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PPDiff: Diffusing in Hybrid Sequence-Structure Space for Protein-Protein Complex Design

arXiv.org Artificial Intelligence

Designing protein-binding proteins with high affinity is critical in biomedical research and biotechnology. Despite recent advancements targeting specific proteins, the ability to create high-affinity binders for arbitrary protein targets on demand, without extensive rounds of wet-lab testing, remains a significant challenge. Here, we introduce PPDiff, a diffusion model to jointly design the sequence and structure of binders for arbitrary protein targets in a non-autoregressive manner. PPDiffbuilds upon our developed Sequence Structure Interleaving Network with Causal attention layers (SSINC), which integrates interleaved self-attention layers to capture global amino acid correlations, k-nearest neighbor (kNN) equivariant graph layers to model local interactions in three-dimensional (3D) space, and causal attention layers to simplify the intricate interdependencies within the protein sequence. To assess PPDiff, we curate PPBench, a general protein-protein complex dataset comprising 706,360 complexes from the Protein Data Bank (PDB). The model is pretrained on PPBenchand finetuned on two real-world applications: target-protein mini-binder complex design and antigen-antibody complex design. PPDiffconsistently surpasses baseline methods, achieving success rates of 50.00%, 23.16%, and 16.89% for the pretraining task and the two downstream applications, respectively. The code, data and models are available at https://github.com/JocelynSong/PPDiff.


RADAR: Benchmarking Language Models on Imperfect Tabular Data

arXiv.org Artificial Intelligence

Language models (LMs) are increasingly being deployed to perform autonomous data analyses. However, their data awareness -- the ability to recognize, reason over, and appropriately handle data artifacts such as missing values, outliers, and logical inconsistencies -- remains underexplored. These artifacts are especially common in real-world tabular data and, if mishandled, can significantly compromise the validity of analytical conclusions. To address this gap, we present RADAR, a benchmark for systematically evaluating data-aware reasoning on tabular data. We develop a framework to simulate data artifacts via programmatic perturbations to enable targeted evaluation of model behavior. RADAR comprises 2980 table query pairs, grounded in real-world data spanning 9 domains and 5 data artifact types. In addition to evaluating artifact handling, RADAR systematically varies table size to study how reasoning performance holds when increasing table size. Our evaluation reveals that, despite decent performance on tables without data artifacts, frontier models degrade significantly when data artifacts are introduced, exposing critical gaps in their capacity for robust, data-aware analysis. Designed to be flexible and extensible, RADAR supports diverse perturbation types and controllable table sizes, offering a valuable resource for advancing tabular reasoning.


Absorb and Converge: Provable Convergence Guarantee for Absorbing Discrete Diffusion Models

arXiv.org Artificial Intelligence

Discrete state space diffusion models have shown significant advantages in applications involving discrete data, such as text and image generation. It has also been observed that their performance is highly sensitive to the choice of rate matrices, particularly between uniform and absorbing rate matrices. While empirical results suggest that absorbing rate matrices often yield better generation quality compared to uniform rate matrices, existing theoretical works have largely focused on the uniform rate matrices case. Notably, convergence guarantees and error analyses for absorbing diffusion models are still missing. In this work, we provide the first finite-time error bounds and convergence rate analysis for discrete diffusion models using absorbing rate matrices. We begin by deriving an upper bound on the KL divergence of the forward process, introducing a surrogate initialization distribution to address the challenge posed by the absorbing stationary distribution, which is a singleton and causes the KL divergence to be ill-defined. We then establish the first convergence guarantees for both the $ฯ„$-leaping and uniformization samplers under absorbing rate matrices, demonstrating improved rates over their counterparts using uniform rate matrices. Furthermore, under suitable assumptions, we provide convergence guarantees without early stopping. Our analysis introduces several new technical tools to address challenges unique to absorbing rate matrices. These include a Jensen-type argument for bounding forward process convergence, novel techniques for bounding absorbing score functions, and a non-divergent upper bound on the score near initialization that removes the need of early-stopping.


Rethinking Metrics and Benchmarks of Video Anomaly Detection

arXiv.org Artificial Intelligence

Video Anomaly Detection (VAD), which aims to detect anomalies that deviate from expectation, has attracted increasing attention in recent years. Existing advancements in VAD primarily focus on model architectures and training strategies, while devoting insufficient attention to evaluation metrics and benchmarks. In this paper, we rethink VAD evaluation methods through comprehensive analyses, revealing three critical limitations in current practices: 1) existing metrics are significantly influenced by single annotation bias; 2) current metrics fail to reward early detection of anomalies; 3) available benchmarks lack the capability to evaluate scene overfitting of fully/weakly-supervised algorithms. To address these limitations, we propose three novel evaluation methods: first, we establish probabilistic AUC/AP (Prob-AUC/AP) metrics utlizing multi-round annotations to mitigate single annotation bias; second, we develop a Latency-aware Average Precision (LaAP) metric that rewards early and accurate anomaly detection; and finally, we introduce two hard normal benchmarks (UCF-HN, MSAD-HN) with videos specifically designed to evaluate scene overfitting. We report performance comparisons of ten state-of-the-art VAD approaches using our proposed evaluation methods, providing novel perspectives for future VAD model development. We release our data and code in https://github.com/Kamino666/RethinkingVAD.


Dynamic Risk Assessments for Offensive Cybersecurity Agents

arXiv.org Artificial Intelligence

Foundation models are increasingly becoming better autonomous programmers, raising the prospect that they could also automate dangerous offensive cyber-operations. Current frontier model audits probe the cybersecurity risks of such agents, but most fail to account for the degrees of freedom available to adversaries in the real world. In particular, with strong verifiers and financial incentives, agents for offensive cybersecurity are amenable to iterative improvement by would-be adversaries. We argue that assessments should take into account an expanded threat model in the context of cybersecurity, emphasizing the varying degrees of freedom that an adversary may possess in stateful and non-stateful environments within a fixed compute budget. We show that even with a relatively small compute budget (8 H100 GPU Hours in our study), adversaries can improve an agent's cybersecurity capability on InterCode CTF by more than 40\% relative to the baseline -- without any external assistance. These results highlight the need to evaluate agents' cybersecurity risk in a dynamic manner, painting a more representative picture of risk.


GAIA: A Foundation Model for Operational Atmospheric Dynamics

arXiv.org Artificial Intelligence

We introduce GAIA (Geospatial Artificial Intelligence for Atmospheres), a hybrid self-supervised geospatial foundation model that fuses Masked Autoencoders (MAE) with self-distillation with no labels (DINO) to generate semantically rich representations from global geostationary satellite imagery. Pre-trained on 15 years of globally-merged infrared observations (2001-2015), GAIA learns disentangled representations that capture atmospheric dynamics rather than trivial diurnal patterns, as evidenced by distributed principal component structure and temporal coherence analysis. We demonstrate robust reconstruction capabilities across varying data availability (30-95% masking), achieving superior gap-filling performance on real missing data patterns. When transferred to downstream tasks, GAIA consistently outperforms an MAE-only baseline: improving atmospheric river segmentation (F1: 0.58 vs 0.52), enhancing tropical cyclone detection (storm-level recall: 81% vs 75%, early detection: 29% vs 17%), and maintaining competitive precipitation estimation performance. Analysis reveals that GAIA's hybrid objectives encourage learning of spatially coherent, object-centric features distributed across multiple principal components rather than concentrated representations focused on reconstruction. This work demonstrates that combining complementary self-supervised objectives yields more transferable representations for diverse atmospheric modeling tasks. Model weights and code are available at: https://huggingface.co/bcg-usra-nasa-gaia/GAIA-v1.


Fair Play for Individuals, Foul Play for Groups? Auditing Anonymization's Impact on ML Fairness

arXiv.org Artificial Intelligence

Machine learning (ML) algorithms are heavily based on the availability of training data, which, depending on the domain, often includes sensitive information about data providers. This raises critical privacy concerns. Anonymization techniques have emerged as a practical solution to address these issues by generalizing features or suppressing data to make it more difficult to accurately identify individuals. Although recent studies have shown that privacy-enhancing technologies can influence ML predictions across different subgroups, thus affecting fair decision-making, the specific effects of anonymization techniques, such as $k$-anonymity, $\ell$-diversity, and $t$-closeness, on ML fairness remain largely unexplored. In this work, we systematically audit the impact of anonymization techniques on ML fairness, evaluating both individual and group fairness. Our quantitative study reveals that anonymization can degrade group fairness metrics by up to fourfold. Conversely, similarity-based individual fairness metrics tend to improve under stronger anonymization, largely as a result of increased input homogeneity. By analyzing varying levels of anonymization across diverse privacy settings and data distributions, this study provides critical insights into the trade-offs between privacy, fairness, and utility, offering actionable guidelines for responsible AI development. Our code is publicly available at: https://github.com/hharcolezi/anonymity-impact-fairness.


AVA: Towards Agentic Video Analytics with Vision Language Models

arXiv.org Artificial Intelligence

AI-driven video analytics has become increasingly important across diverse domains. However, existing systems are often constrained to specific, predefined tasks, limiting their adaptability in open-ended analytical scenarios. The recent emergence of Vision Language Models (VLMs) as transformative technologies offers significant potential for enabling open-ended video understanding, reasoning, and analytics. Nevertheless, their limited context windows present challenges when processing ultra-long video content, which is prevalent in real-world applications. To address this, we introduce AVA, a VLM-powered system designed for open-ended, advanced video analytics. AVA incorporates two key innovations: (1) the near real-time construction of Event Knowledge Graphs (EKGs) for efficient indexing of long or continuous video streams, and (2) an agentic retrieval-generation mechanism that leverages EKGs to handle complex and diverse queries. Comprehensive evaluations on public benchmarks, LVBench and VideoMME-Long, demonstrate that AVA achieves state-of-the-art performance, attaining 62.3% and 64.1% accuracy, respectively-significantly surpassing existing VLM and video Retrieval-Augmented Generation (RAG) systems. Furthermore, to evaluate video analytics in ultra-long and open-world video scenarios, we introduce a new benchmark, AVA-100. This benchmark comprises 8 videos, each exceeding 10 hours in duration, along with 120 manually annotated, diverse, and complex question-answer pairs. On AVA-100, AVA achieves top-tier performance with an accuracy of 75.8%. The source code of AVA is available at https://github.com/I-ESC/Project-Ava. The AVA-100 benchmark can be accessed at https://huggingface.co/datasets/iesc/Ava-100.


Tendon-Actuated Concentric Tube Endonasal Robot (TACTER)

arXiv.org Artificial Intelligence

Endoscopic endonasal approaches (EEA) have become more prevalent for minimally invasive skull base and sinus surgeries. However, rigid scopes and tools significantly decrease the surgeon's ability to operate in tight anatomical spaces and avoid critical structures such as the internal carotid artery and cranial nerves. This paper proposes a novel tendon-actuated concentric tube endonasal robot (TACTER) design in which two tendon-actuated robots are concentric to each other, resulting in an outer and inner robot that can bend independently. The outer robot is a unidirectionally asymmetric notch (UAN) nickel-titanium robot, and the inner robot is a 3D-printed bidirectional robot, with a nickel-titanium bending member. In addition, the inner robot can translate axially within the outer robot, allowing the tool to traverse through structures while bending, thereby executing follow-the-leader motion. A Cosserat-rod based mechanical model is proposed that uses tendon tension of both tendon-actuated robots and the relative translation between the robots as inputs and predicts the TACTER tip position for varying input parameters. The model is validated with experiments, and a human cadaver experiment is presented to demonstrate maneuverability from the nostril to the sphenoid sinus. This work presents the first tendon-actuated concentric tube (TACT) dexterous robotic tool capable of performing follow-the-leader motion within natural nasal orifices to cover workspaces typically required for a successful EEA.


DualOptim: Enhancing Efficacy and Stability in Machine Unlearning with Dual Optimizers

arXiv.org Artificial Intelligence

Existing machine unlearning (MU) approaches exhibit significant sensitivity to hyperparameters, requiring meticulous tuning that limits practical deployment. In this work, we first empirically demonstrate the instability and suboptimal performance of existing popular MU methods when deployed in different scenarios. To address this issue, we propose Dual Optimizer (DualOptim), which incorporates adaptive learning rate and decoupled momentum factors. Empirical and theoretical evidence demonstrates that DualOptim contributes to effective and stable unlearning. Through extensive experiments, we show that DualOptim can significantly boost MU efficacy and stability across diverse tasks, including image classification, image generation, and large language models, making it a versatile approach to empower existing MU algorithms.