A Systematic Approach for Large Language Models Debugging

Large language models (LLMs) have become central to modern AI workflows, powering applications from open-ended text generation to complex agent-based reasoning. However, debugging these models remains a persistent challenge due to their opaque and probabilistic nature and the difficulty of diagnosing errors across diverse tasks and settings. This paper introduces a systematic approach for LLM debugging that treats models as observable systems, providing structured, model-agnostic methods from issue detection to model refinement. By unifying evaluation, interpretability, and error-analysis practices, our approach enables practitioners to iteratively diagnose model weaknesses, refine prompts and model parameters, and adapt data for fine-tuning or assessment, while remaining effective in contexts where standardized benchmarks and evaluation criteria are lacking. We argue that such a structured methodology not only accelerates troubleshooting but also fosters reproducibility, transparency, and scalability in the deployment of LLM-based systems.

STaD: Scaffolded Task Design for Identifying Compositional Skill Gaps in LLMs

Benchmarks are often used as a standard to understand LLM capabilities in different domains. However, aggregate benchmark scores provide limited insight into compositional skill gaps of LLMs and how to improve them. To make these weaknesses visible, we propose Scaffolded Task Design (STaD) framework. STaD generates controlled variations of benchmark tasks based on the concept of scaffolding, which introduces structured, incremental support in a step-by-step manner. Rather than inspecting failures individually, this approach enables systematic and scalable probing of model behavior by identifying the specific reasoning skill compositions they lack. Treating the LLM as a black box, our experiments on six models of varying sizes reveal multiple failure points in three reasoning benchmarks and highlight each model's unique and distinct skill gaps.

LogitScope: A Framework for Analyzing LLM Uncertainty Through Information Metrics

Understanding and quantifying uncertainty in large language model (LLM) outputs is critical for reliable deployment. However, traditional evaluation approaches provide limited insight into model confidence at individual token positions during generation. To address this issue, we introduce LogitScope, a lightweight framework for analyzing LLM uncertainty through token-level information metrics computed from probability distributions. By measuring metrics such as entropy and varentropy at each generation step, LogitScope reveals patterns in model confidence, identifies potential hallucinations, and exposes decision points where models exhibit high uncertainty, all without requiring labeled data or semantic interpretation. We demonstrate LogitScope's utility across diverse applications including uncertainty quantification, model behavior analysis, and production monitoring. The framework is model-agnostic, computationally efficient through lazy evaluation, and compatible with any HuggingFace model, enabling both researchers and practitioners to inspect LLM behavior during inference.

LLMON: An LLM-native Markup Language to Leverage Structure and Semantics at the LLM Interface

Textual Large Language Models (LLMs) provide a simple and familiar interface: a string of text is used for both input and output. However, the information conveyed to an LLM often has a richer structure and semantics, which is not conveyed in a string. For example, most prompts contain both instructions ("Summarize this paper into a paragraph") and data (the paper to summarize), but these are usually not distinguished when passed to the model. This can lead to model confusion and security risks, such as prompt injection attacks. This work addresses this shortcoming by introducing an LLM-native mark-up language, LLMON (LLM Object Notation, pronounced "Lemon"), that enables the structure and semantic metadata of the text to be communicated in a natural way to an LLM. This information can then be used during model training, model prompting, and inference implementation, leading to improvements in model accuracy, safety, and security. This is analogous to how programming language types can be used for many purposes, such as static checking, code generation, dynamic checking, and IDE highlighting. We discuss the general design requirements of an LLM-native markup language, introduce the LLMON markup language and show how it meets these design requirements, describe how the information contained in a LLMON artifact can benefit model training and inference implementation, and provide some preliminary empirical evidence of its value for both of these use cases. We also discuss broader issues and research opportunities that are enabled with an LLM-native approach.

MermaidSeqBench: An Evaluation Benchmark for LLM-to-Mermaid Sequence Diagram Generation

Large language models (LLMs) have demonstrated excellent capabilities in generating structured diagrams from natural language descriptions. In particular, they have shown great promise in generating sequence diagrams for software engineering, typically represented in a text-based syntax such as Mermaid. However, systematic evaluations in this space remain underdeveloped as there is a lack of existing benchmarks to assess the LLM's correctness in this task. To address this shortcoming, we introduce MermaidSeqBench, a human-verified and LLM-synthetically-extended benchmark for assessing an LLM's capabilities in generating Mermaid sequence diagrams from textual prompts. The benchmark consists of a core set of 132 samples, starting from a small set of manually crafted and verified flows. These were expanded via a hybrid methodology combining human annotation, in-context LLM prompting, and rule-based variation generation. Our benchmark uses an LLM-as-a-judge model to assess Mermaid sequence diagram generation across fine-grained metrics, including syntax correctness, activation handling, error handling, and practical usability. We perform initial evaluations on numerous state-of-the-art LLMs and utilize multiple LLM judge models to demonstrate the effectiveness and flexibility of our benchmark. Our results reveal significant capability gaps across models and evaluation modes. Our proposed benchmark provides a foundation for advancing research in structured diagram generation and for developing more rigorous, fine-grained evaluation methodologies.