Abstract--Bioinformatics tools are essential for complex computational biology tasks, yet their integration with emerging AI-agent frameworks is hindered by incompatible interfaces, heterogeneous input-output formats, and inconsistent parameter conventions. The Model Context Protocol (MCP) provides a standardized framework for tool-AI communication, but manually converting hundreds of existing and rapidly growing specialized bioinformatics tools into MCP-compliant servers is labor-intensive and unsustainable. Here, we present BioinfoMCP, a unified platform comprising two components: BioinfoMCP Converter, which automatically generates robust MCP servers from tool documentation using large language models, and BioinfoMCP Benchmark, which systematically validates the reliability and versatility of converted tools across diverse computational tasks. We present a platform of 38 MCP-converted bioinformatics tools, extensively validated to show that 94.7% successfully executed complex workflows across three widely used AI-agent platforms. By removing technical barriers to AI automation, BioinfoMCP enables natural-language interaction with sophisticated bioinformatics analyses without requiring extensive programming expertise, offering a scalable path to intelligent, interoperable computational biology . The bioinformatics landscape is characterized by an extensive ecosystem of specialized tools designed for diverse analytical tasks that serve critical functions in genomics [1], proteomics [2], [3], and molecular biology [4], and so on.

Graph-based Retrieval-Augmented Generation (RAG) has shown great capability in enhancing Large Language Model (LLM)'s answer with an external knowledge base. Compared to traditional RAG, it introduces a graph as an intermediate representation to capture better structured relational knowledge in the corpus, elevating the precision and comprehensiveness of generation results. However, developers usually face challenges in analyzing the effectiveness of GraphRAG on their dataset due to GraphRAG's complex information processing pipeline and the overwhelming amount of LLM invocations involved during graph construction and query, which limits GraphRAG interpretability and accessibility. This research proposes a visual analysis framework that helps RAG developers identify critical recalls of GraphRAG and trace these recalls through the GraphRAG pipeline. Based on this framework, we develop XGraphRAG, a prototype system incorporating a set of interactive visualizations to facilitate users' analysis process, boosting failure cases collection and improvement opportunities identification. Our evaluation demonstrates the effectiveness and usability of our approach. Our work is open-sourced and available at https://github.com/Gk0Wk/XGraphRAG.

Games have been vital test beds for the rapid development of Agent-based research. Remarkable progress has been achieved in the past, but it is unclear if the findings equip for real-world problems. While pressure grows, some of the most critical ecological challenges can find mitigation and prevention solutions through technology and its applications. Most real-world domains include multi-agent scenarios and require machine-machine and human-machine collaboration. Open-source environments have not advanced and are often toy scenarios, too abstract or not suitable for multi-agent research. By mimicking real-world problems and increasing the complexity of environments, we hope to advance state-of-the-art multi-agent research and inspire researchers to work on immediate real-world problems. Here, we present HIVEX, an environment suite to benchmark multi-agent research focusing on ecological challenges. HIVEX includes the following environments: Wind Farm Control, Wildfire Resource Management, Drone-Based Reforestation, Ocean Plastic Collection, and Aerial Wildfire Suppression. We provide environments, training examples, and baselines for the main and sub-tasks. All trained models resulting from the experiments of this work are hosted on Hugging Face. We also provide a leaderboard on Hugging Face and encourage the community to submit models trained on our environment suite.

This report surveys the landscape of potential security threats from malicious uses of AI, and proposes ways to better forecast, prevent, and mitigate these threats. After analyzing the ways in which AI may influence the threat landscape in the digital, physical, and political domains, we make four high-level recommendations for AI researchers and other stakeholders. We also suggest several promising areas for further research that could expand the portfolio of defenses, or make attacks less effective or harder to execute. Finally, we discuss, but do not conclusively resolve, the long-term equilibrium of attackers and defenders.

Large Language Models produce sequences learned as statistical patterns from large corpora. In order not to reproduce corpus biases, after initial training models must be aligned with human values, preferencing certain continuations over others. Alignment, which can be viewed as the superimposition of normative structure onto a statistical model, reveals a conflicted and complex interrelationship between language and technology. This relationship shapes theories of language, linguistic practice and subjectivity, which are especially relevant to the current sophistication in artificially produced text. We examine this practice of structuration as a two-way interaction between users and models by analysing how ChatGPT4 redacts perceived `anomalous' language in fragments of Joyce's Ulysses and the new linguistic practice of prompt engineering. We then situate this alignment problem historically, revisiting earlier postwar linguistic debates which counterposed two views of meaning: as discrete structures, and as continuous probability distributions. We discuss the largely occluded work of the Moscow Linguistic School, which sought to reconcile this opposition. Our attention to the Moscow School and later related arguments by Searle and Kristeva casts the problem of alignment in a new light: as one involving attention to the social structuration of linguistic practice, including structuration of anomalies that, like the Joycean text, exist in defiance of expressive conventions. These debates around the communicative orientation toward language can help explain some of the contemporary behaviours and interdependencies that take place between users and LLMs.

A farmer in Niger tends to a tree sprout growing among his millet crop.Tony Rinaudo/World Vision Australia This story was originally published by Yale Environment 360 and is reproduced here as part of the Climate Desk collaboration. For decades, there have been reports of the deforestation in Africa. And they are true--the continent's forests are disappearing, lost mainly to expanding agriculture, logging, and charcoal-making. Maybe not, according to new satellite data analyzed by artificial intelligence and a growing body of on-the-ground studies. This new research is finding ever more trees outside forests, many of them nurtured by farmers and sprouting on their previously treeless fields.

We approach autonomous drone-based reforestation with a collaborative multi-agent reinforcement learning (MARL) setup. Agents can communicate as part of a dynamically changing network. We explore collaboration and communication on the back of a high-impact problem. Forests are the main resource to control rising CO2 conditions. Unfortunately, the global forest volume is decreasing at an unprecedented rate. Many areas are too large and hard to traverse to plant new trees. To efficiently cover as much area as possible, here we propose a Graph Neural Network (GNN) based communication mechanism that enables collaboration. Agents can share location information on areas needing reforestation, which increases viewed area and planted tree count. We compare our proposed communication mechanism with a multi-agent baseline without the ability to communicate. Results show how communication enables collaboration and increases collective performance, planting precision and the risk-taking propensity of individual agents.

This paper considers multiprocessor task scheduling in a multistage hybrid flow-shop environment. The problem even in its simplest form is NP-hard in the strong sense. The great deal of interest for this problem, besides its theoretical complexity, is animated by needs of various manufacturing and computing systems. We propose a new approach based on limited discrepancy search to solve the problem. Our method is tested with reference to a proposed lower bound as well as the best-known solutions in literature. Computational results show that the developed approach is efficient in particular for large-size problems.