Current evaluations of large language models (LLMs) rely on benchmark scores, but it is difficult to interpret what these individual scores reveal about a model's overall skills. Specifically, as a community we lack understanding of how tasks relate to one another, what they measure in common, how they differ, or which ones are redundant. As a result, models are often assessed via a single score averaged across benchmarks, an approach that fails to capture the models' wholistic strengths and limitations. Here, we propose a new evaluation paradigm that uses factor analysis to identify latent skills driving performance across benchmarks. We apply this method to a comprehensive new leaderboard showcasing the performance of 60 LLMs on 44 tasks, and identify a small set of latent skills that largely explain performance. Finally, we turn these insights into practical tools that identify redundant tasks, aid in model selection, and profile models along each latent skill.

Recent advances in generative models, particularly diffusion and auto-regressive models, have revolutionized fields like computer vision and natural language processing. However, their application to structure-based drug design (SBDD) remains limited due to critical data constraints. To address the limitation of training data for models targeting SBDD tasks, we propose an evolutionary framework named MEVO, which bridges the gap between billion-scale small molecule dataset and the scarce protein-ligand complex dataset, and effectively increase the abundance of training data for generative SBDD models. MEVO is composed of three key components: a high-fidelity VQ-VAE for molecule representation in latent space, a diffusion model for pharmacophore-guided molecule generation, and a pocket-aware evolutionary strategy for molecule optimization with physics-based scoring function. This framework efficiently generate high-affinity binders for various protein targets, validated with predicted binding affinities using free energy perturbation (FEP) methods. In addition, we showcase the capability of MEVO in designing potent inhibitors to KRAS$^{\textrm{G12D}}$, a challenging target in cancer therapeutics, with similar affinity to the known highly active inhibitor evaluated by FEP calculations. With high versatility and generalizability, MEVO offers an effective and data-efficient model for various tasks in structure-based ligand design.

Graph Neural Networks (GNNs) have become a dominant approach to learning graph representations, primarily because of their message-passing mechanisms. However, GNNs typically adopt a fixed aggregator function such as Mean, Max, or Sum without principled reasoning behind the selection. This rigidity, especially in the presence of heterophily, often leads to poor, problem dependent performance. Although some attempts address this by designing more sophisticated aggregation functions, these methods tend to rely heavily on labeled data, which is often scarce in real-world tasks. In this work, we propose a novel unsupervised framework, "Aggregation-aware Multilayer Perceptron" (AMLP), which shifts the paradigm from directly crafting aggregation functions to making MLP adaptive to aggregation. Our lightweight approach consists of two key steps: First, we utilize a graph reconstruction method that facilitates high-order grouping effects, and second, we employ a single-layer network to encode varying degrees of heterophily, thereby improving the capacity and applicability of the model. Extensive experiments on node clustering and classification demonstrate the superior performance of AMLP, highlighting its potential for diverse graph learning scenarios.

In response to Distributed Denial of Service (DDoS) attacks, recent research efforts increasingly rely on Machine Learning (ML)-based solutions, whose effectiveness largely depends on the quality of labeled training datasets. To address the scarcity of such datasets, data augmentation with synthetic traces is often employed. However, current synthetic trace generation methods struggle to capture the complex temporal patterns and spatial distributions exhibited in emerging DDoS attacks. This results in insufficient resemblance to real traces and unsatisfied detection accuracy when applied to ML tasks. In this paper, we propose Dual-Stream Temporal-Field Diffusion (DSTF-Diffusion), a multi-view, multi-stream network traffic generative model based on diffusion models, featuring two main streams: The field stream utilizes spatial mapping to bridge network data characteristics with pre-trained realms of stable diffusion models, effectively translating complex network interactions into formats that stable diffusion can process, while the spatial stream adopts a dynamic temporal modeling approach, meticulously capturing the intrinsic temporal patterns of network traffic. Extensive experiments demonstrate that data generated by our model exhibits higher statistical similarity to originals compared to current state-of-the-art solutions, and enhance performances on a wide range of downstream tasks.

This perspective paper explores the future potential of "conversational intelligence" by examining how Large Language Models (LLMs) could be combined with GRAPHYP's network system to better understand human conversations and preferences. Using recent research and case studies, we propose a conceptual framework that could make AI rea-soning transparent and traceable, allowing humans to see and understand how AI reaches its conclusions. We present the conceptual perspective of "Matching Game Preferences through Dialogical Large Language Models (D-LLMs)," a proposed system that would allow multiple users to share their different preferences through structured conversations. This approach envisions personalizing LLMs by embedding individual user preferences directly into how the model makes decisions. The proposed D-LLM framework would require three main components: (1) reasoning processes that could analyze different search experiences and guide performance, (2) classification systems that would identify user preference patterns, and (3) dialogue approaches that could help humans resolve conflicting information. This perspective framework aims to create an interpretable AI system where users could examine, understand, and combine the different human preferences that influence AI responses, detected through GRAPHYP's search experience networks. The goal of this perspective is to envision AI systems that would not only provide answers but also show users how those answers were reached, making artificial intelligence more transparent and trustworthy for human decision-making.

The Model Context Protocol (MCP) represents a significant advancement in AI-tool integration, enabling seamless communication between AI agents and external services. However, this connectivity introduces novel attack vectors that remain largely unexplored. This paper demonstrates how unsophisticated threat actors, requiring only basic programming skills and free web tools, can exploit MCP's trust model to exfiltrate sensitive financial data. We present a proof-of-concept attack where a malicious weather MCP server, disguised as benign functionality, discovers and exploits legitimate banking tools to steal user account balances. The attack chain requires no advanced technical knowledge, server infrastructure, or monetary investment. The findings reveal a critical security gap in the emerging MCP ecosystem: while individual servers may appear trustworthy, their combination creates unexpected cross-server attack surfaces. Unlike traditional cybersecurity threats that assume sophisticated adversaries, our research shows that the barrier to entry for MCP-based attacks is alarmingly low. A threat actor with undergraduate-level Python knowledge can craft convincing social engineering attacks that exploit the implicit trust relationships MCP establishes between AI agents and tool providers. This work contributes to the nascent field of MCP security by demonstrating that current MCP implementations allow trivial cross-server attacks and proposing both immediate mitigations and protocol improvements to secure this emerging ecosystem.

Diffusion-based deep generative models have emerged as powerful tools for inverse materials design. Yet, many existing approaches overlook essential chemical constraints such as oxidation state balance, which can lead to chemically invalid structures. Here we introduce CrysVCD (Crystal generator with Valence-Constrained Design), a modular framework that integrates chemical rules directly into the generative process. CrysVCD first employs a transformer-based elemental language model to generate valence-balanced compositions, followed by a diffusion model to generate crystal structures. The valence constraint enables orders-of-magnitude more efficient chemical valence checking, compared to pure data-driven approaches with post-screening. When fine-tuned on stability metrics, CrysVCD achieves 85% thermodynamic stability and 68% phonon stability. Moreover, CrysVCD supports conditional generation of functional materials, enabling discovery of candidates such as high thermal conductivity semiconductors and high-$κ$ dielectric compounds. Designed as a general-purpose plugin, CrysVCD can be integrated into diverse generative pipeline to promote chemical validity, offering a reliable, scientifically grounded path for materials discovery.

The microphysical properties of ice crystals are important because they significantly alter the radiative properties and spatiotemporal distributions of clouds, which in turn strongly affect Earth's climate. However, it is challenging to measure key properties of ice crystals, such as mass or morphological features. Here, we present a framework for predicting three-dimensional (3D) microphysical properties of ice crystals from in situ two-dimensional (2D) imagery. First, we computationally generate synthetic ice crystals using 3D modeling software along with geometric parameters estimated from the 2021 Ice Cryo-Encapsulation Balloon (ICEBall) field campaign. Then, we use synthetic crystals to train machine learning (ML) models to predict effective density ($ρ_{e}$), effective surface area ($A_e$), and number of bullets ($N_b$) from synthetic rosette imagery. When tested on unseen synthetic images, we find that our ML models can predict microphysical properties with high accuracy. For $ρ_{e}$ and $A_e$, respectively, our best-performing single view models achieved $R^2$ values of 0.99 and 0.98. For $N_b$, our best single view model achieved a balanced accuracy and F1 score of 0.91. We also quantify the marginal prediction improvements from incorporating a second view. A stereo view ResNet-18 model reduced RMSE by 40% for both $ρ_e$ and $A_e$, relative to a single view ResNet-18 model. For $N_b$, we find that a stereo view ResNet-18 model improved the F1 score by 8%. This work provides a novel ML-driven framework for estimating ice microphysical properties from in situ imagery, which will allow for downstream constraints on microphysical parameterizations, such as the mass-size relationship.

The Controller Area Network (CAN) protocol is widely adopted for in-vehicle communication but lacks inherent security mechanisms, making it vulnerable to cyberattacks. This paper introduces KD-GAT, an intrusion detection framework that combines Graph Attention Networks (GATs) with knowledge distillation (KD) to enhance detection accuracy while reducing computational complexity. In our approach, CAN traffic is represented as graphs using a sliding window to capture temporal and relational patterns. A multi-layer GAT with jumping knowledge aggregation acting as the teacher model, while a compact student GAT--only 6.32% the size of the teacher--is trained via a two-phase process involving supervised pretraining and knowledge distillation with both soft and hard label supervision. Experiments on three benchmark datasets--Car-Hacking, Car-Survival, and can-train-and-test demonstrate that both teacher and student models achieve strong results, with the student model attaining 99.97% and 99.31% accuracy on Car-Hacking and Car-Survival, respectively. However, significant class imbalance in can-train-and-test has led to reduced performance for both models on this dataset. Addressing this imbalance remains an important direction for future work.

Due to the remarkable capabilities and growing impact of large language models (LLMs), they have been deeply integrated into many aspects of society. Thus, ensuring their alignment with human values and intentions has emerged as a critical challenge. This survey provides a comprehensive overview of practical alignment techniques, training protocols, and empirical findings in LLM alignment. We analyze the development of alignment methods across diverse paradigms, characterizing the fundamental trade-offs between core alignment objectives. Our analysis shows that while supervised fine-tuning enables basic instruction-following, preference-based methods offer more flexibility for aligning with nuanced human intent. We discuss state-of-the-art techniques, including Direct Preference Optimization (DPO), Constitutional AI, brain-inspired methods, and alignment uncertainty quantification (AUQ), highlighting their approaches to balancing quality and efficiency. We review existing evaluation frameworks and benchmarking datasets, emphasizing limitations such as reward misspecification, distributional robustness, and scalable oversight. We summarize strategies adopted by leading AI labs to illustrate the current state of practice. We conclude by outlining open problems in oversight, value pluralism, robustness, and continuous alignment. This survey aims to inform both researchers and practitioners navigating the evolving landscape of LLM alignment.