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scCluBench: Comprehensive Benchmarking of Clustering Algorithms for Single-Cell RNA Sequencing

arXiv.org Artificial Intelligence

Cell clustering is crucial for uncovering cellular heterogeneity in single-cell RNA sequencing (scRNA-seq) data by identifying cell types and marker genes. Despite its importance, benchmarks for scRNA-seq clustering methods remain fragmented, often lacking standardized protocols and failing to incorporate recent advances in artificial intelligence. To fill these gaps, we present scCluBench, a comprehensive benchmark of clustering algorithms for scRNA-seq data. First, scCluBench provides 36 scRNA-seq datasets collected from diverse public sources, covering multiple tissues, which are uniformly processed and standardized to ensure consistency for systematic evaluation and downstream analyses. To evaluate performance, we collect and reproduce a range of scRNA-seq clustering methods, including traditional, deep learning-based, graph-based, and biological foundation models. We comprehensively evaluate each method both quantitatively and qualitatively, using core performance metrics as well as visualization analyses. Furthermore, we construct representative downstream biological tasks, such as marker gene identification and cell type annotation, to further assess the practical utility. scCluBench then investigates the performance differences and applicability boundaries of various clustering models across diverse analytical tasks, systematically assessing their robustness and scalability in real-world scenarios. Overall, scCluBench offers a standardized and user-friendly benchmark for scRNA-seq clustering, with curated datasets, unified evaluation protocols, and transparent analyses, facilitating informed method selection and providing valuable insights into model generalizability and application scope.


nuScenes Revisited: Progress and Challenges in Autonomous Driving

arXiv.org Artificial Intelligence

Autonomous Vehicles (AV) and Advanced Driver Assistance Systems (ADAS) have been revolutionized by Deep Learning. As a data-driven approach, Deep Learning relies on vast amounts of driving data, typically labeled in great detail. As a result, datasets, alongside hardware and algorithms, are foundational building blocks for the development of AVs. In this work we revisit one of the most widely used autonomous driving datasets: the nuScenes dataset. nuScenes exemplifies key trends in AV development, being the first dataset to include radar data, to feature diverse urban driving scenes from two continents, and to be collected using a fully autonomous vehicle operating on public roads, while also promoting multi-modal sensor fusion, standardized benchmarks, and a broad range of tasks including perception, localization \& mapping, prediction and planning. We provide an unprecedented look into the creation of nuScenes, as well as its extensions nuImages and Panoptic nuScenes, summarizing many technical details that have hitherto not been revealed in academic publications. Furthermore, we trace how the influence of nuScenes impacted a large number of other datasets that were released later and how it defined numerous standards that are used by the community to this day. Finally, we present an overview of both official and unofficial tasks using the nuScenes dataset and review major methodological developments, thereby offering a comprehensive survey of the autonomous driving literature, with a particular focus on nuScenes.


When Refusals Fail: Unstable Safety Mechanisms in Long-Context LLM Agents

arXiv.org Artificial Intelligence

Solving complex or long-horizon problems often requires large language models (LLMs) to use external tools and operate over a significantly longer context window. New LLMs enable longer context windows and support tool calling capabilities. Prior works have focused mainly on evaluation of LLMs on long-context prompts, leaving agentic setup relatively unexplored, both from capability and safety perspectives. Our work addresses this gap. We find that LLM agents could be sensitive to length, type, and placement of the context, exhibiting unexpected and inconsistent shifts in task performance and in refusals to execute harmful requests. Models with 1M-2M token context windows show severe degradation already at 100K tokens, with performance drops exceeding 50\% for both benign and harmful tasks. Refusal rates shift unpredictably: GPT-4.1-nano increases from $\sim$5\% to $\sim$40\% while Grok 4 Fast decreases from $\sim$80\% to $\sim$10\% at 200K tokens. Our work shows potential safety issues with agents operating on longer context and opens additional questions on the current metrics and paradigm for evaluating LLM agent safety on long multi-step tasks. In particular, our results on LLM agents reveal a notable divergence in both capability and safety performance compared to prior evaluations of LLMs on similar criteria.


QJoin: Transformation-aware Joinable Data Discovery Using Reinforcement Learning

arXiv.org Artificial Intelligence

Discovering which tables in large, heterogeneous repositories can be joined and by what transformations is a central challenge in data integration and data discovery. Traditional join discovery methods are largely designed for equi-joins, which assume that join keys match exactly or nearly so. These techniques, while efficient in clean, well-normalized databases, fail in open or federated settings where identifiers are inconsistently formatted, embedded, or split across multiple columns. Approximate or fuzzy joins alleviate minor string variations but cannot capture systematic transformations. We introduce QJoin, a reinforcement-learning framework that learns and reuses transformation strategies across join tasks. QJoin trains an agent under a uniqueness-aware reward that balances similarity with key distinctiveness, enabling it to explore concise, high-value transformation chains. To accelerate new joins, we introduce two reuse mechanisms: (i) agent transfer, which initializes new policies from pretrained agents, and (ii) transformation reuse, which caches successful operator sequences for similar column clusters. On the AutoJoin Web benchmark (31 table pairs), QJoin achieves an average F1-score of 91.0%. For 19,990 join tasks in NYC+Chicago open datasets, Qjoin reduces runtime by up to 7.4% (13,747 s) by using reusing. These results demonstrate that transformation learning and reuse can make join discovery both more accurate and more efficient.


Boosting Medical Vision-Language Pretraining via Momentum Self-Distillation under Limited Computing Resources

arXiv.org Artificial Intelligence

In medical healthcare, obtaining detailed annotations is challenging, highlighting the need for robust Vision-Language Models (VLMs). Pretrained VLMs enable fine-tuning on small datasets or zero-shot inference, achieving performance comparable to task-specific models. Contrastive learning (CL) is a key paradigm for training VLMs but inherently requires large batch sizes for effective learning, making it computationally demanding and often limited to well-resourced institutions. Moreover, with limited data in healthcare, it is important to prioritize knowledge extraction from both data and models during training to improve performance. Therefore, we focus on leveraging the momentum method combined with distillation to simultaneously address computational efficiency and knowledge exploitation. Our contributions can be summarized as follows: (1) leveraging momentum self-distillation to enhance multimodal learning, and (2) integrating momentum mechanisms with gradient accumulation to enlarge the effective batch size without increasing resource consumption. Our method attains competitive performance with state-of-the-art (SOTA) approaches in zero-shot classification, while providing a substantial boost in the few-shot adaption, achieving over 90% AUC-ROC and improving retrieval tasks by 2-3%. Importantly, our method achieves high training efficiency with a single GPU while maintaining reasonable training time. Our approach aims to advance efficient multimodal learning by reducing resource requirements while improving performance over SOTA methods. The implementation of our method is available at https://github.com/phphuc612/MSD .


LightHCG: a Lightweight yet powerful HSIC Disentanglement based Causal Glaucoma Detection Model framework

arXiv.org Artificial Intelligence

As a representative optic degenerative condition, glaucoma has been a threat to millions due to its irreversibility and severe impact on human vision fields. Mainly characterized by dimmed and blurred visions, or peripheral vision loss, glaucoma is well known to occur due to damages in the optic nerve from increased intraocular pressure (IOP) or neovascularization within the retina. Traditionally, most glaucoma related works and clinical diagnosis focused on detecting these damages in the optic nerve by using patient data from perimetry tests, optic papilla inspections and tonometer-based IOP measurements. Recently, with advancements in computer vision AI models, such as VGG16 or Vision Transformers (ViT), AI-automatized glaucoma detection and optic cup segmentation based on retinal fundus images or OCT recently exhibited significant performance in aiding conventional diagnosis with high performance. However, current AI-driven glaucoma detection approaches still have significant room for improvement in terms of reliability, excessive parameter usage, possibility of spurious correlation within detection, and limitations in applications to intervention analysis or clinical simulations. Thus, this research introduced a novel causal representation driven glaucoma detection model: LightHCG, an extremely lightweight Convolutional VAE-based latent glaucoma representation model that can consider the true causality among glaucoma-related physical factors within the optic nerve region. Using HSIC-based latent space disentanglement and Graph Autoencoder based unsupervised causal representation learning, LightHCG not only exhibits higher performance in classifying glaucoma with 93~99% less weights, but also enhances the possibility of AI-driven intervention analysis, compared to existing advanced vision models such as InceptionV3, MobileNetV2 or VGG16.


Semantic Trading: Agentic AI for Clustering and Relationship Discovery in Prediction Markets

arXiv.org Artificial Intelligence

Prediction markets allow users to trade on outcomes of real-world events, but are prone to fragmentation with overlapping questions, implicit equivalences, and hidden contradictions across markets. We present an agentic AI pipeline that autonomously (i) clusters markets into coherent topical groups using natural-language understanding over contract text and metadata, and (ii) identifies within-cluster market pairs whose resolved outcomes exhibit strong dependence, including "same-outcome" (correlated) and "different-outcome" (anti-correlated) relationships. Using a historical dataset of resolved markets on Poly-market, we evaluate the accuracy of the agent's relational predictions. We then synthesize discovered relationships into a simple trading strategy to quantify how discovered relationships translate into actionable strategies. Results show that agent-identified relationships have around 60-70% accuracy, and their induced trading strategies have an average return of 20% over week-long horizons, highlighting the ability of agen-tic AI and large language models to uncover latent semantic structure within prediction markets.


Quantum feature encoding optimization

arXiv.org Artificial Intelligence

Quantum Machine Learning (QML) holds the promise of enhancing machine learning modeling in terms of both complexity and accuracy. A key challenge in this domain is the encoding of input data, which plays a pivotal role in determining the performance of QML models. In this work, we tackle a largely unaddressed aspect of encoding that is unique to QML modeling -- rather than adjusting the ansatz used for encoding, we consider adjusting how data is conveyed to the ansatz. We specifically implement QML pipelines that leverage classical data manipulation (i.e., ordering, selecting, and weighting features) as a preprocessing step, and evaluate if these aspects of encoding can have a significant impact on QML model performance, and if they can be effectively optimized to improve performance. Our experimental results, applied across a wide variety of data sets, ansatz, and circuit sizes, with a representative QML approach, demonstrate that by optimizing how features are encoded in an ansatz we can substantially and consistently improve the performance of QML models, making a compelling case for integrating these techniques in future QML applications. Finally we demonstrate the practical feasibility of this approach by running it using real quantum hardware with 100 qubit circuits and successfully achieving improved QML modeling performance in this case as well.


The brain-AI convergence: Predictive and generative world models for general-purpose computation

arXiv.org Artificial Intelligence

Recent advances in general-purpose AI systems with attention-based transformers offer a potential window into how the neocortex and cerebellum, despite their relatively uniform circuit architectures, give rise to diverse functions and, ultimately, to human intelligence. This Perspective provides a cross-domain comparison between the brain and AI that goes beyond the traditional focus on visual processing, adopting the emerging perspecive of world-model-based computation. Here, we identify shared computational mechanisms in the attention-based neocortex and the non-attentional cerebellum: both predict future world events from past inputs and construct internal world models through prediction-error learning. These predictive world models are repurposed for seemingly distinct functions -- understanding in sensory processing and generation in motor processing -- enabling the brain to achieve multi-domain capabilities and human-like adaptive intelligence. Notably, attention-based AI has independently converged on a similar learning paradigm and world-model-based computation. We conclude that these shared mechanisms in both biological and artificial systems constitute a core computational foundation for realizing diverse functions including high-level intelligence, despite their relatively uniform circuit structures. Our theoretical insights bridge neuroscience and AI, advancing our understanding of the computational essence of intelligence.


Vehicle Dynamics Embedded World Models for Autonomous Driving

arXiv.org Artificial Intelligence

World models have gained significant attention as a promising approach for autonomous driving. By emulating human-like perception and decision-making processes, these models can predict and adapt to dynamic environments. Existing methods typically map high-dimensional observations into compact latent spaces and learn optimal policies within these latent representations. However, prior work usually jointly learns ego-vehicle dynamics and environmental transition dynamics from the image input, leading to inefficiencies and a lack of robustness to variations in vehicle dynamics. To address these issues, we propose the Vehicle Dynamics embedded Dreamer (VDD) method, which decouples the modeling of ego-vehicle dynamics from environmental transition dynamics. This separation allows the world model to generalize effectively across vehicles with diverse parameters. Additionally, we introduce two strategies to further enhance the robustness of the learned policy: Policy Adjustment during Deployment (PAD) and Policy Augmentation during Training (PAT). Comprehensive experiments in simulated environments demonstrate that the proposed model significantly improves both driving performance and robustness to variations in vehicle dynamics, outperforming existing approaches.