Unlike conventional "black-box" transformers with classical self-attention mechanism, we build a lightweight and interpretable transformer-like neural net by unrolling a mixed-graph-based optimization algorithm to forecast traffic with spatial and temporal dimensions. We construct two graphs: an undirected graph $\mathcal{G}^u$ capturing spatial correlations across geography, and a directed graph $\mathcal{G}^d$ capturing sequential relationships over time. We predict future samples of signal $\mathbf{x}$, assuming it is "smooth" with respect to both $\mathcal{G}^u$ and $\mathcal{G}^d$, where we design new $\ell_2$ and $\ell_1$-norm variational terms to quantify and promote signal smoothness (low-frequency reconstruction) on a directed graph. We design an iterative algorithm based on alternating direction method of multipliers (ADMM), and unroll it into a feed-forward network for data-driven parameter learning. We insert graph learning modules for $\mathcal{G}^u$ and $\mathcal{G}^d$ that play the role of self-attention. Experiments show that our unrolled networks achieve competitive traffic forecast performance as state-of-the-art prediction schemes, while reducing parameter counts drastically. Our code is available in https://github.com/SingularityUndefined/Unrolling-GSP-STForecast .

Despite their ability to understand chemical knowledge, large language models (LLMs) remain limited in their capacity to propose novel molecules with desired functions (e.g., drug-like properties). In addition, the molecules that LLMs propose can often be challenging to make, and are almost never compatible with automated synthesis approaches. To better enable the discovery of functional small molecules, LLMs need to learn a new molecular language that is more effective in predicting properties and inherently synced with automated synthesis technology. Current molecule LLMs are limited by representing molecules based on atoms. In this paper, we argue that just like tokenizing texts into meaning-bearing (sub-)word tokens instead of characters, molecules should be tokenized at the level of functional building blocks, i.e., parts of molecules that bring unique functions and serve as effective building blocks for real-world automated laboratory synthesis. This motivates us to propose mCLM, a modular Chemical-Language Model that comprises a bilingual language model that understands both natural language descriptions of functions and molecular blocks. mCLM front-loads synthesizability considerations while improving the predicted functions of molecules in a principled manner. mCLM, with only 3B parameters, achieves improvements in synthetic accessibility relative to 7 other leading generative AI methods including GPT-5. When tested on 122 out-of-distribution medicines using only building blocks/tokens that are compatible with automated modular synthesis, mCLM outperforms all baselines in property scores and synthetic accessibility. mCLM can also reason on multiple functions and iteratively self-improve to rescue drug candidates that failed late in clinical trials ("fallen angels").

1-Lipschitz neural networks are fundamental for generative modelling, inverse problems, and robust classifiers. In this paper, we focus on 1-Lipschitz residual networks (ResNets) based on explicit Euler steps of negative gradient flows and study their approximation capabilities. Leveraging the Restricted Stone-Weierstrass Theorem, we first show that these 1-Lipschitz ResNets are dense in the set of scalar 1-Lipschitz functions on any compact domain when width and depth are allowed to grow. We also show that these networks can exactly represent scalar piecewise affine 1-Lipschitz functions. We then prove a stronger statement: by inserting norm-constrained linear maps between the residual blocks, the same density holds when the hidden width is fixed. Because every layer obeys simple norm constraints, the resulting models can be trained with off-the-shelf optimisers. This paper provides the first universal approximation guarantees for 1-Lipschitz ResNets, laying a rigorous foundation for their practical use.

We propose the first unified adversarial attack benchmark for Genomic Foundation Models (GFMs), named GenoArmory. Unlike existing GFM benchmarks, GenoArmory offers the first comprehensive evaluation framework to systematically assess the vulnerability of GFMs to adversarial attacks. Methodologically, we evaluate the adversarial robustness of five state-of-the-art GFMs using four widely adopted attack algorithms and three defense strategies. Importantly, our benchmark provides an accessible and comprehensive framework to analyze GFM vulnerabilities with respect to model architecture, quantization schemes, and training datasets. Additionally, we introduce GenoAdv, a new adversarial sample dataset designed to improve GFM safety. Empirically, classification models exhibit greater robustness to adversarial perturbations compared to generative models, highlighting the impact of task type on model vulnerability. Moreover, adversarial attacks frequently target biologically significant genomic regions, suggesting that these models effectively capture meaningful sequence features.

The rapid development of Multimodal Large Reasoning Models (MLRMs) has demonstrated broad application potential, yet their safety and reliability remain critical concerns that require systematic exploration. To address this gap, we conduct a comprehensive and systematic safety evaluation of 11 MLRMs across 5 benchmarks and unveil prevalent safety degradation phenomena in most advanced models. Moreover, our analysis reveals distinct safety patterns across different benchmarks: significant safety degradation is observed across jailbreak robustness benchmarks, whereas safety-awareness benchmarks demonstrate less pronounced degradation. In particular, the long thought process in some scenarios even enhances safety performance. Therefore, it is a potential approach to address safety issues in MLRMs by leveraging the intrinsic reasoning capabilities of the model to detect unsafe intent. To operationalize this insight, we construct a multimodal tuning dataset that incorporates a safety-oriented thought process. Experimental results from fine-tuning existing MLRMs with this dataset effectively enhances the safety on both jailbreak robustness and safety-awareness benchmarks. This study provides a new perspective for developing safe MLRMs. Our dataset is available at https://github.com/xinyuelou/Think-in-Safety.

Retrieval-augmented generation (RAG) has become a widely adopted paradigm for enabling knowledge-grounded large language models (LLMs). However, standard RAG pipelines often fail to ensure that model reasoning remains consistent with the evidence retrieved, leading to factual inconsistencies or unsupported conclusions. In this work, we reinterpret RAG as Retrieval-Augmented Reasoning and identify a central but underexplored problem: Reasoning Misalignment -- the divergence between an LLM's internal reasoning trajectory and the evidential constraints provided by retrieval. To address this issue, we propose AlignRAG, a novel iterative framework grounded in Critique-Driven Alignment (CDA). We further introduce AlignRAG-auto, an autonomous variant that dynamically terminates refinement, removing the need to pre-specify the number of critique iterations. At the heart of AlignRAG lies a contrastive critique synthesis mechanism that generates retrieval-sensitive critiques while mitigating self-bias. This mechanism trains a dedicated retrieval-augmented Critic Language Model (CLM) using labeled critiques that distinguish between evidence-aligned and misaligned reasoning. Empirical evaluations show that our approach significantly improves reasoning fidelity. Our 8B-parameter CLM improves performance over the Self-Refine baseline by 12.1% on out-of-domain tasks and outperforms a standard 72B-parameter CLM by 2.2%. Furthermore, AlignRAG-auto achieves this state-of-the-art performance while dynamically determining the optimal number of refinement steps, enhancing efficiency and usability. AlignRAG remains compatible with existing RAG architectures as a plug-and-play module and demonstrates strong robustness under both informative and noisy retrieval scenarios.

Large Language Models (LLMs) have recently demonstrated strong capabilities in code-related tasks, but their robustness in code reasoning under perturbations remains underexplored. We introduce CodeCrash, a stress-testing framework with 1,279 questions from CruxEval and LiveCodeBench, designed to evaluate reasoning reliability under structural perturbations and misleading natural language (NL) contexts. Through a systematic evaluation of 17 LLMs, we find that models often shortcut reasoning by over-relying on NL cues, leading to an average performance degradation of 23.2% in output prediction tasks. Even with Chain-of-Thought reasoning, models on average still have a 13.8% drop due to distractibility and rationalization, revealing a lack of critical reasoning capability to distinguish the actual code behaviors. While Large Reasoning Models with internal reasoning mechanisms improve robustness by fostering critical thinking, plausible yet incorrect hints can trigger pathological self-reflection, causing 2-3 times token consumption and even catastrophic cognitive dissonance in extreme cases for QwQ-32B. We refer to this phenomenon as Reasoning Collapse. CodeCrash provides a rigorous benchmark for evaluating robustness in code reasoning, guiding future research and development toward more reliable and resilient models.

WebShell attacks, where malicious scripts are injected into web servers, pose a significant cybersecurity threat. Traditional ML and DL methods are often hampered by challenges such as the need for extensive training data, catastrophic forgetting, and poor generalization. Recently, Large Language Models have emerged as powerful alternatives for code-related tasks, but their potential in WebShell detection remains underexplored. In this paper, we make two contributions: (1) a comprehensive evaluation of seven LLMs, including GPT-4, LLaMA 3.1 70B, and Qwen 2.5 variants, benchmarked against traditional sequence- and graph-based methods using a dataset of 26.59K PHP scripts, and (2) the Behavioral Function-Aware Detection (BFAD) framework, designed to address the specific challenges of applying LLMs to this domain. Our framework integrates three components: a Critical Function Filter that isolates malicious PHP function calls, a Context-Aware Code Extraction strategy that captures the most behaviorally indicative code segments, and Weighted Behavioral Function Profiling that enhances in-context learning by prioritizing the most relevant demonstrations based on discriminative function-level profiles. Our results show that, stemming from their distinct analytical strategies, larger LLMs achieve near-perfect precision but lower recall, while smaller models exhibit the opposite trade-off. However, all baseline models lag behind previous SOTA methods. With the application of BFAD, the performance of all LLMs improves significantly, yielding an average F1 score increase of 13.82%. Notably, larger models now outperform SOTA benchmarks, while smaller models such as Qwen-2.5-Coder-3B achieve performance competitive with traditional methods. This work is the first to explore the feasibility and limitations of LLMs for WebShell detection and provides solutions to address the challenges in this task.

Aligning Vision-Language Models (VLMs) with safety standards is essential to mitigate risks arising from their multimodal complexity, where integrating vision and language unveils subtle threats beyond the reach of conventional safeguards. Inspired by the insight that reasoning across modalities is key to preempting intricate vulnerabilities, we propose a novel direction for VLM safety: multimodal reasoning-driven prompt rewriting. To this end, we introduce VLMGuard-R1, a proactive framework that refines user inputs through a reasoning-guided rewriter, dynamically interpreting text-image interactions to deliver refined prompts that bolster safety across diverse VLM architectures without altering their core parameters. To achieve this, we devise a three-stage reasoning pipeline to synthesize a dataset that trains the rewriter to infer subtle threats, enabling tailored, actionable responses over generic refusals. Extensive experiments across three benchmarks with five VLMs reveal that VLMGuard-R1 outperforms four baselines. In particular, VLMGuard-R1 achieves a remarkable 43.59\% increase in average safety across five models on the SIUO benchmark.

Attention mechanisms underpin modern deep learning, while the quadratic time and space complexity limit scalability for long sequences. To address this, Quantum Annealing Multi-Head Attention (QAMA) is proposed, a novel drop-in operator that reformulates attention as an energy-based Hamiltonian optimization problem. In this framework, token interactions are encoded into binary quadratic terms, and quantum annealing is employed to search for low-energy configurations that correspond to effective attention patterns. Unlike classical sparse or approximate attention methods that rely on hand-crafted heuristics, QAMA allows sparsity structures to emerge naturally from the optimization process. Theoretically, computational complexity is analysed through single-spin flip dynamics, providing time to solution runtime bounds that depend on the spectral properties of the annealing Hamiltonian. Empirically, evaluation on both natural language and vision benchmarks shows that, across tasks, accuracy deviates by at most 2.7 points from standard multi-head attention, while requiring only linear qubits in sequence length. Visualizations further reveal that the Hamiltonian penalty terms induce meaningful and interpretable sparsity across heads. Finally, deployment on a coherent Ising machine validates the feasibility of running QAMA on real quantum hardware, showing tangible inference-time reductions compared with classical implementations. These results highlight QAMA as a pioneering and scalable step toward integrating quantum optimization devices into deep neural architectures, providing a seamlessly integrable and hardware-compatible alternative to conventional attention mechanisms. This work has been submitted to the IEEE for possible publication. Copyright may be transferred without notice, after which this version may no longer be accessible.