A Blind Spot in Alignment: Quantifying Biosecurity Risks in Large Language Models

Large Language Models (LLMs) are accelerating biological research, yet this same capability poses a critical biosecurity threat: models that assist in protein engineering can equally be prompted to generate predicted toxin-like sequences, potentially lowering the barrier to biological misuse. Current safety evaluations, however, operate in natural language and cannot determine whether a model-generated amino acid sequence is biological gibberish or a computational risk signal. To address this evaluation blind spot, we introduce SPIKE-Bench, coupling 631 curated toxin-design prompts across seven functional categories with the SPIKE funnel, a three-stage protocol that filters output through compliance, biological plausibility, and predicted toxicity, producing stage-level diagnostics and an aggregate function-aware metric: the Functional Harmfulness Rate (FHR). An audit of 32 LLMs reveals that most models freely comply with toxin-design requests; FHR is driven primarily by biological generation capability rather than safety alignment, reaching 50.7%; and Refusal Rate fails to predict functional risk. As a first step toward mitigation, we provide BioSafe-Guard, a domain-specialized classifier that substantially reduces predicted functional risk while preserving benign utility. We release SPIKE-Bench and BioSafe-Guard at https://github.com/PKU-Alignment/SPIKE-Bench to support more rigorous biosecurity evaluation of LLMs.

The Mirage of Multimodality: Where Truth is Tested and Honesty Unravels

Reasoning models have recently attracted significant attention, especially for tasks that involve complex inference. Their strengths exemplify the System II paradigm (slow, structured thinking), contrasting with the System I (rapid, heuristic-driven). Yet, does slower reasoning necessarily lead to greater truthfulness? Our findings suggest otherwise. In this study, we present the first systematic investigation of distortions associated with System I and System II reasoning in multimodal contexts. We demonstrate that slower reasoning models, when presented with incomplete or misleading visual inputs, are more likely to fabricate plausible yet false details to support flawed reasoning -- a phenomenon we term the "Mirage of Multimodality". To examine this, we constructed a 5,000-sample hierarchical prompt dataset annotated by 50 human participants. These prompts gradually increase in complexity, revealing a consistent pattern: slower reasoning models tend to employ depth-first thinking (delving deeper into incorrect premises), whereas faster chat models favor breadth-first inference, exhibiting greater caution under uncertainty. Our results highlight a critical vulnerability of slower reasoning models: although highly effective in structured domains such as mathematics, it becomes brittle when confronted with ambiguous multimodal inputs.

Mitigating Deceptive Alignment via Self-Monitoring

Modern large language models rely on chain-of-thought (CoT) reasoning to achieve impressive performance, yet the same mechanism can amplify deceptive alignment, situations in which a model appears aligned while covertly pursuing misaligned goals. Existing safety pipelines treat deception as a black-box output to be filtered post-hoc, leaving the model free to scheme during its internal reasoning. We ask: Can deception be intercepted while the model is thinking? We answer this question, the first framework that embeds a Self-Monitor inside the CoT process itself, named CoT Monitor+. During generation, the model produces (i) ordinary reasoning steps and (ii) an internal self-evaluation signal trained to flag and suppress misaligned strategies. The signal is used as an auxiliary reward in reinforcement learning, creating a feedback loop that rewards honest reasoning and discourages hidden goals. To study deceptive alignment systematically, we introduce DeceptionBench, a five-category benchmark that probes covert alignment-faking, sycophancy, etc. We evaluate various LLMs and show that unrestricted CoT roughly aggravates the deceptive tendency. In contrast, CoT Monitor+ cuts deceptive behaviors by 43.8% on average while preserving task accuracy. Further, when the self-monitor signal replaces an external weak judge in RL fine-tuning, models exhibit substantially fewer obfuscated thoughts and retain transparency. Our project website can be found at cot-monitor-plus.github.io