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SpliceBind: Isoform-Aware Prediction of Binding Pocket Druggability

arXiv:2606.04020v1 Announce Type: cross Abstract: Splice-mediated drug resistance occurs in up to 40% of patients on targeted kinase inhibitors, yet state-of-the-art druggability tools operate on single structures and cannot compare across isoforms. We introduce SpliceBind, a graph neural network framework for isoform-aware druggability prediction. Beyond improving prediction accuracy (AUROC 0.703 vs. P2Rank 0.634, p = 0.026), we address a more fundamental question: when do structural...

arXiv CS 6d ago

Hallucination Is Linearly Decodable from Mid-Layer Hidden States in Quantized LLMs

arXiv:2606.02628v1 Announce Type: new Abstract: We investigate whether open-source LLMs encode a linearly separable truthfulness signal in their hidden states, and at which network depth this signal is strongest. Across three $7$B--$8$B instruction-tuned models (Llama-3.1-8B, Mistral-7B, Qwen2.5-7B) loaded in $4$-bit NF4 quantization, we extract per-layer hidden states on four hallucination benchmarks (TruthfulQA, HaluEval-QA, FEVER, and a controlled synthetic set) and compare four detection...

arXiv CS 7d ago

Localizing Prompt Ambiguity in Large Language Models with Probe-Targeted Attribution

arXiv:2606.05486v1 Announce Type: new Abstract: Prompt ambiguity is a common source of failure in large language models, but is difficult to localize because it is a latent property of the prompt, while existing attribution methods are designed to explain observable outputs such as logits or generated tokens. We introduce PRIG, a gradient attribution method that uses a probe logit to attribute latent ambiguity to token positions. Specifically, PRIG trains a linear probe to distinguish clear...

arXiv CS 5d ago

When Does Structure Help? The Information Bonus of AlphaFold2 Representations over Protein Language Models

arXiv:2606.04228v1 Announce Type: new Abstract: AI scientist systems increasingly choose biological foundation models before they choose experiments. In protein pipelines, this creates a concrete engineering and scientific question: when is the cost of structural inference worth paying over a cheaper sequence-only model? We introduce the information bonus (IB), a task-level metric that measures the linearly accessible advantage of frozen single-sequence AlphaFold2 Evoformer representations...

arXiv CS 6d ago

Normality-Preserving Continual Industrial Anomaly Detection via Orthogonal LoRA Banks

Announce Type: new Abstract: Continual industrial anomaly detection with diffusion models suffers from historical normality prior drift and catastrophic forgetting. Existing continual diffusion methods preserve previous knowledge through replay or constrained optimization, but they lack an explicit mechanism for isolating and protecting category-specific normality priors during sequential adaptation. Although low-rank adaptation provides modular residual updates, standard LoRA neither...

arXiv CS 8d ago

Self-Commitment Latency: A Reward-Free Probe for Prompted Implicit Hacking

Announce Type: new Abstract: Implicit reward hacking is hard to audit when a language model's chain of thought appears benign: a final answer may be anchored by a prompt shortcut while the written reasoning still resembles ordinary problem solving. Verifier-based probes expose such behavior by measuring how early truncated reasoning contexts obtain high reward, but require a task-specific reward signal. This paper proposes a weaker-input alternative, self-commitment latency, which measures...

arXiv CS 5d ago

Structure-Aware Prediction of PROTAC-Mediated Protein Degradability via Graph Neural Networks

Announce Type: cross Abstract: Proteolysis-targeting chimeras (PROTACs) can selectively degrade disease-causing proteins, yet predicting which targets are amenable to degradation remains a critical bottleneck: existing computational methods require the complete PROTAC molecular structure, information unavailable before synthesis. We present DegradoMap, a graph neural network that predicts PROTAC-mediated degradability from protein structure and E3 ligase identity alone -- the minimal...

arXiv CS 6d ago

Multi-Agent Reasoning with Consistency Verification Improves Uncertainty Calibration in Medical MCQA

arXiv:2603.24481v2 Announce Type: replace Abstract: Miscalibrated confidence scores are a practical obstacle to deploying AI in clinical settings. A model that is always overconfident offers no useful signal for deferral.

arXiv CS 2d ago

GuardNet: Ensemble Strategies of Shallow Neural Networks for Robust Prompt Injection and Jailbreak Detection

arXiv:2606.05566v1 Announce Type: new Abstract: Large Language Models (LLMs) have transformed natural language processing, but they remain vulnerable to Prompt Injection (PI) and Jailbreak (JB) attacks. In addition, benchmark evaluations may be affected by contamination and partial information leakage, compromising performance estimates.

arXiv CS 5d ago

Quantifying Rodda and Graham Gait Classification from 3D Markerless Kinematics derived from a Single-view Video in a Heterogeneous Pediatric Clinical Cohort

arXiv:2605.11314v3 Announce Type: replace Abstract: Cerebral Palsy (CP) is a neurological disorder of movement and the most common cause of lifelong physical disability in childhood. Approximately 75% of children with CP are ambulatory, and accurate gait assessment is central to preserving walking function, which deteriorates by mid-adulthood in a quarter to half of adults with CP. The Rodda and Graham classification system quantifies sagittal-plane gait deviations using ankle and knee...

arXiv CS 1d ago