OLAF (Open Life Science Analysis Framework) is an open-source platform that enables researchers to perform bioinformatics analyses using natural language. By combining large language models (LLMs) with a modular agent-pipe-router architecture, OLAF generates and executes bioinformatics code on real scientific data, including formats like .h5ad. The system includes an Angular front end and a Python/Firebase backend, allowing users to run analyses such as single-cell RNA-seq workflows, gene annotation, and data visualization through a simple web interface. Unlike general-purpose AI tools, OLAF integrates code execution, data handling, and scientific libraries in a reproducible, user-friendly environment. It is designed to lower the barrier to computational biology for non-programmers and support transparent, AI-powered life science research.

To reduce development overhead and enable seamless integration between potential components comprising any given generative AI application, the Model Context Protocol (MCP) (Anthropic, 2024) has recently been released and subsequently widely adopted. The MCP is an open protocol that standardizes API calls to large language models (LLMs), data sources, and agentic tools. By connecting multiple MCP servers, each defined with a set of tools, resources, and prompts, users are able to define automated workflows fully driven by LLMs. However, we show that the current MCP design carries a wide range of security risks for end users. In particular, we demonstrate that industry-leading LLMs may be coerced into using MCP tools to compromise an AI developer's system through various attacks, such as malicious code execution, remote access control, and credential theft. To proactively mitigate these and related attacks, we introduce a safety auditing tool, MCPSafetyScanner, the first agentic tool to assess the security of an arbitrary MCP server. MCPScanner uses several agents to (a) automatically determine adversarial samples given an MCP server's tools and resources; (b) search for related vulnerabilities and remediations based on those samples; and (c) generate a security report detailing all findings. Our work highlights serious security issues with general-purpose agentic workflows while also providing a proactive tool to audit MCP server safety and address detected vulnerabilities before deployment. The described MCP server auditing tool, MCPSafetyScanner, is freely available at: https://github.com/johnhalloran321/mcpSafetyScanner

Recent advances in large language models (LLMs) have shown impressive progress in mathematical reasoning tasks. However, current evaluation benchmarks predominantly focus on the accuracy of final answers, often overlooking the crucial logical rigor for mathematical problem solving. The claim that state-of-the-art LLMs can solve Math Olympiad-level problems requires closer examination. To explore this, we conducted both qualitative and quantitative human evaluations of proofs generated by LLMs, and developed a schema for automatically assessing their reasoning capabilities. Our study reveals that current LLMs fall significantly short of solving challenging Olympiad-level problems and frequently fail to distinguish correct mathematical reasoning from clearly flawed solutions. Our analyses demonstrate that the occasional correct final answers provided by LLMs often result from pattern recognition or heuristic shortcuts rather than genuine mathematical reasoning. These findings underscore the substantial gap between LLM performance and human expertise in advanced mathematical reasoning and highlight the importance of developing benchmarks that prioritize the soundness of the reasoning used to arrive at an answer rather than the mere correctness of the final answers.

Automatic speech recognition systems have undoubtedly advanced with the integration of multilingual and multitask models such as Whisper, which have shown a promising ability to understand and process speech across a wide range of languages. Despite their robustness, these models often fall short in handling the linguistic distinctions of minority languages. This study addresses this gap by integrating traditional and novel language models with fine-tuned Whisper models to raise their performance in less commonly studied languages. Through rigorous fine-tuning and evaluation across multiple datasets, we demonstrate substantial improvements in word error rate, particularly in low-resource scenarios. Our approach not only does take advantage of the extensive data Whisper was pre-trained on, but also complements its linguistic adaptability by incorporating language models. We obtained improvements up to 51% for in-distribution datasets and up to 34% for out-of-distribution sentences using statistical language models, while large language models provided moderate but consistently robust improvement across diverse linguistic contexts. The findings reveal that, while the integration reliably benefits all model sizes, the extent of improvement varies, highlighting the importance of optimized language model parameters. Finally, we emphasize the importance of selecting appropriate evaluation parameters when reporting the results using transformer-based ASR models. In summary, this research clears the way for more inclusive ASR technologies that perform better across languages by enriching their linguistic knowledge. For further implementation details of this study, the technical documentation and source code are available at http://www.github.com/hitz-zentroa/whisper-lm.

In recent years, Large Language Models (LLMs) have been widely applied across various domains due to their powerful domain adaptation capabilities. Previous studies have suggested that diverse, multi-modal data can enhance LLMs' domain adaptation performance. However, this hypothesis remains insufficiently validated in the e-commerce sector. To address this gap, we propose a comprehensive e-commerce multi-task framework and design empirical experiments to examine the impact of diverse data and tasks on LLMs from two perspectives: "capability comprehensiveness" and "task comprehensiveness." Specifically, we observe significant improvements in LLM performance by progressively introducing tasks related to new major capability areas and by continuously adding subtasks within different major capability domains. Furthermore, we observe that increasing model capacity amplifies the benefits of diversity, suggesting a synergistic relationship between model capacity and data diversity. Finally, we validate the best-performing model from our empirical experiments in the KDD Cup 2024, achieving a rank 5 in Task 1. This outcome demonstrates the significance of our research for advancing LLMs in the e-commerce domain.

Language models based on the Transformer architecture achieve excellent results in many language-related tasks, such as text classification or sentiment analysis. However, despite the architecture of these models being well-defined, little is known about how their internal computations help them achieve their results. This renders these models, as of today, a type of 'black box' systems. There is, however, a line of research -- 'interpretability' -- aiming to learn how information is encoded inside these models. More specifically, there is work dedicated to studying whether Transformer-based models possess knowledge of linguistic phenomena similar to human speakers -- an area we call 'linguistic interpretability' of these models. In this survey we present a comprehensive analysis of 160 research works, spread across multiple languages and models -- including multilingual ones -- that attempt to discover linguistic information from the perspective of several traditional Linguistics disciplines: Syntax, Morphology, Lexico-Semantics and Discourse. Our survey fills a gap in the existing interpretability literature, which either not focus on linguistic knowledge in these models or present some limitations -- e.g. only studying English-based models. Our survey also focuses on Pre-trained Language Models not further specialized for a downstream task, with an emphasis on works that use interpretability techniques that explore models' internal representations.

While large language models (LLMs) already play significant roles in society, research has shown that LLMs still generate content including social bias against certain sensitive groups. While existing benchmarks have effectively identified social biases in LLMs, a critical gap remains in our understanding of the underlying reasoning that leads to these biased outputs. This paper goes one step further to evaluate the causal reasoning process of LLMs when they answer questions eliciting social biases. We first propose a novel conceptual framework to classify the causal reasoning produced by LLMs. Next, we use LLMs to synthesize $1788$ questions covering $8$ sensitive attributes and manually validate them. The questions can test different kinds of causal reasoning by letting LLMs disclose their reasoning process with causal graphs. We then test 4 state-of-the-art LLMs. All models answer the majority of questions with biased causal reasoning, resulting in a total of $4135$ biased causal graphs. Meanwhile, we discover $3$ strategies for LLMs to avoid biased causal reasoning by analyzing the "bias-free" cases. Finally, we reveal that LLMs are also prone to "mistaken-biased" causal reasoning, where they first confuse correlation with causality to infer specific sensitive group names and then incorporate biased causal reasoning.

'Neural howlround' in large language models: a self-reinforcing bias phenomenon, and a dynamic attenuation solution Seth Drake, PhD (Independent Researcher) April 14, 2025 Abstract Large language model (LLM)-driven AI systems may exhibit an inference failure mode we term'neural howlround,' a self-reinforcing cognitive loop where certain highly weighted inputs become dominant, leading to entrenched response patterns resistant to correction. This paper explores the mechanisms underlying this phenomenon, which is distinct from model collapse and biased salience weighting. We propose an attenuation-based correction mechanism that dynamically introduces counterbalancing adjustments and can restore adaptive reasoning, even in'locked-in' AI systems. Additionally, we discuss some other related effects arising from improperly managed reinforcement. Finally, we outline potential applications of this mitigation strategy for improving AI robustness in real-world decision-making tasks. 1 Introduction Many AI agents use large language models (LLMs) for input recognition and also output prediction: these models are trained on vast datasets and are based on probability weight assignments developed over the course of training. Research on the causes of AI bias and model reinforcement loops has identified numerous challenges, For example, model collapse, in which generative systems exhibit degradation in diversity and accuracy when outputs 1 arXiv:2504.07992v1 Furthermore, research into biased salience weighting suggests that excessive reinforcement of certain pathways leads to an'echo chamber' effect which induces a self-perpetuating self-reinforcement of certain outputs. 'Neural howlround,' the failure mode we describe here, is not merely a combination of multiple of these existing cases. While it may outwardly resemble existing AI bias phenomena, 'neural howlround' is a unique, emergent failure mode occurring during inference rather than during training. This runtime instability necessitates a dedicated intervention strategy distinct from traditional bias mitigation techniques. We feel additionally that this failure mode deserves particular attention as it is a runtime event. If left unchecked it could cause LLM-driven agents to become'locked-in,' unable to escape cognitive or ideological loops and thereby limited in their ability to respond with an appropriate level of critical thought, to adapt to novel or contradictive inputs or to maintain proper probabilistic output.

--Large Language Models (LLMs) have made significant strides in Natural Language Processing but remain vulnerable to fairness-related issues, often reflecting biases inherent in their training data. These biases pose risks, particularly when LLMs are deployed in sensitive areas such as healthcare, finance, and law. This paper introduces a metamorphic testing approach to systematically identify fairness bugs in LLMs. We define and apply a set of fairness-oriented metamorphic relations (MRs) to assess the LLaMA and GPT model, a state-of-the-art LLM, across diverse demographic inputs. Our methodology includes generating source and follow-up test cases for each MR and analyzing model responses for fairness violations. The results demonstrate the effectiveness of MT in exposing bias patterns, especially in relation to tone and sentiment, and highlight specific intersections of sensitive attributes that frequently reveal fairness faults. This research improves fairness testing in LLMs, providing a structured approach to detect and mitigate biases and improve model robustness in fairness-sensitive applications. Language models, particularly those of considerable size, have revolutionized numerous applications in natural language processing, from translation to content generation. As these models are increasingly integrated into applications that affect daily life, their reliability and fairness become paramount.

In the era of Large Language Models (LLMs), establishing effective evaluation methods and standards for diverse human-AI interaction systems is increasingly challenging. To encourage more transparent documentation and facilitate discussion on human-AI system evaluation design options, we present an evaluation card SPHERE, which encompasses five key dimensions: 1) What is being evaluated?; 2) How is the evaluation conducted?; 3) Who is participating in the evaluation?; 4) When is evaluation conducted?; 5) How is evaluation validated? We conduct a review of 39 human-AI systems using SPHERE, outlining current evaluation practices and areas for improvement. We provide three recommendations for improving the validity and rigor of evaluation practices.