This paper addresses the critical challenge of deriving interpretable confidence scores from generative language models (LLMs) when applied to multi-label content safety classification. While models like LLaMA Guard are effective for identifying unsafe content and its categories, their generative architecture inherently lacks direct class-level probabilities, which hinders model confidence assessment and performance interpretation. This limitation complicates the setting of dynamic thresholds for content moderation and impedes fine-grained error analysis. This research proposes and evaluates three novel token-level probability estimation approaches to bridge this gap. The aim is to enhance model interpretability and accuracy, and evaluate the generalizability of this framework across different instruction-tuned models. Through extensive experimentation on a synthetically generated, rigorously annotated dataset, it is demonstrated that leveraging token logits significantly improves the interpretability and reliability of generative classifiers, enabling more nuanced content safety moderation.

Designing proteins de novo with tailored structural, physicochemical, and functional properties remains a grand challenge in biotechnology, medicine, and materials science, due to the vastness of sequence space and the complex coupling between sequence, structure, and function. Current state-of-the-art generative methods, such as protein language models (PLMs) and diffusion-based architectures, often require extensive fine-tuning, task-specific data, or model reconfiguration to support objective-directed design, thereby limiting their flexibility and scalability. To overcome these limitations, we present a decentralized, agent-based framework inspired by swarm intelligence for de novo protein design. In this approach, multiple large language model (LLM) agents operate in parallel, each assigned to a specific residue position. These agents iteratively propose context-aware mutations by integrating design objectives, local neighborhood interactions, and memory and feedback from previous iterations. This position-wise, decentralized coordination enables emergent design of diverse, well-defined sequences without reliance on motif scaffolds or multiple sequence alignments, validated with experiments on proteins with alpha helix and coil structures. Through analyses of residue conservation, structure-based metrics, and sequence convergence and embeddings, we demonstrate that the framework exhibits emergent behaviors and effective navigation of the protein fitness landscape. Our method achieves efficient, objective-directed designs within a few GPU-hours and operates entirely without fine-tuning or specialized training, offering a generalizable and adaptable solution for protein design. Beyond proteins, the approach lays the groundwork for collective LLM-driven design across biomolecular systems and other scientific discovery tasks.

Numerical simulations have revolutionized the industrial design process by reducing prototyping costs, design iterations, and enabling product engineers to explore the design space more efficiently. However, the growing scale of simulations demands substantial expert knowledge, computational resources, and time. A key challenge is identifying input parameters that yield optimal results, as iterative simulations are costly and can have a large environmental impact. This paper presents an AI-assisted workflow that reduces expert involvement in parameter optimization through the use of Bayesian optimization. Furthermore, we present an active learning variant of the approach, assisting the expert if desired. A deep learning model provides an initial parameter estimate, from which the optimization cycle iteratively refines the design until a termination condition (e.g., energy budget or iteration limit) is met. We demonstrate our approach, based on a sheet metal forming process, and show how it enables us to accelerate the exploration of the design space while reducing the need for expert involvement.

Forecasting tumor growth is critical for optimizing treatment. Classical growth models such as the Gompertz and Bertalanffy equations capture general tumor dynamics but may fail to adapt to patient-specific variability, particularly with limited data available. In this study, we leverage Neural Ordinary Differential Equations (Neural ODEs) and Universal Differential Equations (UDEs), two pillars of Scientific Machine Learning (SciML), to construct adaptive tumor growth models capable of learning from experimental data. Using the Gompertz model as a baseline, we replace rigid terms with adaptive neural networks to capture hidden dynamics through robust modeling in the Julia programming language. We use our models to perform forecasting under data constraints and symbolic recovery to transform the learned dynamics into explicit mathematical expressions. Our approach has the potential to improve predictive accuracy, guiding dynamic and effective treatment strategies for improved clinical outcomes.

Large language models (LLMs) have shown remarkable ability to generate code, yet their outputs often violate syntactic or semantic constraints when guided only through natural language prompts. We introduce TreeCoder, the most general and flexible framework to date for exploring decoding strategies, constraints, and hyperparameters in LLMs, and use it in code generation to enforce correctness and structure during decoding rather than relying on prompt engineering. TreeCoder represents decoding as a tree search over candidate programs, where both decoding strategies and constraint functions - such as style, syntax, execution - are treated as first-class, optimisable components. This design enables systematic exploration and automatic tuning of decoding configurations using standard optimisation techniques. Experiments on the MBPP (Python) and SQL-Spider benchmarks show that TreeCoder consistently improves accuracy across open-source models such as CodeLlama, Mistral and DeepSeek, often outperforming their unconstrained baselines by considerable margins.

Large Language models are revolutionizing the conversational recommender systems through their impressive capabilities in instruction comprehension, reasoning, and human interaction. A core factor underlying effective recommendation dialogue is the ability to infer and reason about users' mental states (such as desire, intention, and belief), a cognitive capacity commonly referred to as Theory of Mind. Despite growing interest in evaluating ToM in LLMs, current benchmarks predominantly rely on synthetic narratives inspired by Sally-Anne test, which emphasize physical perception and fail to capture the complexity of mental state inference in realistic conversational settings. Moreover, existing benchmarks often overlook a critical component of human ToM: behavioral prediction, the ability to use inferred mental states to guide strategic decision-making and select appropriate conversational actions for future interactions. To better align LLM-based ToM evaluation with human-like social reasoning, we propose RecToM, a novel benchmark for evaluating ToM abilities in recommendation dialogues. RecToM focuses on two complementary dimensions: Cognitive Inference and Behavioral Prediction. The former focus on understanding what has been communicated by inferring the underlying mental states. The latter emphasizes what should be done next, evaluating whether LLMs can leverage these inferred mental states to predict, select, and assess appropriate dialogue strategies. Extensive experiments on state-of-the-art LLMs demonstrate that RecToM poses a significant challenge. While the models exhibit partial competence in recognizing mental states, they struggle to maintain coherent, strategic ToM reasoning throughout dynamic recommendation dialogues, particularly in tracking evolving intentions and aligning conversational strategies with inferred mental states.

Machine learning, and in particular its modern incarnation of deep learning (DL) [1, 2], has become an indispensable tool in particle physics, a field that routinely handles vast datasets and nonlinear relationships among observables [3-6]. In recent years, advances in DL have expanded the scope of data-driven progress across the energy, intensity, accelerator, and cosmic frontiers [7, 8]. Despite remarkable advancements, most current DL applications in particle physics are supervised, relying either on Monte Carlo (MC) simulations or on labeled experimental data. However, because simulations cannot fully capture the complexity of the real world, a persistent gap between MC and Data leads to training bias. Direct training on real data, in turn, demands extensive human labeling, which is labor-intensive and hard to scale [9]. For this reason, the development of unsupervised DL [10, 11] is integral for particle physics. Unsupervised learning has achieved remarkable success in tasks such as clustering [12, 13], anomaly detection [14, 15], and learning representations [16, 17].

The interaction between proteins and nucleic acids is crucial for processes that sustain cellular function, including DNA maintenance and the regulation of gene expression and translation. Amino acid mutat ions in protein - nucleic acid complexes often lead to vital disease s . Experimental techniques have their own specific limitations in predicting mutational effects in protein - nucleic acid complexes . In this study, we compiled a large dataset of 1951 mutations including both protein - DNA and protein - RNA complexes and integrate d structural and sequential features to build a deep learning - based regression model named DeepPNI . This model estimates mutation - induced binding free energy changes in protein - nucleic aci d complexes . The structural feature s are encoded via edge - aware RGCN and the sequential feature s are extracted using protein language model ESM - 2. W e have achieved a high average Pearson correlation coeffi cient (PCC) of 0.76 in the large dataset via five - fold cross - validation. Consistent performance across individual dataset of protein - DNA, protein - RNA complexes, and different experimental temperature split dataset make the model g eneralizable . Our model showed g ood performance in complex - based five - fold cross - validation, which prove d its robustness. In addition, DeepPNI outperform ed in e xternal dataset validation, and compar ison with existing tools .

The standard theory of model-free reinforcement learning assumes that the environment dynamics are stationary and that agents are decoupled from their environment, such that policies are treated as being separate from the world they inhabit. This leads to theoretical challenges in the multi-agent setting where the non-stationarity induced by the learning of other agents demands prospective learning based on prediction models. To accurately model other agents, an agent must account for the fact that those other agents are, in turn, forming beliefs about it to predict its future behavior, motivating agents to model themselves as part of the environment. Here, building upon foundational work on universal artificial intelligence (AIXI), we introduce a mathematical framework for prospective learning and embedded agency centered on self-prediction, where Bayesian RL agents predict both future perceptual inputs and their own actions, and must therefore resolve epistemic uncertainty about themselves as part of the universe they inhabit. We show that in multi-agent settings, self-prediction enables agents to reason about others running similar algorithms, leading to new game-theoretic solution concepts and novel forms of cooperation unattainable by classical decoupled agents. Moreover, we extend the theory of AIXI, and study universally intelligent embedded agents which start from a Solomonoff prior. We show that these idealized agents can form consistent mutual predictions and achieve infinite-order theory of mind, potentially setting a gold standard for embedded multi-agent learning.

Online pornography and gambling have consistently posed regulatory challenges for governments, threatening both personal assets and privacy. Therefore, it is imperative to research the classification of the newly registered Pornographic and Gambling Domain Names (PGDN). However, scholarly investigation into this topic is limited. Previous efforts in PGDN classification pursue high accuracy using ideal sample data, while others employ up-to-date data from real-world scenarios but achieve lower classification accuracy. This paper introduces the Real-PGDN method, which accomplishes a complete process of timely and comprehensive real-data crawling, feature extraction with feature-missing tolerance, precise PGDN classification, and assessment of application effects in actual scenarios. Our two-level classifier, which integrates CoSENT (BERT-based), Multilayer Perceptron (MLP), and traditional classification algorithms, achieves a 97.88% precision. The research process amasses the NRD2024 dataset, which contains continuous detection information over 20 days for 1,500,000 newly registered domain names across 6 directions. Results from our case study demonstrate that this method also maintains a forecast precision of over 70% for PGDN that are delayed in usage after registration.