Prompts in the Wild: A Large Analyzed Collection of Transactional Prompts in Code

The behavior of contemporary generative Large Language Models (LLMs) is directly shaped by prompts, unstructured texts that describe the desired output and model behavior. In this paper we argue that prompts are linguistic objects that merit investigation in their own right. To this end, we collect 57.5K unique samples of prompts from GitHub. Specifically, we focus on transactional prompts: reproducible natural language instructions that are integrated into software. To enable the empirical, quantitative study of prompts, we introduce a structured ontology, capturing the properties of prompts as well as their formal and semantic components. Based on this ontology, we transform prompts from unstructured raw texts into richly structured linguistic objects. Analysis of these structured data reveals significant diversity of usage patterns across languages, domains, tasks, and modalities, in a typical Zipf-like distribution where some clearly prevail and others, more diverse, appear in the long tail. To validate the reliability of the ontology-based annotation of the prompts, we perform a comprehensive error analysis across all fields, providing a detailed assessment of annotation quality. We release the dataset together with a browsing and exploration interface (https://github.com/OnlpLab/transactionalPromptsCollection ).

MANCE: Manifold Aware Concept Erasure

Concept erasure aims to remove a target concept from a representation while preserving the other information encoded in it. This is difficult because representations encode many concepts that are often correlated with the erasure target, so removing the target risks damaging them. We propose the Manifold Constraint Hypothesis (MCH): if natural representations concentrate on a structured, lower-dimensional manifold, then interventions should be constrained to that manifold and better preserve other information encoded in the representation during interventions. We instantiate MCH in a new concept erasure method: MANifold aware Concept Erasure (MANCE). MANCE performs iterative updates to the representations using signals from a classifier that predicts a target concept. We estimate the manifold using representations obtained from natural inputs, and then we project the concept removal update to the estimated manifold. We perform extensive evaluation on 119 settings spanning text and vision, including 13 language models, three NLP concepts, and 40 CelebA-CLIP attributes. Employing MANCE on top of previous methods shows consistent improved leakage results. We also introduce MANCE+ and MANCE++, which prepend a closed-form erasure algorithm before employing MANCE, achieving better leakage--surgicality tradeoffs relative to matched full-space updates. MANCE++, our best method, achieves state-of-the-art results on nonlinear concept erasure. These results support MCH in the erasure setting: interventions should be constrained to the natural representation manifold.

Factual Retrieval in LLMs Is a Redundant, Distributed and Non-Contiguous Process

Large language models (LLMs) store and recall factual knowledge, yet the precise mechanism of how entity representations are transformed to enable specific attribute retrieval remains underexplored. In this work, we investigate this mechanism through the lens of an "attribute-computation path"-a sequence of computational steps over the entity representation required to elicit a target attribute. We then propose an iterative patching protocol to identify a minimal subset of layers necessary for this computation. Applying our method to LLaMA 3.1 8B and Qwen3 8B, we find that these paths are non-contiguous, often skipping layers, and that models possess multiple, functionally-equivalent paths for the same entity and fact, highlighting a high degree of redundancy in attribute computation. This implies that knowledge computation is highly distributed, potentially explaining the localization-editing mismatch and suggesting that knowledge storage and retrieval in LLMs is far from being well understood.

Forecasting Future Behavior as a Learning Task

Trust in an AI system is often anchored by explanations of how it works, which one then uses to forecast its behavior on new inputs. For large reasoning models (LRMs), this conventional route is particularly difficult to follow: explanation methods for single token generations do not naturally generalize to long trajectories, and the trajectories themselves are often not faithful when read as natural language. We propose an alternative that bypasses the explanation step: treat behavior forecasting as a learnable task and train Behavior Forecasters that operates on a single reasoning trajectory to make the same forecasts one would typically seek from an explanation. The forecaster's training data is obtained by querying the LRM with no human annotation, and its inference is done in a single forward pass. We instantiate this approach on two tasks: how likely the LRM is to repeat its answer on re-runs, and how removing parts of the input changes its answer. We evaluate this approach on both tasks across three diverse reasoning datasets and find that trained Behavior Forecasters are more accurate than GPT-5.4 and Claude Opus-4.6 reading the same trajectories as naive readers, at a small fraction of their inference cost. We find that fine-tuning the backbone end-to-end and initializing it from the target LRM are each necessary for strong performance. These results show that the reasoning trajectory carries information about the LRM's future behavior that goes beyond what naive reading conveys.

A Language for Describing Agentic LLM Contexts

Large language models are increasingly used within larger systems ("LLM agents"). These make a sequence of LLM calls, each call providing the LLM with a combination of instructions, observations, and interaction history. The design of the encoded information and its structure play a central role in the quality of the resulting system, leading to efforts spent on context engineering. It is therefore critical to communicate the composition of the LLM context in a system, and how it evolves over time. Yet, no standard exists for doing so: context construction is typically conveyed through informal prose, ad hoc diagrams, or direct inspection of code, none of which precisely capture how a prompt evolves across interaction steps or how two context representation strategies differ. To remedy this, we introduce the Agentic Context Description Language (ACDL), a language for specifying the structure and dynamics of LLM input contexts in a precise, readable, and standard manner, along with visualizations. ACDL provides constructs for specifying context aspects such as role message sequences, dynamic content, time-indexed references, and conditional or iterative structure, capturing the full architecture of a prompt independently of any particular implementation. ACDL diagrams can be hand drawn on a whiteboard, or written in formal language which can then be rendered. We describe the language, demonstrate it by documenting several existing systems and their variants, and encourage the community to adopt it for describing LLM systems context, both in day-to-day communication and in papers. Tooling, examples and documentation are available at www.acdlang.org.

PRISM: PRIor from corpus Statistics for topic Modeling

Topic modeling seeks to uncover latent semantic structure in text, with LDA providing a foundational probabilistic framework. While recent methods often incorporate external knowledge (e.g., pre-trained embeddings), such reliance limits applicability in emerging or underexplored domains. We introduce \textbf{PRISM}, a corpus-intrinsic method that derives a Dirichlet parameter from word co-occurrence statistics to initialize LDA without altering its generative process. Experiments on text and single cell RNA-seq data show that PRISM improves topic coherence and interpretability, rivaling models that rely on external knowledge. These results underscore the value of corpus-driven initialization for topic modeling in resource-constrained settings. Code is available at: https://github.com/shaham-lab/PRISM.

Understanding Usage and Engagement in AI-Powered Scientific Research Tools: The Asta Interaction Dataset

AI-powered scientific research tools are rapidly being integrated into research workflows, yet the field lacks a clear lens into how researchers use these systems in real-world settings. We present and analyze the Asta Interaction Dataset, a large-scale resource comprising over 200,000 user queries and interaction logs from two deployed tools (a literature discovery interface and a scientific question-answering interface) within an LLM-powered retrieval-augmented generation platform. Using this dataset, we characterize query patterns, engagement behaviors, and how usage evolves with experience. We find that users submit longer and more complex queries than in traditional search, and treat the system as a collaborative research partner, delegating tasks such as drafting content and identifying research gaps. Users treat generated responses as persistent artifacts, revisiting and navigating among outputs and cited evidence in non-linear ways. With experience, users issue more targeted queries and engage more deeply with supporting citations, although keyword-style queries persist even among experienced users. We release the anonymized dataset and analysis with a new query intent taxonomy to inform future designs of real-world AI research assistants and to support realistic evaluation.

State over Tokens: Characterizing the Role of Reasoning Tokens

Large Language Models (LLMs) can generate reasoning tokens before their final answer to boost performance on complex tasks. While these sequences seem like human thought processes, empirical evidence reveals that they are not a faithful explanation of the model's actual reasoning process. To address this gap between appearance and function, we introduce the State over Tokens (SoT) conceptual framework. SoT reframes reasoning tokens not as a linguistic narrative, but as an externalized computational state -- the sole persistent information carrier across the model's stateless generation cycles. This explains how the tokens can drive correct reasoning without being a faithful explanation when read as text and surfaces previously overlooked research questions on these tokens. We argue that to truly understand the process that LLMs do, research must move beyond reading the reasoning tokens as text and focus on decoding them as state.

AstaBench: Rigorous Benchmarking of AI Agents with a Scientific Research Suite

AI agents hold the potential to revolutionize scientific productivity by automating literature reviews, replicating experiments, analyzing data, and even proposing new directions of inquiry; indeed, there are now many such agents, ranging from general-purpose "deep research" systems to specialized science-specific agents, such as AI Scientist and AIGS. Rigorous evaluation of these agents is critical for progress. Yet existing benchmarks fall short on several fronts: they (1) fail to provide holistic, product-informed measures of real-world use cases such as science research; (2) lack reproducible agent tools necessary for a controlled comparison of core agentic capabilities; (3) do not account for confounding variables such as model cost and tool access; (4) do not provide standardized interfaces for quick agent prototyping and evaluation; and (5) lack comprehensive baseline agents necessary to identify true advances. In response, we define principles and tooling for more rigorously benchmarking agents. Using these, we present AstaBench, a suite that provides the first holistic measure of agentic ability to perform scientific research, comprising 2400+ problems spanning the entire scientific discovery process and multiple scientific domains, and including many problems inspired by actual user requests to deployed Asta agents. Our suite comes with the first scientific research environment with production-grade search tools that enable controlled, reproducible evaluation, better accounting for confounders. Alongside, we provide a comprehensive suite of nine science-optimized classes of Asta agents and numerous baselines. Our extensive evaluation of 57 agents across 22 agent classes reveals several interesting findings, most importantly that despite meaningful progress on certain individual aspects, AI remains far from solving the challenge of science research assistance.

Efficient Decoding Methods for Language Models on Encrypted Data

Large language models (LLMs) power modern AI applications, but processing sensitive data on untrusted servers raises privacy concerns. Homomorphic encryption (HE) enables computation on encrypted data for secure inference. However, neural text generation requires decoding methods like argmax and sampling, which are non-polynomial and thus computationally expensive under encryption, creating a significant performance bottleneck. We introduce cutmax, an HE-friendly argmax algorithm that reduces ciphertext operations compared to prior methods, enabling practical greedy decoding under encryption. We also propose the first HE-compatible nucleus (top-p) sampling method, leveraging cutmax for efficient stochastic decoding with provable privacy guarantees. Both techniques are polynomial, supporting efficient inference in privacy-preserving settings. Moreover, their differentiability facilitates gradient-based sequence-level optimization as a polynomial alternative to straight-through estimators. We further provide strong theoretical guarantees for cutmax, proving it converges globally to a unique two-level fixed point, independent of the input values beyond the identity of the maximizer, which explains its rapid convergence in just a few iterations. Evaluations on realistic LLM outputs show latency reductions of 24x-35x over baselines, advancing secure text generation.