Research groups face persistent challenges in capturing, storing, and retrieving knowledge that is distributed across team members. Although structured data intended for analysis and publication is often well managed, much of a group's collective knowledge remains informal, fragmented, or undocumented--often passed down orally through meetings, mentoring, and day-to-day collaboration. This includes private resources such as emails, meeting notes, training materials, and ad hoc documentation. Together, these reflect the group's tacit knowledge--the informal, experience-based expertise that underlies much of their work. Accessing this knowledge can be difficult, requiring significant time and insider understanding. Retrieval-augmented generation (RAG) systems offer promising solutions by enabling users to query and generate responses grounded in relevant source material. However, most current RAG-LLM systems are oriented toward public documents and overlook the privacy concerns of internal research materials. We introduce AquiLLM (pronounced ah-quill-em), a lightweight, modular RAG system designed to meet the needs of research groups. AquiLLM supports varied document types and configurable privacy settings, enabling more effective access to both formal and informal knowledge within scholarly groups.

Attention sink (AS) is a consistent pattern in transformer attention maps where certain tokens (often special tokens or positional anchors) disproportionately attract attention from other tokens. We show that in transformers, AS is not an architectural artifact, but it is the manifestation of a fundamental geometric principle: the establishment of reference frames that anchor representational spaces. We analyze several architectures and identify three distinct reference frame types, centralized, distributed, and bidirectional, that correlate with the attention sink phenomenon. We show that they emerge during the earliest stages of training as optimal solutions to the problem of establishing stable coordinate systems in high-dimensional spaces. We show the influence of architecture components, particularly position encoding implementations, on the specific type of reference frame. This perspective transforms our understanding of transformer attention mechanisms and provides insights for both architecture design and the relationship with AS.

With the rapid evolution of multimodal large language models, the capacity to deeply understand and interpret human intentions has emerged as a critical capability, which demands detailed and thoughtful reasoning. In recent studies, Reinforcement Learning (RL) has demonstrated potential in enhancing the reasoning capabilities of Large Language Models (LLMs). Nonetheless, the challenges associated with adapting RL to multimodal data and formats remain largely unaddressed. In this paper, we identify two issues in existing multimodal reasoning models: insufficient global context understanding and shortcut problems. Insufficient context understanding can happen when a model misinterprets multimodal context, resulting in incorrect answers. The shortcut problem occurs when the model overlooks crucial clues in multimodal inputs, directly addressing the query without considering the multimodal information. To tackle these issues, we emphasize the necessity for the model to reason with a clear understanding of the global context within multimodal inputs. This global context understanding can effectively prevent the model from overlooking key multimodal cues and ensure a thorough reasoning process. To ensure the accurate interpretation of multimodal context information, we implement a context reward judged by a large language model, alongside format and accuracy rewards. Additionally, to improve complex reasoning capability, we employ the LLM to assess the logical reward, determining whether the reasoning process successfully integrates multimodal information with logical methods. We also introduce a reasoning omni-modal benchmark, IntentBench, aimed at evaluating models in understanding complex human intentions and emotions. Our proposed method demonstrates advanced performance across multiple omni-modal benchmarks compared to other open-source omni-modal models.

Large language models (LLMs) have shown significant potential to change how we write, communicate, and create, leading to rapid adoption across society. This dissertation examines how individuals and institutions are adapting to and engaging with this emerging technology through three research directions. First, I demonstrate how the institutional adoption of AI detectors introduces systematic biases, particularly disadvantaging writers of non-dominant language varieties, highlighting critical equity concerns in AI governance. Second, I present novel population-level algorithmic approaches that measure the increasing adoption of LLMs across writing domains, revealing consistent patterns of AI-assisted content in academic peer reviews, scientific publications, consumer complaints, corporate communications, job postings, and international organization press releases. Finally, I investigate LLMs' capability to provide feedback on research manuscripts through a large-scale empirical analysis, offering insights into their potential to support researchers who face barriers in accessing timely manuscript feedback, particularly early-career researchers and those from under-resourced settings.

Summarizing long-form narratives--such as books, movies, and TV scripts--requires capturing intricate plotlines, character interactions, and thematic coherence, a task that remains challenging for existing LLMs. We introduce NexusSum, a multi-agent LLM framework for narrative summarization that processes long-form text through a structured, sequential pipeline--without requiring fine-tuning. Our approach introduces two key innovations: (1) Dialogue-to-Description Transformation: A narrative-specific preprocessing method that standardizes character dialogue and descriptive text into a unified format, improving coherence. (2) Hierarchical Multi-LLM Summarization: A structured summarization pipeline that optimizes chunk processing and controls output length for accurate, high-quality summaries. Our method establishes a new state-of-the-art in narrative summarization, achieving up to a 30.0% improvement in BERTScore (F1) across books, movies, and TV scripts. These results demonstrate the effectiveness of multi-agent LLMs in handling long-form content, offering a scalable approach for structured summarization in diverse storytelling domains.

The general public often encounters complex texts but does not have the time or expertise to fully understand them, leading to the spread of misinformation. Automatic Text Simplification (ATS) helps make information more accessible, but its evaluation methods have not kept up with advances in text generation, especially with Large Language Models (LLMs). In particular, recent studies have shown that current ATS metrics do not correlate with the presence of errors. Manual inspections have further revealed a variety of errors, underscoring the need for a more nuanced evaluation framework, which is currently lacking. This resource paper addresses this gap by introducing a test collection for detecting and classifying errors in simplified texts. First, we propose a taxonomy of errors, with a formal focus on information distortion. Next, we introduce a parallel dataset of automatically simplified scientific texts. This dataset has been human-annotated with labels based on our proposed taxonomy. Finally, we analyze the quality of the dataset, and we study the performance of existing models to detect and classify errors from that taxonomy. These contributions give researchers the tools to better evaluate errors in ATS, develop more reliable models, and ultimately improve the quality of automatically simplified texts.

The Unlearning Sensitive Content from Large Language Models task aims to remove targeted datapoints from trained models while minimally affecting their general knowledge. In our work, we leverage parameter-efficient, gradient-based unlearning using low-rank (LoRA) adaptation and layer-focused fine-tuning. To further enhance unlearning effectiveness, we employ data chunking, splitting forget data into disjoint partitions and merging them with cyclically sampled retain samples at a pre-defined ratio. Our task-agnostic method achieves an outstanding forget-retain balance, ranking first on leaderboards and significantly outperforming baselines and competing systems.

Purpose: We present a virtual model to optimize point of entry (POE) in lung biopsy planning systems. Our model allows to compute the quality of a biopsy sample taken from potential POE, taking into account the margin of error that arises from discrepancies between the orientation in the planning simulation and the actual orientation during the operation. Additionally, the study examines the impact of the characteristics of the lesion. Methods: The quality of the biopsy is given by a heatmap projected onto the skeleton of a patient-specific model of airways. The skeleton provides a 3D representation of airways structure, while the heatmap intensity represents the potential amount of tissue that it could be extracted from each POE. This amount of tissue is determined by the intersection of the lesion with a cone that represents the uncertainty area in the introduction of biopsy instruments. The cone, lesion, and skeleton are modelled as graphical objects that define a 3D scene of the intervention. Results: We have simulated different settings of the intervention scene from a single anatomy extracted from a CT scan and two lesions with regular and irregular shapes. The different scenarios are simulated by systematic rotation of each lesion placed at different distances from airways. Analysis of the heatmaps for the different settings show a strong impact of lesion orientation for irregular shape and the distance for both shapes. Conclusion: The proposed heatmaps help to visually assess the optimal POE and identify whether multiple optimal POEs exist in different zones of the bronchi. They also allow us to model the maximum allowable error in navigation systems and study which variables have the greatest influence on the success of the operation. Additionally, they help determine at what point this influence could potentially jeopardize the operation.

Many important scientific problems involve multivariate optimization coupled with slow and laborious experimental measurements. These complex, high-dimensional searches can be defined by non-convex optimization landscapes that resemble needle-in-a-haystack surfaces, leading to entrapment in local minima. Contextualizing optimizers with human domain knowledge is a powerful approach to guide searches to localized fruitful regions. However, this approach is susceptible to human confirmation bias and it is also challenging for domain experts to keep track of the rapidly expanding scientific literature. Here, we propose the use of Large Language Models (LLMs) for contextualizing Bayesian optimization (BO) via a hybrid optimization framework that intelligently and economically blends stochastic inference with domain knowledge-based insights from the LLM, which is used to suggest new, better-performing areas of the search space for exploration. Our method fosters user engagement by offering real-time commentary on the optimization progress, explaining the reasoning behind the search strategies. We validate the effectiveness of our approach on synthetic benchmarks with up to 15 independent variables and demonstrate the ability of LLMs to reason in four real-world experimental tasks where context-aware suggestions boost optimization performance substantially.

This paper introduces CaseSumm, a novel dataset for long-context summarization in the legal domain that addresses the need for longer and more complex datasets for summarization evaluation. We collect 25.6K U.S. Supreme Court (SCOTUS) opinions and their official summaries, known as "syllabuses." Our dataset is the largest open legal case summarization dataset, and is the first to include summaries of SCOTUS decisions dating back to 1815. We also present a comprehensive evaluation of LLM-generated summaries using both automatic metrics and expert human evaluation, revealing discrepancies between these assessment methods. Our evaluation shows Mistral 7b, a smaller open-source model, outperforms larger models on most automatic metrics and successfully generates syllabus-like summaries. In contrast, human expert annotators indicate that Mistral summaries contain hallucinations. The annotators consistently rank GPT-4 summaries as clearer and exhibiting greater sensitivity and specificity. Further, we find that LLM-based evaluations are not more correlated with human evaluations than traditional automatic metrics. Furthermore, our analysis identifies specific hallucinations in generated summaries, including precedent citation errors and misrepresentations of case facts. These findings demonstrate the limitations of current automatic evaluation methods for legal summarization and highlight the critical role of human evaluation in assessing summary quality, particularly in complex, high-stakes domains. CaseSumm is available at https://huggingface.co/datasets/ChicagoHAI/CaseSumm