Contrastive Domain Generalization for Cross-Instrument Molecular Identification in Mass Spectrometry

Identifying molecules from mass spectrometry (MS) data remains a fundamental challenge due to the semantic gap between physical spectral peaks and underlying chemical structures. Existing deep learning approaches often treat spectral matching as a closed-set recognition task, limiting their ability to generalize to unseen molecular scaffolds. To overcome this limitation, we propose a cross-modal alignment framework that directly maps mass spectra into the chemically meaningful molecular structure embedding space of a pretrained chemical language model. On a strict scaffold-disjoint benchmark, our model achieves a Top-1 accuracy of 42.2% in fixed 256-way zero-shot retrieval and demonstrates strong generalization under a global retrieval setting. Moreover, the learned embedding space demonstrates strong chemical coherence, reaching 95.4% accuracy in 5-way 5-shot molecular re-identification. These results suggest that explicitly integrating physical spectral resolution with molecular structure embedding is key to solving the generalization bottleneck in molecular identification from MS data.

Co-CoT: A Prompt-Based Framework for Collaborative Chain-of-Thought Reasoning

Due to the proliferation of short-form content and the rapid adoption of AI, opportunities for deep, reflective thinking have significantly diminished, undermining users' critical thinking and reducing engagement with the reasoning behind AI-generated outputs. To address this issue, we propose an Interactive Chain-of-Thought (CoT) Framework that enhances human-centered explainability and responsible AI usage by making the model's inference process transparent, modular, and user-editable. The framework decomposes reasoning into clearly defined blocks that users can inspect, modify, and re-execute, encouraging active cognitive engagement rather than passive consumption. It further integrates a lightweight edit-adaptation mechanism inspired by preference learning, allowing the system to align with diverse cognitive styles and user intentions. Ethical transparency is ensured through explicit metadata disclosure, built-in bias checkpoint functionality, and privacy-preserving safeguards. This work outlines the design principles and architecture necessary to promote critical engagement, responsible interaction, and inclusive adaptation in AI systems aimed at addressing complex societal challenges.

LLMs as Deceptive Agents: How Role-Based Prompting Induces Semantic Ambiguity in Puzzle Tasks

Recent advancements in Large Language Models (LLMs) have not only showcased impressive creative capabilities but also revealed emerging agentic behaviors that exploit linguistic ambiguity in adversarial settings. In this study, we investigate how an LLM, acting as an autonomous agent, leverages semantic ambiguity to generate deceptive puzzles that mislead and challenge human users. Inspired by the popular puzzle game "Connections", we systematically compare puzzles produced through zero-shot prompting, role-injected adversarial prompts, and human-crafted examples, with an emphasis on understanding the underlying agent decision-making processes. Employing computational analyses with HateBERT to quantify semantic ambiguity, alongside subjective human evaluations, we demonstrate that explicit adversarial agent behaviors significantly heighten semantic ambiguity -- thereby increasing cognitive load and reducing fairness in puzzle solving. These findings provide critical insights into the emergent agentic qualities of LLMs and underscore important ethical considerations for evaluating and safely deploying autonomous language systems in both educational technologies and entertainment.