Research Papers

In complex molecular systems, the reaction coordinate (RC) that characterizes transition pathways is essential to understand underlying molecular mechanisms. This review surveys a framework for identifying the RC by applying deep learning to the committor, which provides the most reliable measure of the progress along a transition path. The inputs to the neural network are collective variables (CVs) expressed as functions of atomic coordinates of the system, and the corresponding RC is predicted as the output by training the network on the committor as the learning target. Because deep learning models typically operate in a black-box manner, it is difficult to determine which input variables govern the predictions. The incorporation of eXplainable Artificial Intelligence (XAI) techniques enables quantitative assessment of the contributions of individual input variables to the predictions. This approach allows the identification of CVs that play dominant roles and demonstrates that the committor distribution on the surface using important CVs is separated by well-defined boundaries. The framework provides an explainable deep learning strategy for assigning a molecular mechanism from the RC and is applicable to a wide range of complex molecular systems.

AI-mediated communication is increasingly being utilized to help facilitate interactions; however, in privacy sensitive domains, an AI mediator has the additional challenge of considering how to preserve privacy. In these contexts, a mediator may redact or withhold information, raising questions about how users perceive these interventions and whether explanations of system behavior can improve trust. In this work, we investigate how explanations of redaction operations can affect user trust in AI-mediated communication. We devise a scenario where a validated system removes sensitive content from messages and generates explanations of varying detail to communicate its decisions to recipients. We then conduct a user study with $180$ participants that studies how user trust and preferences vary for cases with different amounts of redacted content and different levels of explanation detail. Our results show that participants believed our system was more effective at preserving privacy when explanations were provided ($p<0.05$, Cohen's $d \approx 0.3$). We also found that contextual factors had an impact; participants relied more on explanations and found them more helpful when the system performed extensive redactions ($p<0.05$, Cohen's $f \approx 0.2$). We also found that explanation preferences depended on individual differences as well, and factors such as age and baseline familiarity with AI affected user trust in our system. These findings highlight the importance and challenge of balancing transparency and privacy in AI-mediated communications and suggest that adaptive, context-aware explanations are essential for designing privacy-aware, trustworthy AI systems.

Diabetic retinopathy screening traditionally relies on fundus photography, requiring specialized equipment and expertise often unavailable in primary care and resource limited settings. We developed and validated a deep learning (DL) system for automated diabetic classification using anterior segment ocular imaging a readily accessible alternative utilizing standard photography equipment. The system leverages visible biomarkers in the iris, sclera, and conjunctiva that correlate with systemic diabetic status. We systematically evaluated five contemporary architectures (EfficientNet-V2-S with self-supervised learning (SSL), Vision Transformer, Swin Transformer, ConvNeXt-Base, and ResNet-50) on 2,640 clinically annotated anterior segment images spanning Normal, Controlled Diabetic, and Uncontrolled Diabetic categories. A tailored preprocessing pipeline combining specular reflection mitigation and contrast limited adaptive histogram equalization (CLAHE) was implemented to enhance subtle vascular and textural patterns critical for classification. SSL using SimCLR on domain specific ocular images substantially improved model performance.EfficientNet-V2-S with SSL achieved optimal performance with an F1-score of 98.21%, precision of 97.90%, and recall of 98.55% a substantial improvement over ImageNet only initialization (94.63% F1). Notably, the model attained near perfect precision (100%) for Normal classification, critical for minimizing unnecessary clinical referrals.

Computational argumentation offers formal frameworks for transparent, verifiable reasoning but has traditionally been limited by its reliance on domain-specific information and extensive feature engineering. In contrast, LLMs excel at processing unstructured text, yet their opaque nature makes their reasoning difficult to evaluate and trust. We argue that the convergence of these fields will lay the foundation for a new paradigm: Argumentative Human-AI Decision-Making. We analyze how the synergy of argumentation framework mining, argumentation framework synthesis, and argumentative reasoning enables agents that do not just justify decisions, but engage in dialectical processes where decisions are contestable and revisable -- reasoning with humans rather than for them. This convergence of computational argumentation and LLMs is essential for human-aware, trustworthy AI in high-stakes domains.

Large language models appear to develop internal representations of emotion -- "emotion circuits," "emotion neurons," and structured emotional manifolds have been reported across multiple model families. But every study making these claims uses stimuli signalled by explicit emotion keywords, leaving a fundamental question unanswered: do these circuits detect genuine emotional meaning, or do they detect the word "devastated"? We present the first clinical validity test of emotion circuit claims using mechanistic interpretability methods grounded in clinical psychology -- clinical vignettes that evoke emotions through situational and behavioural cues alone, emotion keywords removed. Across six models (Llama-3.2-1B, Llama-3-8B, Gemma-2-9B; base and instruct variants), we apply four convergent mechanistic interpretability methods -- linear probing, causal activation patching, knockout experiments, and representational geometry -- and discover two dissociable emotion processing mechanisms. Affect reception -- detecting emotionally significant content -- operates with near-perfect accuracy (AUROC 1.000), consistent with early-layer saturation, and replicates across all six models. Emotion categorization -- mapping affect to specific emotion labels -- is partially keyword-dependent, dropping 1-7% without keywords and improving with scale. Causal activation patching confirms keyword-rich and keyword-free stimuli share representational space, transferring affective salience rather than emotion-category identity. These findings falsify the keyword-spotting hypothesis, establish a novel mechanistic dissociation, and introduce clinical stimulus methodology as a rigorous standard for testing emotion processing claims in large language models -- with direct implications for AI safety evaluation and alignment. All stimuli, code, and data are released for replication.

PET theranostics is transforming precision oncology, yet treatment response varies substantially; many patients receiving 177Lu-PSMA radioligand therapy (RLT) for metastatic castration-resistant prostate cancer (mCRPC) fail to respond, demanding reliable pre-therapy prediction. While LLM-based agents have shown remarkable potential in complex medical diagnosis, their application to PET theranostic outcome prediction remains unexplored, which faces three key challenges: (1) data and knowledge scarcity: RLT was only FDA-approved in 2022, yielding few training cases and insufficient domain knowledge in general LLMs; (2) heterogeneous information integration: robust prediction hinges on structured knowledge extraction from PET/CT, laboratory tests, and free-text clinical documentation; (3) evidence-grounded reasoning: clinical decisions must be anchored in trial evidence rather than LLM hallucinations. In this paper, we present TheraAgent, to our knowledge, the first agentic framework for PET theranostics, with three core innovations: (1) Multi-Expert Feature Extraction with Confidence-Weighted Consensus, where three specialized experts process heterogeneous inputs with uncertainty quantification; (2) Self-Evolving Agentic Memory (SEA-Mem), which learns prognostic patterns from accumulated cases, enabling case-based reasoning from limited data; (3) Evidence-Calibrated Reasoning, integrating a curated theranostics knowledge base to ground predictions in VISION/TheraP trial evidence. Evaluated on 35 real patients and 400 synthetic cases, TheraAgent achieves 75.7% overall accuracy on real patients and 87.0% on synthetic cases, outperforming MDAgents and MedAgent-Pro by over 20%. These results highlight a promising blueprint for trustworthy AI agents in PET theranostics, enabling trial-calibrated, multi-source decision support. Code will be released upon acceptance.

Large Language Model (LLM)-based coding agents show promise in automating software development tasks, yet they frequently fail in ways that are difficult for developers to understand and debug. While general-purpose LLMs like GPT can provide ad-hoc explanations of failures, raw execution traces remain challenging to interpret even for experienced developers. We present a systematic explainable AI (XAI) approach that transforms raw agent execution traces into structured, human-interpretable explanations. Our method consists of three key components: (1) a domain-specific failure taxonomy derived from analyzing real agent failures, (2) an automatic annotation system that classifies failures using defined annotation schema, (3) a hybrid explanation generator that produces visual execution flows, natural language explanations, and actionable recommendations. Through a user study with 20 participants (10 technical, 10 non-technical), we demonstrate that our approach enables users to identify failure root causes 2.8 times faster and propose correct fixes with 73% higher accuracy compared to raw execution traces. Importantly, our structured approach outperforms ad-hoc state of the art models explanations by providing consistent, domain-specific insights with integrated visualizations. Our work establishes a framework for systematic agent failure analysis, addressing the critical need for interpretable AI systems in software development workflows

Accurate fault detection in high-dimensional industrial environments remains a major challenge due to the inherent complexity, noise, and redundancy in sensor data. This paper introduces CLAIRE, i.e., a hybrid end-to-end learning framework that integrates unsupervised deep representation learning with supervised classification for intelligent quality control in smart manufacturing systems. It employs an optimized deep autoencoder to transform raw input into a compact latent space, effectively capturing the intrinsic data structure while suppressing irrelevant or noisy features. The learned representations are then fed into a downstream classifier to perform binary fault prediction. Experimental results on a high-dimensional dataset demonstrate that CLAIRE significantly outperforms conventional classifiers trained directly on raw features. Moreover, the framework incorporates a post hoc phase, using a game-theory-based interpretability technique, to analyze the latent space and identify the most informative input features contributing to fault predictions. The proposed framework highlights the potential of integrating explainable AI with feature-aware regularization for robust fault detection. The modular and interpretable nature of the proposed framework makes it highly adaptable, offering promising applications in other domains characterized by complex, high-dimensional data, such as healthcare, finance, and environmental monitoring.

Explainable Artificial Intelligence (XAI) seeks to enhance the transparency and accountability of machine learning systems, yet most methods follow a one-size-fits-all paradigm that neglects user differences in expertise, goals, and cognitive needs. Although Large Language Models can translate technical explanations into natural language, they introduce challenges related to faithfulness and hallucinations. To address these challenges, we present PONTE (Personalized Orchestration for Natural language Trustworthy Explanations), a human-in-the-loop framework for adaptive and reliable XAI narratives. PONTE models personalization as a closed-loop validation and adaptation process rather than prompt engineering. It combines: (i) a low-dimensional preference model capturing stylistic requirements; (ii) a preference-conditioned generator grounded in structured XAI artifacts; and (iii) verification modules enforcing numerical faithfulness, informational completeness, and stylistic alignment, optionally supported by retrieval-grounded argumentation. User feedback iteratively updates the preference state, enabling quick personalization. Automatic and human evaluations across healthcare and finance domains show that the verification-refinement loop substantially improves completeness and stylistic alignment over validation-free generation. Human studies further confirm strong agreement between intended preference vectors and perceived style, robustness to generation stochasticity, and consistently positive quality assessments.

Vision-Language Models (VLMs) transfer visual and textual data into a shared embedding space. In so doing, they enable a wide range of multimodal tasks, while also raising critical questions about the nature of machine 'understanding.' In this paper, we examine how Explainable Artificial Intelligence (XAI) methods can render the visual reasoning of a VLM - namely, CLIP - legible in art-historical contexts. To this end, we evaluate seven methods, combining zero-shot localization experiments with human interpretability studies. Our results indicate that, while these methods capture some aspects of human interpretation, their effectiveness hinges on the conceptual stability and representational availability of the examined categories.

Chain-of-thought (CoT) reasoning is fundamental to modern LLM architectures and represents a critical intervention point for AI safety. However, CoT reasoning may exhibit failure modes that we note as pathologies, which prevent it from being useful for monitoring. Prior work has identified three distinct pathologies: post-hoc rationalization, where models generate plausible explanations backwards from predetermined answers; encoded reasoning, where intermediate steps conceal information within seemingly interpretable text; and internalized reasoning, where models replace explicit reasoning with meaningless filler tokens while computing internally. To better understand and discriminate between these pathologies, we create a set of concrete metrics that are simple to implement, computationally inexpensive, and task-agnostic. To validate our approach, we develop model organisms deliberately trained to exhibit specific CoT pathologies. Our work provides a practical toolkit for assessing CoT pathologies, with direct implications for training-time monitoring.

We make three contributions in this paper. First, we present an approach for compiling a random forest classifier into a set of circuits, where each circuit directly encodes the instances in some class of the classifier. We show empirically that our proposed approach is significantly more efficient than existing similar approaches. Next, we utilize this approach to further obtain circuits that are tractable for computing the complete and general reasons of a decision, which are instance abstractions that play a fundamental role in computing explanations. Finally, we propose algorithms for computing the robustness of a decision and all shortest ways to flip it. We illustrate the utility of our contributions by using them to enumerate all sufficient reasons, necessary reasons and contrastive explanations of decisions; to compute the robustness of decisions; and to identify all shortest ways to flip the decisions made by random forest classifiers learned from a wide range of datasets.