Muhan Gao

Muhan Gao, Jash Shah, Weiqi Wang et al.

Scientific knowledge is growing rapidly, making it difficult to track progress and high-level conceptual links across broad disciplines. While tools like citation networks and search engines help retrieve related papers, they lack the abstraction needed to capture the needed to represent the density and structure of activity across subfields. We motivate SCIENCE HIERARCHOGRAPHY, the goal of organizing scientific literature into a high-quality hierarchical structure that spans multiple levels of abstraction -- from broad domains to specific studies. Such a representation can provide insights into which fields are well-explored and which are under-explored. To achieve this goal, we develop a hybrid approach that combines efficient embedding-based clustering with LLM-based prompting, striking a balance between scalability and semantic precision. Compared to LLM-heavy methods like iterative tree construction, our approach achieves superior quality-speed trade-offs. Our hierarchies capture different dimensions of research contributions, reflecting the interdisciplinary and multifaceted nature of modern science. We evaluate its utility by measuring how effectively an LLM-based agent can navigate the hierarchy to locate target papers. Results show that our method improves interpretability and offers an alternative pathway for exploring scientific literature beyond traditional search methods. Code, data and demo are available: https://github.com/JHU-CLSP/science-hierarchography

Muhan Gao, Zih-Ching Chen, Kuan-Hao Huang

As large language models are increasingly deployed in retrieval-augmented generation and agentic systems that accumulate extensive context, understanding how distracting information affects long-context performance becomes critical. Prior work shows that semantically relevant yet misleading documents degrade performance, but the quantitative relationship between the proportion of distractors and performance remains unstudied. In this work, we systematically vary the hard-distractor proportion in fixed-length contexts, revealing a striking nonlinear pattern: as the proportion of hard distractors increases, performance drops sharply within the first small fraction, while the remainder of the range yields only marginal additional decline. We term this ''The First Drop of Ink'' effect, analogous to how a single drop of ink contaminates water. Our theoretical and empirical analyses grounded in attention mechanics show that hard distractors capture disproportionate attention even at small proportions, with diminishing marginal impact as their proportion grows. Controlled experiments further show that filtering gains mainly come from context-length reduction rather than distractor removal; substantial recovery requires reducing the hard-distractor proportion to near zero, highlighting the importance of upstream retrieval precision.

Zhouxiang Fang, Aayush Mishra, Muhan Gao et al.

Recent works have suggested that In-Context Learning (ICL) operates in dual modes, i.e. task retrieval (remember learned patterns from pre-training) and task learning (inference-time ''learning'' from demonstrations). However, disentangling these the two modes remains a challenging goal. We introduce ICL CIPHERS, a class of task reformulations based on substitution ciphers borrowed from classic cryptography. In this approach, a subset of tokens in the in-context inputs are substituted with other (irrelevant) tokens, rendering English sentences less comprehensible to human eye. However, by design, there is a latent, fixed pattern to this substitution, making it reversible. This bijective (reversible) cipher ensures that the task remains a well-defined task in some abstract sense, despite the transformations. It is a curious question if LLMs can solve tasks reformulated by ICL CIPHERS with a BIJECTIVE mapping, which requires ''deciphering'' the latent cipher. We show that LLMs are better at solving tasks reformulated by ICL CIPHERS with BIJECTIVE mappings than the NON-BIJECTIVE (irreversible) baseline, providing a novel approach to quantify ''learning'' in ICL. While this gap is small, it is consistent across the board on four datasets and six models. Finally, we examine LLMs' internal representations and identify evidence in their ability to decode the ciphered inputs.

Taiming Lu, Muhan Gao, Kuai Yu et al.

Large Language Models (LLMs) exhibit positional bias, struggling to utilize information from the middle or end of long contexts. Our study explores LLMs' long-context reasoning by probing their hidden representations. We find that while LLMs encode the position of target information, they often fail to leverage this in generating accurate responses. This reveals a disconnect between information retrieval and utilization, a "know but don't tell" phenomenon. We further analyze the relationship between extraction time and final accuracy, offering insights into the underlying mechanics of transformer models.