Logical reasoning is a core capability for large language models (LLMs), yet existing benchmarks that rely solely on final-answer accuracy fail to capture the quality of the reasoning process. To address this, we introduce FineLogic, a fine-grained evaluation framework that assesses logical reasoning across three dimensions: overall accuracy, stepwise soundness, and representation-level probing. Leveraging this framework, we conduct a comprehensive study on how different supervision formats in fine-tuning shape reasoning abilities. We fine-tune LLMs on four supervision styles: one in natural language and three symbolic variants. We find a key trade-off: natural language supervision excels at generalization to out-of-distribution and long-chain problems, whereas symbolic supervision is superior at instilling structurally sound, atomic reasoning steps. Furthermore, our probing analysis indicates that fine-tuning primarily refines the model's step-by-step generation process, rather than improving its ability to converge on an answer early. Together, our framework and analysis provide a more rigorous lens for evaluating and improving logical reasoning in LLMs. The code is available at https://github.com/YujunZhou/FineLogic.

Bidirectional language models have better context understanding and perform better than unidirectional models on natural language understanding tasks, yet the theoretical reasons behind this advantage remain unclear. In this work, we investigate this disparity through the lens of the Information Bottleneck (IB) principle, which formalizes a trade-off between compressing input information and preserving task-relevant content. We propose FlowNIB, a dynamic and scalable method for estimating mutual information during training that addresses key limitations of classical IB approaches, including computational intractability and fixed trade-off schedules. Theoretically, we show that bidirectional models retain more mutual information and exhibit higher effective dimensionality than unidirectional models. To support this, we present a generalized framework for measuring representational complexity and prove that bidirectional representations are strictly more informative under mild conditions. We further validate our findings through extensive experiments across multiple models and tasks using FlowNIB, revealing how information is encoded and compressed throughout training. Together, our work provides a principled explanation for the effectiveness of bidirectional architectures and introduces a practical tool for analyzing information flow in deep language models.

Diffusion language models offer parallel token generation and inherent bidirectionality, promising more efficient and powerful sequence modeling compared to autoregressive approaches. However, state-of-the-art diffusion models (e.g., Dream 7B, LLaDA 8B) suffer from slow inference. While they match the quality of similarly sized autoregressive (AR) models (e.g., Qwen2.5 7B, Llama3 8B), their iterative denoising requires multiple full-sequence forward passes, resulting in high computational costs and latency, particularly for long input prompts and long-context scenarios. Furthermore, parallel token generation introduces token incoherence problems, and current sampling heuristics suffer from significant quality drops with decreasing denoising steps. We address these limitations with two training-free techniques. First, we propose FreeCache, a Key-Value (KV) approximation caching technique that reuses stable KV projections across denoising steps, effectively reducing the computational cost of DLM inference. Second, we introduce Guided Diffusion, a training-free method that uses a lightweight pretrained autoregressive model to supervise token unmasking, dramatically reducing the total number of denoising iterations without sacrificing quality. We conduct extensive evaluations on open-source reasoning benchmarks, and our combined methods deliver an average of 12.14x end-to-end speedup across various tasks with negligible accuracy degradation. For the first time, diffusion language models achieve a comparable and even faster latency as the widely adopted autoregressive models. Our work successfully paved the way for scaling up the diffusion language model to a broader scope of applications across different domains.

Large Language Models (LLMs) are predominantly evaluated on Standard American English (SAE), often overlooking the diversity of global English varieties. This narrow focus may raise fairness concerns as degraded performance on non-standard varieties can lead to unequal benefits for users worldwide. Therefore, it is critical to extensively evaluate the linguistic robustness of LLMs on multiple non-standard English varieties. We introduce Trans-EnV, a framework that automatically transforms SAE datasets into multiple English varieties to evaluate the linguistic robustness. Our framework combines (1) linguistics expert knowledge to curate variety-specific features and transformation guidelines from linguistic literature and corpora, and (2) LLM-based transformations to ensure both linguistic validity and scalability. Using Trans-EnV, we transform six benchmark datasets into 38 English varieties and evaluate seven state-of-the-art LLMs. Our results reveal significant performance disparities, with accuracy decreasing by up to 46.3% on non-standard varieties. These findings highlight the importance of comprehensive linguistic robustness evaluation across diverse English varieties. Each construction of Trans-EnV was validated through rigorous statistical testing and consultation with a researcher in the field of second language acquisition, ensuring its linguistic validity. Our code and datasets are publicly available at https://github.com/jiyounglee-0523/TransEnV and https://huggingface.co/collections/jiyounglee0523/transenv-681eadb3c0c8cf363b363fb1.

Existing interpretability methods for Large Language Models (LLMs) often fall short by focusing on linear directions or isolated features, overlooking the high-dimensional, nonlinear, and relational geometry within model representations. This study focuses on how adversarial inputs systematically affect the internal representation spaces of LLMs, a topic which remains poorly understood. We propose persistent homology (PH), a tool from topological data analysis, as a principled framework to characterize the multi-scale dynamics within LLM activations. Using PH, we systematically analyze six state-of-the-art models under two distinct adversarial conditions, indirect prompt injection and backdoor fine-tuning, and identify a consistent topological signature of adversarial influence. Across architectures and model sizes, adversarial inputs induce ``topological compression'', where the latent space becomes structurally simpler, collapsing from varied, compact, small-scale features into fewer, dominant, and more dispersed large-scale ones. This topological signature is statistically robust across layers, highly discriminative, and provides interpretable insights into how adversarial effects emerge and propagate. By quantifying the shape of activations and neuronal information flow, our architecture-agnostic framework reveals fundamental invariants of representational change, offering a complementary perspective to existing interpretability methods.

Biomedical researchers increasingly rely on large-scale structured databases for complex analytical tasks. However, current text-to-SQL systems often struggle to map qualitative scientific questions into executable SQL, particularly when implicit domain reasoning is required. We introduce BiomedSQL, the first benchmark explicitly designed to evaluate scientific reasoning in text-to-SQL generation over a real-world biomedical knowledge base. BiomedSQL comprises 68,000 question/SQL query/answer triples generated from templates and grounded in a harmonized BigQuery knowledge base that integrates gene-disease associations, causal inference from omics data, and drug approval records. Each question requires models to infer domain-specific criteria, such as genome-wide significance thresholds, effect directionality, or trial phase filtering, rather than rely on syntactic translation alone. We evaluate a range of open- and closed-source LLMs across prompting strategies and interaction paradigms. Our results reveal a substantial performance gap: GPT-o3-mini achieves 59.0% execution accuracy, while our custom multi-step agent, BMSQL, reaches 62.6%, both well below the expert baseline of 90.0%. BiomedSQL provides a new foundation for advancing text-to-SQL systems capable of supporting scientific discovery through robust reasoning over structured biomedical knowledge bases. Our dataset is publicly available at https://huggingface.co/datasets/NIH-CARD/BiomedSQL, and our code is open-source at https://github.com/NIH-CARD/biomedsql.

Agentic Retrieval-Augmented Generation (RAG) systems enhance Large Language Models (LLMs) by enabling dynamic, multi-step reasoning and information retrieval. However, these systems often exhibit sub-optimal search behaviors like over-search (retrieving redundant information) and under-search (failing to retrieve necessary information), which hinder efficiency and reliability. This work formally defines and quantifies these behaviors, revealing their prevalence across multiple QA datasets and agentic RAG systems (e.g., one model could have avoided searching in 27.7% of its search steps). Furthermore, we demonstrate a crucial link between these inefficiencies and the models' uncertainty regarding their own knowledge boundaries, where response accuracy correlates with model's uncertainty in its search decisions. To address this, we propose $β$-GRPO, a reinforcement learning-based training method that incorporates confidence threshold to reward high-certainty search decisions. Experiments on seven QA benchmarks show that $β$-GRPO enable a 3B model with better agentic RAG ability, outperforming other strong baselines with a 4% higher average exact match score.

Large Language Models (LLMs) are prone to hallucination, particularly in long-form generations. A promising direction to mitigate hallucination is to teach LLMs to express uncertainty explicitly when they lack sufficient knowledge. However, existing work lacks direct and fair evaluation of LLMs' ability to express uncertainty effectively in long-form generation. To address this gap, we first introduce UNCLE, a benchmark designed to evaluate uncertainty expression in both long- and short-form question answering (QA). UNCLE covers five domains and includes more than 1,000 entities, each with paired short- and long-form QA items. Our dataset is the first to directly link short- and long-form QA through aligned questions and gold-standard answers. Along with UNCLE, we propose a suite of new metrics to assess the models' capabilities to selectively express uncertainty. We then demonstrate that current models fail to convey uncertainty appropriately in long-form generation. We further explore both prompt-based and training-based methods to improve models' performance, with the training-based methods yielding greater gains. Further analysis of alignment gaps between short- and long-form uncertainty expression highlights promising directions for future research using UNCLE.

Most LLM fingerprinting methods teach the model to respond to a few fixed queries with predefined atypical responses (keys). This memorization often does not survive common deployment steps such as finetuning or quantization, and such keys can be easily detected and filtered from LLM responses, ultimately breaking the fingerprint. To overcome these limitations we introduce LLM fingerprinting via semantically conditioned watermarks, replacing fixed query sets with a broad semantic domain, and replacing brittle atypical keys with a statistical watermarking signal diffused throughout each response. After teaching the model to watermark its responses only to prompts from a predetermined domain e.g., French language, the model owner can use queries from that domain to reliably detect the fingerprint and verify ownership. As we confirm in our thorough experimental evaluation, our fingerprint is both stealthy and robust to all common deployment scenarios.

Media framing refers to the emphasis on specific aspects of perceived reality to shape how an issue is defined and understood. Its primary purpose is to shape public perceptions often in alignment with the authors' opinions and stances. However, the interaction between stance and media frame remains largely unexplored. In this work, we apply an interdisciplinary approach to conceptualize and computationally explore this interaction with internet memes on climate change. We curate CLIMATEMEMES, the first dataset of climate-change memes annotated with both stance and media frames, inspired by research in communication science. CLIMATEMEMES includes 1,184 memes sourced from 47 subreddits, enabling analysis of frame prominence over time and communities, and sheds light on the framing preferences of different stance holders. We propose two meme understanding tasks: stance detection and media frame detection. We evaluate LLaVA-NeXT and Molmo in various setups, and report the corresponding results on their LLM backbone. Human captions consistently enhance performance. Synthetic captions and human-corrected OCR also help occasionally. Our findings highlight that VLMs perform well on stance, but struggle on frames, where LLMs outperform VLMs. Finally, we analyze VLMs' limitations in handling nuanced frames and stance expressions on climate change internet memes.