VILLA: Versatile Information Retrieval From Scientific Literature Using Large LAnguage Models

The lack of high-quality ground truth datasets to train machine learning (ML) models impedes the potential of artificial intelligence (AI) for science research. Scientific information extraction (SIE) from the literature using LLMs is emerging as a powerful approach to automate the creation of these datasets. However, existing LLM-based approaches and benchmarking studies for SIE focus on broad topics such as biomedicine and chemistry, are limited to choice-based tasks, and focus on extracting information from short and well-formatted text. The potential of SIE methods in complex, open-ended tasks is considerably under-explored. In this study, we used a domain that has been virtually ignored in SIE, namely virology, to address these research gaps. We design a unique, open-ended SIE task of extracting mutations in a given virus that modify its interaction with the host. We develop a new, multi-step retrieval augmented generation (RAG) framework called VILLA for SIE. In parallel, we curate a novel dataset of 629 mutations in ten influenza A virus proteins obtained from 239 scientific publications to serve as ground truth for the mutation extraction task. Finally, we demonstrate VILLA's superior performance using a novel and comprehensive evaluation and comparison with vanilla RAG and other state-of-the art RAG- and agent-based tools for SIE.

When AI Shows Its Work, Is It Actually Working? Step-Level Evaluation Reveals Frontier Language Models Frequently Bypass Their Own Reasoning

Language models increasingly "show their work" by writing step-by-step reasoning before answering. But are these reasoning steps genuinely used, or decorative narratives generated after the model has already decided? Consider: a medical AI writes "The patient's eosinophilia and livedo reticularis following catheterization suggest cholesterol embolization syndrome. Answer: B." If we remove the eosinophilia observation, does the diagnosis change? For most frontier models, the answer is no - the step was decorative. We introduce step-level evaluation: remove one reasoning sentence at a time and check whether the answer changes. This simple test requires only API access -- no model weights -- and costs approximately $1-2 per model per task. Testing 10 frontier models (GPT-5.4, Claude Opus, DeepSeek-V3.2, MiniMax-M2.5, Kimi-K2.5, and others) across sentiment, mathematics, topic classification, and medical QA (N=376-500 each), the majority produce decorative reasoning: removing any step changes the answer less than 17% of the time, while any single step alone recovers the answer. This holds even on math, where smaller models (0.8-8B) show genuine step dependence (55% necessity). Two models break the pattern: MiniMax-M2.5 on sentiment (37% necessity) and Kimi-K2.5 on topic classification (39%) - but both shortcut other tasks. Faithfulness is model-specific and task-specific. We also discover "output rigidity": on the same medical questions, Claude Opus writes 11 diagnostic steps while GPT-OSS-120B outputs a single token. Mechanistic analysis (attention patterns) confirms that CoT attention drops more in late layers for decorative tasks (33%) than faithful ones (20%). Implications: step-by-step explanations from frontier models are largely decorative, per-model per-domain evaluation is essential, and training objectives - not scale - determine whether reasoning is genuine.

Reddit After Roe: A Computational Analysis of Abortion Narratives and Barriers in the Wake of Dobbs

The 2022 U.S. Supreme Court decision in Dobbs v. Jackson Women's Health Organization reshaped the reproductive rights landscape, introducing new uncertainty and barriers to abortion access. We present a large-scale computational analysis of abortion discourse on Reddit, examining how barriers to access are articulated across information-seeking and information-sharing behaviors, different stages of abortion (before, during, after), and three phases of the Dobbs decision in 2022. Drawing on more than 17,000 posts from four abortion-related subreddits, we employed a multi-step pipeline to classify posts by information type, abortion stage, barrier category, and expressed emotions. Using a codebook of eight barrier types, including legal, financial, emotional, and social obstacles, we analyzed their associations with emotions and information behaviors. Topic modeling of model-generated barrier rationales further revealed how discourse evolved in response to shifting legal and cultural contexts. Our findings show that emotional and psychological barriers consistently dominate abortion narratives online, with emotions such as nervousness, confusion, fear, and sadness prevalent across discourse. By linking information behaviors, barriers, emotions, and temporal dynamics, this study provides a multi-dimensional account of how abortion is navigated in online communities.

Knowledge Access Beats Model Size: Memory Augmented Routing for Persistent AI Agents

Production AI agents frequently receive user-specific queries that are highly repetitive, with up to 47\% being semantically similar to prior interactions, yet each query is typically processed with the same computational cost. We argue that this redundancy can be exploited through conversational memory, transforming repetition from a cost burden into an efficiency advantage. We propose a memory-augmented inference framework in which a lightweight 8B-parameter model leverages retrieved conversational context to answer all queries via a low-cost inference path. Without any additional training or labeled data, this approach achieves 30.5\% F1, recovering 69\% of the performance of a full-context 235B model while reducing effective cost by 96\%. Notably, a 235B model without memory (13.7\% F1) underperforms even the standalone 8B model (15.4\% F1), indicating that for user-specific queries, access to relevant knowledge outweighs model scale. We further analyze the role of routing and confidence. At practical confidence thresholds, routing alone already directs 96\% of queries to the small model, but yields poor accuracy (13.0\% F1) due to confident hallucinations. Memory does not substantially alter routing decisions; instead, it improves correctness by grounding responses in retrieved user-specific information. As conversational memory accumulates over time, coverage of recurring topics increases, further narrowing the performance gap. We evaluate on 152 LoCoMo questions (Qwen3-8B/235B) and 500 LongMemEval questions. Incorporating hybrid retrieval (BM25 + cosine similarity) improves performance by an additional +7.7 F1, demonstrating that retrieval quality directly enhances end-to-end system performance. Overall, our results highlight that memory, rather than model size, is the primary driver of accuracy and efficiency in persistent AI agents.

On the Failure of Topic-Matched Contrast Baselines in Multi-Directional Refusal Abliteration

Inasmuch as the removal of refusal behavior from instruction-tuned language models by directional abliteration requires the extraction of refusal-mediating directions from the residual stream activation space, and inasmuch as the construction of the contrast baseline against which harmful prompt activations are compared has been treated in the existing literature as an implementation detail rather than a methodological concern, the present work investigates whether a topically matched contrast baseline yields superior refusal directions. The investigation is carried out on the Qwen~3.5 2B model using per-category matched prompt pairs, per-class Self-Organizing Map extraction, and Singular Value Decomposition orthogonalization. It was found that topic-matched contrast produces no functional refusal directions at any tested weight level on any tested layer, while unmatched contrast on the same model, same extraction code, and same evaluation protocol achieves complete refusal elimination on six layers. The geometric analysis of the failure establishes that topic-matched subtraction cancels the dominant activation component shared between harmful and harmless prompts of the same subject, reducing the extracted direction magnitude below the threshold at which weight-matrix projection perturbs the residual stream. The implications for the design of contrast baselines in abliteration research are discussed.

AwesomeLit: Towards Hypothesis Generation with Agent-Supported Literature Research

There are different goals for literature research, from understanding an unfamiliar topic to generate hypothesis for the next research project. The nature of literature research also varies according to user's familiarity level of the topic. For inexperienced researchers, identifying gaps in the existing literature and generating feasible hypothesis are crucial but challenging. While general ``deep research'' tools can be used, they are not designed for such use case, thus often not effective. In addition, the ``black box" nature and hallucination of Large Language Models (LLMs) often lead to distrust. In this paper, we introduce a human-agent collaborative visualization system AwesomeLit to address this need. It has several novel features: a transparent user-steerable agentic workflow; a dynamically generated query exploring tree, visualizing the exploration path and provenance; and a semantic similarity view, depicting the relationships between papers. It enables users to transition from general intentions to detailed research topics. Finally, a qualitative study involving several early researchers showed that AwesomeLit is effective in helping users explore unfamiliar topics, identify promising research directions, and improve confidence in research results.

When Documents Disagree: Measuring Institutional Variation in Transplant Guidance with Retrieval-Augmented Language Models

Patient education materials for solid-organ transplantation vary substantially across U.S. centers, yet no systematic method exists to quantify this heterogeneity at scale. We introduce a framework that grounds the same patient questions in different centers' handbooks using retrieval-augmented language models and compares the resulting answers using a five-label consistency taxonomy. Applied to 102 handbooks from 23 centers and 1,115 benchmark questions, the framework quantifies heterogeneity across four dimensions: question, topic, organ, and center. We find that 20.8% of non-absent pairwise comparisons exhibit clinically meaningful divergence, concentrated in condition monitoring and lifestyle topics. Coverage gaps are even more prominent: 96.2% of question-handbook pairs miss relevant content, with reproductive health at 95.1% absence. Center-level divergence profiles are stable and interpretable, where heterogeneity reflects systematic institutional differences, likely due to patient diversity. These findings expose an information gap in transplant patient education materials, with document-grounded medical question answering highlighting opportunities for content improvement.

Conversation Tree Architecture: A Structured Framework for Context-Aware Multi-Branch LLM Conversations

Large language models (LLMs) are increasingly deployed for extended, multi-topic conversations, yet the flat, append-only structure of current conversation interfaces introduces a fundamental limitation: all context accumulates in a single unbounded window, causing topically distinct threads to bleed into one another and progressively degrade response quality. We term this failure mode logical context poisoning. In this paper, we introduce the Conversation Tree Architecture (CTA), a hierarchical framework that organizes LLM conversations as trees of discrete, context-isolated nodes. Each node maintains its own local context window; structured mechanisms govern how context flows between parent and child nodes, downstream on branch creation and upstream on branch deletion. We additionally introduce volatile nodes, transient branches whose local context must be selectively merged upward or permanently discarded before purging. We formalize the architecture's primitives, characterize the open design problems in context flow, relate our framework to prior work in LLM memory management, and describe a working prototype implementation. The CTA provides a principled foundation for structured conversational context management and extends naturally to multi-agent settings.

HiCI: Hierarchical Construction-Integration for Long-Context Attention

Long-context language modeling is commonly framed as a scalability challenge of token-level attention, yet local-to-global information structuring remains largely implicit in existing approaches. Drawing on cognitive theories of discourse comprehension, we propose HiCI (Hierarchical Construction--Integration), a hierarchical attention module that constructs segment-level representations, integrates them into a shared global context, and broadcasts both to condition segment-level attention. We validate HiCI through parameter-efficient adaptation of LLaMA-2 with only <5.5% additional parameters, extending context from 4K to 100K tokens (7B) and 64K tokens (13B). Across language modeling, retrieval, and instruction-following benchmarks, HiCI yields consistent improvements over strong baselines, including matching proprietary models on topic retrieval and surpassing GPT-3.5-Turbo-16K on code comprehension. These results demonstrate the effectiveness of explicit hierarchical structuring as an inductive bias for long-context modeling.

Hybrid topic modelling for computational close reading: Mapping narrative themes in Pushkin's Evgenij Onegin

This study presents a hybrid topic modelling framework for computational literary analysis that integrates Latent Dirichlet Allocation (LDA) with sparse Partial Least Squares Discriminant Analysis (sPLS-DA) to model thematic structure and longitudinal dynamics in narrative poetry. As a case study, we analyse Evgenij Onegin-Aleksandr S. Pushkin's novel in verse-using an Italian translation, testing whether unsupervised and supervised lexical structures converge in a small-corpus setting. The poetic text is segmented into thirty-five documents of lemmatised content words, from which five stable and interpretable topics emerge. To address small-corpus instability, a multi-seed consensus protocol is adopted. Using sPLS-DA as a supervised probe enhances interpretability by identifying lexical markers that refine each theme. Narrative hubs-groups of contiguous stanzas marking key episodes-extend the bag-of-words approach to the narrative level, revealing how thematic mixtures align with the poem's emotional and structural arc. Rather than replacing traditional literary interpretation, the proposed framework offers a computational form of close reading, illustrating how lightweight probabilistic models can yield reproducible thematic maps of complex poetic narratives, even when stylistic features such as metre, phonology, or native morphology are abstracted away. Despite relying on a single lemmatised translation, the approach provides a transparent methodological template applicable to other high-density literary texts in comparative studies.