January 2026

arXiv:2601.15458v1 Announce Type: new Abstract: Motivation: The multiple sequence alignment (MSA) problem has been extensively studied, with numerous approaches developed over recent years. With the rapid growth of sequence data, there is an increasing need for fast and accurate MSA tools that scale effectively to large datasets. Building on our previous work on CLAM, we are able to use exact dynamic programming (Needleman-Wunsch) while scaling to large datasets. We introduce MuSAlS (Multiple Sequence Alignment at Scale), a fast […]

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arXiv:2601.15457v1 Announce Type: new Abstract: The integration of Large Language Models (LLMs) into the public health policy sector offers a transformative approach to navigating the vast repositories of regulatory guidance maintained by agencies such as the Centers for Disease Control and Prevention (CDC). However, the propensity for LLMs to generate hallucinations, defined as plausible but factually incorrect assertions, presents a critical barrier to the adoption of these technologies in high-stakes environments where information integrity is non-negotiable. This empirical […]

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arXiv:2601.15455v1 Announce Type: new Abstract: In their 1991 paper “Algebraic Reconstruction of Types and Effects,” Pierre Jouvelot and David Gifford presented a type-and-effect reconstruction algorithm based on an algebraic structure of effects. Their work is considered a milestone in the development of type-and-effect systems, and has inspired numerous subsequent works in the area of static analysis. However, unlike the later research it spawned, the original algorithm considered a language with higher-rank polymorphism, a feature which is challenging to […]

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arXiv:2601.15453v1 Announce Type: new Abstract: Few-normal shot anomaly detection (FNSAD) aims to detect abnormal regions in images using only a few normal training samples, making the task highly challenging due to limited supervision and the diversity of potential defects. Recent approaches leverage vision-language models such as CLIP with prompt-based learning to align image and text features. However, existing methods often exhibit weak discriminability between normal and abnormal prompts and lack principled scoring mechanisms for patch-level anomalies. We propose […]

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arXiv:2601.15445v1 Announce Type: new Abstract: Reflexive Thematic Analysis (RTA) is a critical method for generating deep interpretive insights. Yet its core tenets, including researcher reflexivity, tangible analytical evolution, and productive disagreement, are often poorly supported by software tools that prioritize speed and consensus over interpretive depth. To address this gap, we introduce Reflexis, a collaborative workspace that centers these practices. It supports reflexivity by integrating in-situ reflection prompts, makes code evolution transparent and tangible, and scaffolds collaborative interpretation […]

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arXiv:2601.15441v1 Announce Type: new Abstract: Internal activations of diffusion models encode rich semantic information, but interpreting such representations remains challenging. While Sparse Autoencoders (SAEs) have shown promise in disentangling latent representations, existing SAE-based methods for diffusion model understanding rely on unsupervised approaches that fail to align sparse features with human-understandable concepts. This limits their ability to provide reliable semantic control over generated images. We introduce CASL (Concept-Aligned Sparse Latents), a supervised framework that aligns sparse latent dimensions of […]

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arXiv:2601.15437v1 Announce Type: new Abstract: Large Language Models (LLMs) like ChatGPT offer potential support for autistic people, but this potential requires understanding the implicit perspectives these models might carry, including their biases and assumptions about autism. Moving beyond single-agent prompting, we utilized LLM-based multi-agent systems to investigate complex social scenarios involving autistic and non-autistic agents. In our study, agents engaged in group-task conversations and answered structured interview questions, which we analyzed to examine ChatGPT’s biases and how it […]

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arXiv:2601.15436v1 Announce Type: new Abstract: We propose a novel way to evaluate sycophancy of LLMs in a direct and neutral way, mitigating various forms of uncontrolled bias, noise, or manipulative language, deliberately injected to prompts in prior works. A key novelty in our approach is the use of LLM-as-a-judge, evaluation of sycophancy as a zero-sum game in a bet setting. Under this framework, sycophancy serves one individual (the user) while explicitly incurring cost on another. Comparing four leading […]

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arXiv:2601.15434v1 Announce Type: new Abstract: The evolution of digital manufacturing requires intelligent Question Answering (QA) systems that can seamlessly integrate and analyze complex multi-modal data, such as text, images, formulas, and tables. Conventional Retrieval Augmented Generation (RAG) methods often fall short in handling this complexity, resulting in subpar performance. We introduce ManuRAG, an innovative multi-modal RAG framework designed for manufacturing QA, incorporating specialized techniques to improve answer accuracy, reliability, and interpretability. To benchmark performance, we evaluate ManuRAG on […]

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arXiv:2601.15432v1 Announce Type: new Abstract: Scientific research metadata is vital to ensure the validity, reusability, and cost-effectiveness of research efforts. The MEDFORD metadata language was previously introduced to simplify the process of writing and maintaining metadata for non-programmers. However, barriers to entry and usability remain, including limited automatic validation, difficulty of data transport, and user unfamiliarity with text file editing. To address these issues, we introduce MEDFORD-in-a-Box (MIAB), a documentation ecosystem to facilitate researcher adoption and earlier metadata […]

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