhysicsMind: Sim and Real Mechanics Benchmarking for Physical Reasoning and Prediction in Foundational VLMs and World Models

Modern foundational Multimodal Large Language Models (MLLMs) and video world models have advanced significantly in mathematical, common-sense, and visual reasoning, but their grasp of the underlying physics remains underexplored. Existing benchmarks attempting to measure this matter rely on synthetic, Visual Question Answer templates or focus on perceptual video quality that is tangential to measuring how well the video abides by physical laws. To address this fragmentation, we introduce PhysicsMind, a unified benchmark with both real and simulation environments that evaluates law-consistent reasoning and generation over three canonical principles: Center of Mass, Lever Equilibrium, and Newton's First Law. PhysicsMind comprises two main tasks: i) VQA tasks, testing whether models can reason and determine physical quantities and values from images or short videos, and ii) Video Generation(VG) tasks, evaluating if predicted motion trajectories obey the same center-of-mass, torque, and inertial constraints as the ground truth. A broad range of recent models and video generation models is evaluated on PhysicsMind and found to rely on appearance heuristics while often violating basic mechanics. These gaps indicate that current scaling and training are still insufficient for robust physical understanding, underscoring PhysicsMind as a focused testbed for physics-aware multimodal models. Our data will be released upon acceptance.

Adaptive Disentangled Representation Learning for Incomplete Multi-View Multi-Label Classification

Multi-view multi-label learning frequently suffers from simultaneous feature absence and incomplete annotations, due to challenges in data acquisition and cost-intensive supervision. To tackle the complex yet highly practical problem while overcoming the existing limitations of feature recovery, representation disentanglement, and label semantics modeling, we propose an Adaptive Disentangled Representation Learning method (ADRL). ADRL achieves robust view completion by propagating feature-level affinity across modalities with neighborhood awareness, and reinforces reconstruction effectiveness by leveraging a stochastic masking strategy. Through disseminating category-level association across label distributions, ADRL refines distribution parameters for capturing interdependent label prototypes. Besides, we formulate a mutual-information-based objective to promote consistency among shared representations and suppress information overlap between view-specific representation and other modalities. Theoretically, we derive the tractable bounds to train the dual-channel network. Moreover, ADRL performs prototype-specific feature selection by enabling independent interactions between label embeddings and view representations, accompanied by the generation of pseudo-labels for each category. The structural characteristics of the pseudo-label space are then exploited to guide a discriminative trade-off during view fusion. Finally, extensive experiments on public datasets and real-world applications demonstrate the superior performance of ADRL.

Adaptive Detector-Verifier Framework for Zero-Shot Polyp Detection in Open-World Settings

Polyp detectors trained on clean datasets often underperform in real-world endoscopy, where illumination changes, motion blur, and occlusions degrade image quality. Existing approaches struggle with the domain gap between controlled laboratory conditions and clinical practice, where adverse imaging conditions are prevalent. In this work, we propose AdaptiveDetector, a novel two-stage detector-verifier framework comprising a YOLOv11 detector with a vision-language model (VLM) verifier. The detector adaptively adjusts per-frame confidence thresholds under VLM guidance, while the verifier is fine-tuned with Group Relative Policy Optimization (GRPO) using an asymmetric, cost-sensitive reward function specifically designed to discourage missed detections -- a critical clinical requirement. To enable realistic assessment under challenging conditions, we construct a comprehensive synthetic testbed by systematically degrading clean datasets with adverse conditions commonly encountered in clinical practice, providing a rigorous benchmark for zero-shot evaluation. Extensive zero-shot evaluation on synthetically degraded CVC-ClinicDB and Kvasir-SEG images demonstrates that our approach improves recall by 14 to 22 percentage points over YOLO alone, while precision remains within 0.7 points below to 1.7 points above the baseline. This combination of adaptive thresholding and cost-sensitive reinforcement learning achieves clinically aligned, open-world polyp detection with substantially fewer false negatives, thereby reducing the risk of missed precancerous polyps and improving patient outcomes.

GTCN-G: A Residual Graph-Temporal Fusion Network for Imbalanced Intrusion Detection (Preprint)

The escalating complexity of network threats and the inherent class imbalance in traffic data present formidable challenges for modern Intrusion Detection Systems (IDS). While Graph Neural Networks (GNNs) excel in modeling topological structures and Temporal Convolutional Networks (TCNs) are proficient in capturing time-series dependencies, a framework that synergistically integrates both while explicitly addressing data imbalance remains an open challenge. This paper introduces a novel deep learning framework, named Gated Temporal Convolutional Network and Graph (GTCN-G), engineered to overcome these limitations. Our model uniquely fuses a Gated TCN (G-TCN) for extracting hierarchical temporal features from network flows with a Graph Convolutional Network (GCN) designed to learn from the underlying graph structure. The core innovation lies in the integration of a residual learning mechanism, implemented via a Graph Attention Network (GAT). This mechanism preserves original feature information through residual connections, which is critical for mitigating the class imbalance problem and enhancing detection sensitivity for rare malicious activities (minority classes). We conducted extensive experiments on two public benchmark datasets, UNSW-NB15 and ToN-IoT, to validate our approach. The empirical results demonstrate that the proposed GTCN-G model achieves state-of-the-art performance, significantly outperforming existing baseline models in both binary and multi-class classification tasks.

Attention and Risk-Aware Decision Framework for Safe Autonomous Driving

Autonomous driving has attracted great interest due to its potential capability in full-unsupervised driving. Model-based and learning-based methods are widely used in autonomous driving. Model-based methods rely on pre-defined models of the environment and may struggle with unforeseen events. Proximal policy optimization (PPO), an advanced learning-based method, can adapt to the above limits by learning from interactions with the environment. However, existing PPO faces challenges with poor training results, and low training efficiency in long sequences. Moreover, the poor training results are equivalent to collisions in driving tasks. To solve these issues, this paper develops an improved PPO by introducing the risk-aware mechanism, a risk-attention decision network, a balanced reward function, and a safety-assisted mechanism. The risk-aware mechanism focuses on highlighting areas with potential collisions, facilitating safe-driving learning of the PPO. The balanced reward function adjusts rewards based on the number of surrounding vehicles, promoting efficient exploration of the control strategy during training. Additionally, the risk-attention network enhances the PPO to hold channel and spatial attention for the high-risk areas of input images. Moreover, the safety-assisted mechanism supervises and prevents the actions with risks of collisions during the lane keeping and lane changing. Simulation results on a physical engine demonstrate that the proposed algorithm outperforms benchmark algorithms in collision avoidance, achieving higher peak reward with less training time, and shorter driving time remaining on the risky areas among multiple testing traffic flow scenarios.