Daily Papers

Artificial intelligence models have shown great potential in structure-based drug design, generating ligands with high binding affinities. However, existing models have often overlooked a crucial physical constraint: atoms must maintain a minimum pairwise distance to avoid separation violation, a phenomenon governed by the balance of attractive and repulsive forces. To mitigate such separation violations, we propose NucleusDiff. It models the interactions between atomic nuclei and their surrounding electron clouds by enforcing the distance constraint between the nuclei and manifolds. We quantitatively evaluate NucleusDiff using the CrossDocked2020 dataset and a COVID-19 therapeutic target, demonstrating that NucleusDiff reduces violation rate by up to 100.00% and enhances binding affinity by up to 22.16%, surpassing state-of-the-art models for structure-based drug design. We also provide qualitative analysis through manifold sampling, visually confirming the effectiveness of NucleusDiff in reducing separation violations and improving binding affinities.

We introduce the Discrete Min-Max Violation (DMMV) as a general optimization problem which seeks an assignment of discrete values to variables that minimizes the largest constraint violation. This context-free mathematical formulation is applicable to a wide range of use cases that have worst-case performance requirements. After defining the DMMV problem mathematically, we explore its properties to establish a foundational understanding. To tackle DMMV instance sizes of practical relevance, we develop a GPU-accelerated heuristic that takes advantage of the mathematical properties of DMMV for speeding up the solution process. We demonstrate the versatile applicability of our heuristic by solving three optimization problems as use cases: (1) post-training quantization of language models, (2) discrete tomography, and (3) Finite Impulse Response (FIR) filter design. In quantization without outlier separation, our heuristic achieves 14% improvement on average over existing methods. In discrete tomography, it reduces reconstruction error by 16% under uniform noise and accelerates computations by a factor of 6 on GPU. For FIR filter design, it nearly achieves 50% ripple reduction compared to using the commercial integer optimization solver, Gurobi. Our comparative results point to the benefits of studying DMMV as a context-free optimization problem and the advantages that our proposed heuristic offers on three distinct problems. Our GPU-accelerated heuristic will be made open-source to further stimulate research on DMMV and its other applications. The code is available at https://anonymous.4open.science/r/AMVM-5F3E/

This paper proposes a neuro-symbolic framework for G-code generation that seeks to integrate the neural generative capabilities of the GLLM method (Abdelaal et al., 2025) with formal verification via a Separation Logic (SL) prover. To establish a reliable physical baseline, the framework extracts deterministic boundary representations from 3D CAD models (STEP files) using the OpenCASCADE framework. This extracted geometric data supports a two-component architecture: the LLM serves as an initial code generator, while the SL Prover, utilizing a Spatial Heap model, evaluates the output. By conceptualizing physical collisions as logical Spatial Data Races -- violations of the separating conjunction in SL -- our framework translates proof failures into structured mathematical feedback. These failures are condensed into bounding boxes that serve as directives for the LLM's iterative self-correction. Ultimately, this work aims to develop a self-correcting system that reduces the need for human supervision, leading to safer and verified autonomous manufacturing.

We present a straightforward statistical test to detect certain violations of the assumption that the data are Independent and Identically Distributed (IID). The specific form of violation considered is common across real-world applications: whether the examples are ordered in the dataset such that almost adjacent examples tend to have more similar feature values (e.g. due to distributional drift, or attractive interactions between datapoints). Based on a k-Nearest Neighbors estimate, our approach can be used to audit any multivariate numeric data as well as other data types (image, text, audio, etc.) that can be numerically represented, perhaps with model embeddings. Compared with existing methods to detect drift or auto-correlation, our approach is both applicable to more types of data and also able to detect a wider variety of IID violations in practice. Code: https://github.com/cleanlab/cleanlab

We propose a theoretical framework demonstrating that popular Large Language Model (LLM) alignment methods, including Reinforcement Learning from Human Feedback (RLHF) and alternatives, fundamentally function as divergence estimators between aligned (preferred or safe) and unaligned (less-preferred or harmful) distributions. This explains the separation phenomenon between safe and harmful prompts in the model hidden representation after alignment. Inspired by the theoretical results, we identify that some alignment methods are better than others in terms of separation and, introduce a new method, KLDO, and further demonstrate the implication of our theories. We advocate for compliance-refusal datasets over preference datasets to enhance safety alignment, supported by both theoretical reasoning and empirical evidence. Additionally, to quantify safety separation, we leverage a distance metric in the representation space and statistically validate its efficacy as a statistical significant indicator of LLM resilience against jailbreak attacks.

This paper presents a program logic for reasoning about multithreaded Java-like programs with dynamic thread creation, thread joining and reentrant object monitors. The logic is based on concurrent separation logic. It is the first detailed adaptation of concurrent separation logic to a multithreaded Java-like language. The program logic associates a unique static access permission with each heap location, ensuring exclusive write accesses and ruling out data races. Concurrent reads are supported through fractional permissions. Permissions can be transferred between threads upon thread starting, thread joining, initial monitor entrancies and final monitor exits. In order to distinguish between initial monitor entrancies and monitor reentrancies, auxiliary variables keep track of multisets of currently held monitors. Data abstraction and behavioral subtyping are facilitated through abstract predicates, which are also used to represent monitor invariants, preconditions for thread starting and postconditions for thread joining. Value-parametrized types allow to conveniently capture common strong global invariants, like static object ownership relations. The program logic is presented for a model language with Java-like classes and interfaces, the soundness of the program logic is proven, and a number of illustrative examples are presented.

Separation provision and collision avoidance to avoid other air traffic are fundamental components of the layered conflict management system to ensure safe and efficient operations. Pilots have visual-based separation responsibilities to see and be seen to maintain separation between aircraft. To safely integrate into the airspace, drones should be required to have a minimum level of performance based on the safety achieved as baselined by crewed aircraft seen and be seen interactions. Drone interactions with crewed aircraft should not be more hazardous than interactions between traditional aviation aircraft. Accordingly, there is need for a methodology to design and evaluate detect and avoid systems, to be equipped by drones to mitigate the risk of a midair collision, where the methodology explicitly addresses, both semantically and mathematically, the appropriate operating rules associated with see and be seen. In response, we simulated how onboard pilots safely operate through see and be seen interactions using an updated visual acquisition model that was originally developed by J.W. Andrews decades ago. Monte Carlo simulations were representative two aircraft flying under visual flight rules and results were analyzed with respect to drone detect and avoid performance standards.

Large language models are increasingly deployed as *deep agents* that plan, maintain persistent state, and invoke external tools, shifting safety failures from unsafe text to unsafe *trajectories*. We introduce **AgentFence**, an architecture-centric security evaluation that defines 14 trust-boundary attack classes spanning planning, memory, retrieval, tool use, and delegation, and detects failures via *trace-auditable conversation breaks* (unauthorized or unsafe tool use, wrong-principal actions, state/objective integrity violations, and attack-linked deviations). Holding the base model fixed, we evaluate eight agent archetypes under persistent multi-turn interaction and observe substantial architectural variation in mean security break rate (MSBR), ranging from 0.29 pm 0.04 (LangGraph) to 0.51 pm 0.07 (AutoGPT). The highest-risk classes are operational: Denial-of-Wallet (0.62 pm 0.08), Authorization Confusion (0.54 pm 0.10), Retrieval Poisoning (0.47 pm 0.09), and Planning Manipulation (0.44 pm 0.11), while prompt-centric classes remain below 0.20 under standard settings. Breaks are dominated by boundary violations (SIV 31%, WPA 27%, UTI+UTA 24%, ATD 18%), and authorization confusion correlates with objective and tool hijacking (ρapprox 0.63 and ρapprox 0.58). AgentFence reframes agent security around what matters operationally: whether an agent stays within its goal and authority envelope over time.

Universal sound separation faces a fundamental misalignment: models optimized for low-level signal metrics often produce semantically contaminated outputs, failing to suppress perceptually salient interference from acoustically similar sources. We introduce a preference alignment perspective, analogous to aligning LLMs with human intent. To address this, we introduce MARS-Sep, a reinforcement learning framework that reformulates separation as decision making. Instead of simply regressing ground-truth masks, MARS-Sep learns a factorized Beta mask policy that is steered by a preference reward model and optimized by a stable, clipped trust-region surrogate. The reward, derived from a progressively-aligned audio-text-vision encoder, directly incentivizes semantic consistency with query prompts. Extensive experiments on multiple benchmarks demonstrate consistent gains in Text-, Audio-, and Image-Queried separation, with notable improvements in signal metrics and semantic quality. Our code is available at https://github.com/mars-sep/MARS-Sep. Sound separation samples are available at https://mars-sep.github.io/.