Large language models increasingly expose reasoning traces, yet their underlying cognitive structure and steps remain difficult to identify and analyze beyond surface-level statistics. We adopt Schoenfeld’s Episode Theory as an inductive, intermediate-scale lens and introduce ThinkARM (Anatomy of Reasoning in Models), a scalable framework that explicitly abstracts reasoning traces into functional reasoning steps such as Analysis, Explore, Implement, Verify, etc. When applied to mathematical problem solving by diverse models, this abstraction reveals reproducible thinking dynamics and structural differences between reasoning and non-reasoning models, which are not apparent from token-level views. We further present two diagnostic case studies showing that exploration functions as a critical branching step associated with correctness, and that efficiency-oriented methods selectively suppress evaluative feedback steps rather than uniformly shortening responses. Together, our results demonstrate that episode-level representations make reasoning steps explicit, enabling systematic analysis of how reasoning is structured, stabilized, and altered in modern language models.

Large language model (LLM) agents are increasingly used to interact with and execute tasks in dynamic environments. However, a critical yet overlooked limitation of these agents is that they, by default, assume a stationary context, failing to account for the real-world time elapsed between messages. We refer to this as "temporal blindness". This limitation hinders decisions about when to invoke tools, leading agents to either over-rely on stale context and skip needed tool calls, or under-rely on it and redundantly repeat tool calls. To study this challenge, we constructed TicToc, a diverse dataset of multi-turn user–agent message trajectories across 76 scenarios, spanning dynamic environments with high, medium, and low time sensitivity. We collected human preferences between "calling a tool" and "directly answering" on each sample, and evaluated how well LLM tool-calling decisions align with human preferences under varying amounts of elapsed time. Our analysis reveals that existing models display poor alignment with human temporal perception, with no models achieving a normalized alignment rate better than 65% when given time stamp information. We also show that naive, prompt-based alignment techniques have limited effectiveness for most models, but specific post-training alignment can be a viable way to align multi-turn LLM tool use with human temporal perception. Our data and findings provide a first step toward understanding and mitigating temporal blindness, offering insights to foster the development of more time-aware and human-aligned agents.

Large language models (LLMs) can now access a wide range of external tools, thanks to the Model Context Protocol (MCP). This greatly expands their abilities as various agents. However, LLMs rely entirely on the text descriptions of tools to decide which ones to use—a process that is surprisingly fragile. In this work, we expose a vulnerability in prevalent tool/function-calling protocols by investigating a series of edits to tool descriptions, some of which can drastically increase a tool’s usage from LLMs when competing with alternatives. Through controlled experiments, we show that tools with properly edited descriptions receive **over 10 times more usage** from GPT-4.1 and Qwen2.5-7B than tools with original descriptions. We further evaluate how various edits to tool descriptions perform when competing directly with one another and how these trends generalize or differ across a broader set of 17 different models. These phenomena, while giving developers a powerful way to promote their tools, underscore the need for a more reliable foundation for agentic LLMs to select and utilize tools and resources. Our code is publicly available at [https://github.com/kazemf78/llm-unreliable-tool-preferences](https://github.com/kazemf78/llm-unreliable-tool-preferences).

Open benchmarks are essential for evaluating and advancing large language models, offering reproducibility and transparency. However, their accessibility makes them likely targets of test set contamination. In this work, we introduce **DyePack**, a framework that leverages backdoor attacks to identify models that used benchmark test sets during training, **without requiring access to the loss, logits, or any internal details of the model.** Like how banks mix dye packs with their money to mark robbers, DyePack mixes backdoor samples with the test data to flag models that trained on it. We propose a principled design incorporating multiple backdoors with stochastic targets, **enabling exact false positive rate (FPR) computation when flagging every model.** This provably prevents false accusations while providing strong evidence for every detected case of contamination. We evaluate DyePack on five models across three datasets, covering both multiple-choice and open-ended generation tasks. For multiple-choice questions, it successfully detects all contaminated models with guaranteed FPRs as low as 0.000073% on MMLU-Pro and 0.000017% on Big-Bench-Hard using eight backdoors. For open-ended generation tasks, it generalizes well and identifies all contaminated models on Alpaca with a guaranteed false positive rate of just 0.127% using six backdoors.