Vision-language models (VLMs) often produce chain-of-thought (CoT) explanations that sound plausible yet fail to reflect the underlying decision process, undermining trust in high-stakes clinical use. Existing evaluations rarely catch this misalignment, prioritizing answer accuracy or adherence to formats. We present a clinically grounded framework for chest X-ray visual question answering (VQA) that probes CoT faithfulness via controlled text and image modifications across three axes: clinical fidelity, causal attribution, and confidence calibration. In a reader study (n=4), evaluator-radiologist correlations fall within the observed inter-radiologist range for all axes, with strong alignment for attribution (Kendall's $τ_b=0.670$), moderate alignment for fidelity ($τ_b=0.387$), and weak alignment for confidence tone ($τ_b=0.091$), which we report with caution. Benchmarking six VLMs shows that answer accuracy and explanation quality can be decoupled, acknowledging injected cues does not ensure grounding, and text cues shift explanations more than visual cues. While some open-source models match final answer accuracy, proprietary models score higher on attribution (25.0% vs. 1.4%) and often on fidelity (36.1% vs. 31.7%), highlighting deployment risks and the need to evaluate beyond final answer accuracy.

Retrieval-Augmented Generation (RAG) is widely used to mitigate hallucinations of Large Language Models (LLMs) by leveraging external knowledge. While effective for simple queries, traditional RAG systems struggle with large-scale, unstructured corpora where information is fragmented. Recent advances incorporate knowledge graphs to capture relational structures, enabling more comprehensive retrieval for complex, multi-hop reasoning tasks. However, existing graph-based RAG (GraphRAG) methods rely on unstable and costly relation extraction for graph construction, often producing noisy graphs with incorrect or inconsistent relations that degrade retrieval quality. In this paper, we revisit the pipeline of existing GraphRAG systems and propose LinearRAG (Linear Graph-based Retrieval-Augmented Generation), an efficient framework that enables reliable graph construction and precise passage retrieval. Specifically, LinearRAG constructs a relation-free hierarchical graph, termed Tri-Graph, using only lightweight entity extraction and semantic linking, avoiding unstable relation modeling. This new paradigm of graph construction scales linearly with corpus size and incurs no extra token consumption, providing an economical and reliable indexing of the original passages. For retrieval, LinearRAG adopts a two-stage strategy: (i) relevant entity activation via local semantic bridging, followed by (ii) passage retrieval through global importance aggregation. Extensive experiments on four datasets demonstrate that LinearRAG significantly outperforms baseline models. Our code and datasets are available at https://github.com/DEEP-PolyU/LinearRAG.

Genomic Selection (GS) uses whole-genome information to predict crop phenotypes and accelerate breeding. Traditional GS methods, however, struggle with prediction accuracy for complex traits and large datasets. We propose DPCformer, a deep learning model integrating convolutional neural networks with a self-attention mechanism to model complex genotype-phenotype relationships. We applied DPCformer to 13 traits across five crops (maize, cotton, tomato, rice, chickpea). Our approach uses an 8-dimensional one-hot encoding for SNP data, ordered by chromosome, and employs the PMF algorithm for feature selection. Evaluations show DPCformer outperforms existing methods. In maize datasets, accuracy for traits like days to tasseling and plant height improved by up to 2.92%. For cotton, accuracy gains for fiber traits reached 8.37%. On small-sample tomato data, the Pearson Correlation Coefficient for a key trait increased by up to 57.35%. In chickpea, the yield correlation was boosted by 16.62%. DPCformer demonstrates superior accuracy, robustness in small-sample scenarios, and enhanced interpretability, providing a powerful tool for precision breeding and addressing global food security challenges.

Real-world evaluation of perception-based planning models for robotic systems, such as autonomous vehicles, can be safely and inexpensively conducted offline, i.e. by computing model prediction error over a pre-collected validation dataset with ground-truth annotations. However, extrapolating from offline model performance to online settings remains a challenge. In these settings, seemingly minor errors can compound and result in test-time infractions or collisions. This relationship is understudied, particularly across diverse closed-loop metrics and complex urban maneuvers. In this work, we revisit this undervalued question in policy evaluation through an extensive set of experiments across diverse conditions and metrics. Based on analysis in simulation, we find an even worse correlation between offline and online settings than reported by prior studies, casting doubts on the validity of current evaluation practices and metrics for driving policies. Next, we bridge the gap between offline and online evaluation. We investigate an offline metric based on epistemic uncertainty, which aims to capture events that are likely to cause errors in closed-loop settings. The resulting metric achieves over 13% improvement in correlation compared to previous offline metrics. We further validate the generalization of our findings beyond the simulation environment in real-world settings, where even greater gains are observed.

This work presents a systematic investigation into the latent knowledge encoded within Network Foundation Models (NFMs) that focuses on hidden representations analysis rather than pure downstream task performance. Different from existing efforts, we analyze the models through a three-part evaluation: Embedding Geometry Analysis to assess representation space utilization, Metric Alignment Assessment to measure correspondence with domain-expert features, and Causal Sensitivity Testing to evaluate robustness to protocol perturbations. Using five diverse network datasets spanning controlled and real-world environments, we evaluate four state-of-the-art NFMs, revealing that they all exhibit significant anisotropy, inconsistent feature sensitivity patterns, an inability to separate the high-level context, payload dependency, and other properties. Our work identifies numerous limitations across all models and demonstrates that addressing them can significantly improve model performance (by up to +0.35 $F_1$ score without architectural changes).

This article presents two corpora of English and Czech texts generated with large language models (LLMs). The motivation is to create a resource for comparing human-written texts with LLM-generated text linguistically. Emphasis was placed on ensuring these resources are multi-genre and rich in terms of topics, authors, and text types, while maintaining comparability with existing human-created corpora. These generated corpora replicate reference human corpora: BE21 by Paul Baker, which is a modern version of the original Brown Corpus, and Koditex corpus that also follows the Brown Corpus tradition but in Czech. The new corpora were generated using models from OpenAI, Anthropic, Alphabet, Meta, and DeepSeek, ranging from GPT-3 (davinci-002) to GPT-4.5, and are tagged according to the Universal Dependencies standard (i.e., they are tokenized, lemmatized, and morphologically and syntactically annotated). The subcorpus size varies according to the model used (the English part contains on average 864k tokens per model, 27M tokens altogether, the Czech partcontains on average 768k tokens per model, 21.5M tokens altogether). The corpora are freely available for download under the CC BY 4.0 license (the annotated data are under CC BY-NC-SA 4.0 licence) and are also accessible through the search interface of the Czech National Corpus.

Hydrogen is the most abundant element in our Universe. The first generation of stars and galaxies produced photons that ionized hydrogen gas, driving a cosmological event known as the Epoch of Reionization (EoR). The upcoming Square Kilometre Array Observatory (SKAO) will map the distribution of neutral hydrogen during this era, aiding in the study of the properties of these first-generation objects. Extracting astrophysical information will be challenging, as SKAO will produce a tremendous amount of data where the hydrogen signal will be contaminated with undesired foreground contamination and instrumental systematics. To address this, we develop the latest deep learning techniques to extract information from the 2D power spectra of the hydrogen signal expected from SKAO. We apply a series of neural network models to these measurements and quantify their ability to predict the history of cosmic hydrogen reionization, which is connected to the increasing number and efficiency of early photon sources. We show that the study of the early Universe benefits from modern deep learning technology. In particular, we demonstrate that dedicated machine learning algorithms can achieve more than a $0.95$ $R^2$ score on average in recovering the reionization history. This enables accurate and precise cosmological and astrophysical inference of structure formation in the early Universe.

Long context training is crucial for LLM's context extension. Existing schemes, such as sequence parallelism, incur substantial communication overhead. Pipeline parallelism (PP) reduces this cost, but its effectiveness hinges on partitioning granularity. Batch-level PP dividing input samples exhibits high memory consumption in long-context scenario, whereas token-level PP splitting sequences into slices alleviates memory overhead but may incur hardware under-utilization. This trade-off motivates adaptively selecting PP granularity to match resource and workload characteristics. Moreover, sequence length distribution of the real-world dataset exhibits skewness, posing a challenge on PP's workload balance and efficient scheduling. Current static PP scheduling methods overlook the variance of sequence length, leading to suboptimal performance. In this paper, we propose Elastic Pipeline Parallelism (EPP) that orchestrates token-level PP and batch-level PP to adapt to resource and workload heterogeneity. We build InfiniPipe, a distributed training system that unleashes the potential of EPP via (1) a resource-aware and workload-balanced sequence processor that splits long sequences and packs short ones; and (2) a co-optimization methodology that jointly optimizes pipeline schedule and gradient checkpointing via a mechanism named stage-aware chunk-level adaptive checkpointing. Comprehensive experiments demonstrate that InfiniPipe achieves a 1.69x speedup over state-of-the-art systems.

The emergence of Vision Language Action (VLA) models marks a paradigm shift from traditional policy-based control to generalized robotics, reframing Vision Language Models (VLMs) from passive sequence generators into active agents for manipulation and decision-making in complex, dynamic environments. This survey delves into advanced VLA methods, aiming to provide a clear taxonomy and a systematic, comprehensive review of existing research. It presents a comprehensive analysis of VLA applications across different scenarios and classifies VLA approaches into several paradigms: autoregression-based, diffusion-based, reinforcement-based, hybrid, and specialized methods; while examining their motivations, core strategies, and implementations in detail. In addition, foundational datasets, benchmarks, and simulation platforms are introduced. Building on the current VLA landscape, the review further proposes perspectives on key challenges and future directions to advance research in VLA models and generalizable robotics. By synthesizing insights from over three hundred recent studies, this survey maps the contours of this rapidly evolving field and highlights the opportunities and challenges that will shape the development of scalable, general-purpose VLA methods.

Graph-based Retrieval-augmented generation (RAG) has become a widely studied approach for improving the reasoning, accuracy, and factuality of Large Language Models (LLMs). However, many existing graph-based RAG systems overlook the high cost associated with LLM token usage during graph construction, hindering large-scale adoption. To address this, we propose TERAG, a simple yet effective framework designed to build informative graphs at a significantly lower cost. Inspired by HippoRAG, we incorporate Personalized PageRank (PPR) during the retrieval phase, and we achieve at least 80% of the accuracy of widely used graph-based RAG methods while consuming only 3%-11% of the output tokens. With its low token footprint and efficient construction pipeline, TERAG is well-suited for large-scale and cost-sensitive deployment scenarios.