MetaboT: AI-based agent for natural language-based interaction with metabolomics knowledge graphs

Mass spectrometry metabolomics generates vast amounts of data requiring advanced methods for interpretation. Knowledge graphs address these challenges by structuring mass spectrometry data, metabolite information, and their relationships into a connected network (Gaudry et al. 2024). However, effective use of a knowledge graph demands an in-depth understanding of its ontology and its query language syntax. To overcome this, we designed MetaboT, an AI system utilizing large language models (LLMs) to translate user questions into SPARQL semantic query language for operating on knowledge graphs (Steve Harris 2013). We demonstrate its effectiveness using the Experimental Natural Products Knowledge Graph (ENPKG), a large-scale public knowledge graph for plant natural products (Gaudry et al. 2024).MetaboT employs specialized AI agents for handling user queries and interacting with the knowledge graph by breaking down complex tasks into discrete components, each managed by a specialised agent (Fig. 1a). The multi-agent system is constructed using the LangChain and LangGraph libraries, which facilitate the integration of LLMs with external tools and information sources (LangChain, n.d.). The query generation process follows a structured workflow. First, the Entry Agent determines if the question is new or a follow-up to previous interactions. New questions are forwarded to the Validator Agent, which verifies if the question is related to the knowledge graph. Then, the valid question is sent to the Supervisor Agent, which identifies if the question requires chemical conversions or standardized identifiers. In this case it delegates the question to the Knowledge Graph Agent, which can use tools to extract necessary details, such as URIs or taxonomies of chemical names, from the user query. Finally, an agent responsible for crafting the SPARQL queries equipped with the ontology of the knowledge graph uses the provided identifiers to generate the query. Then, the system executes the generated query against the metabolomics knowledge graph and returns structured results to the user (Fig. 1b). To assess the performance of MetaboT we have curated 50 metabolomics-related questions and their expected answers. In addition to submitting these questions to MetaboT, we evaluated a baseline by submitting them to a standard LLM (GPT-4o) with a prompt that incorporated the knowledge graph ontology but did not provide specific entity IDs. This baseline achieved only 8.16% accuracy, compared to MetaboT's 83.67%, underscoring the necessity of our multi-agent system for accurately retrieving entities and generating correct SPARQL queries. MetaboT demonstrates promising performance as a conversational question-answering assistant, enabling researchers to retrieve structured metabolomics data through natural language queries. By automating the generation and execution of SPARQL queries, it removes technical barriers that have traditionally hindered access to knowledge graphs. Importantly, MetaboT leverages the capabilities of LLMs while maintaining experimentally grounded query generation, ensuring that outputs remain aligned with domain-specific standards and data structures. This approach facilitates data-driven discoveries by bridging the gap between complex semantic technologies and user-friendly interaction. MetaboT is accessible at [https://metabot.holobiomicslab.eu/], and its source code is available at [https://github.com/HolobiomicsLab/MetaboT].

Measuring and Controlling the Spectral Bias for Self-Supervised Image Denoising

Current self-supervised denoising methods for paired noisy images typically involve mapping one noisy image through the network to the other noisy image. However, after measuring the spectral bias of such methods using our proposed Image Pair Frequency-Band Similarity, it suffers from two practical limitations. Firstly, the high-frequency structural details in images are not preserved well enough. Secondly, during the process of fitting high frequencies, the network learns high-frequency noise from the mapped noisy images. To address these challenges, we introduce a Spectral Controlling network (SCNet) to optimize self-supervised denoising of paired noisy images. First, we propose a selection strategy to choose frequency band components for noisy images, to accelerate the convergence speed of training. Next, we present a parameter optimization method that restricts the learning ability of convolutional kernels to high-frequency noise using the Lipschitz constant, without changing the network structure. Finally, we introduce the Spectral Separation and low-rank Reconstruction module (SSR module), which separates noise and high-frequency details through frequency domain separation and low-rank space reconstruction, to retain the high-frequency structural details of images. Experiments performed on synthetic and real-world datasets verify the effectiveness of SCNet.

Back to Ear: Perceptually Driven High Fidelity Music Reconstruction

Variational Autoencoders (VAEs) are essential for large-scale audio tasks like diffusion-based generation. However, existing open-source models often neglect auditory perceptual aspects during training, leading to weaknesses in phase accuracy and stereophonic spatial representation. To address these challenges, we propose {\epsilon}ar-VAE, an open-source music signal reconstruction model that rethinks and optimizes the VAE training paradigm. Our contributions are threefold: (i) A K-weighting perceptual filter applied prior to loss calculation to align the objective with auditory perception. (ii) Two novel phase losses: a Correlation Loss for stereo coherence, and a Phase Loss using its derivatives--Instantaneous Frequency and Group Delay--for precision. (iii) A new spectral supervision paradigm where magnitude is supervised by all four Mid/Side/Left/Right components, while phase is supervised only by the LR components. Experiments show {\epsilon}ar-VAE at 44.1kHz substantially outperforms leading open-source models across diverse metrics, showing particular strength in reconstructing high-frequency harmonics and the spatial characteristics.

Kimi K2: Open Agentic Intelligence

We introduce Kimi K2, a Mixture-of-Experts (MoE) large language model with 32 billion activated parameters and 1 trillion total parameters. We propose the MuonClip optimizer, which improves upon Muon with a novel QK-clip technique to address training instability while enjoying the advanced token efficiency of Muon. Based on MuonClip, K2 was pre-trained on 15.5 trillion tokens with zero loss spike. During post-training, K2 undergoes a multi-stage post-training process, highlighted by a large-scale agentic data synthesis pipeline and a joint reinforcement learning (RL) stage, where the model improves its capabilities through interactions with real and synthetic environments. Kimi K2 achieves state-of-the-art performance among open-source non-thinking models, with strengths in agentic capabilities. Notably, K2 obtains 66.1 on Tau2-Bench, 76.5 on ACEBench (En), 65.8 on SWE-Bench Verified, and 47.3 on SWE-Bench Multilingual -- surpassing most open and closed-sourced baselines in non-thinking settings. It also exhibits strong capabilities in coding, mathematics, and reasoning tasks, with a score of 53.7 on LiveCodeBench v6, 49.5 on AIME 2025, 75.1 on GPQA-Diamond, and 27.1 on OJBench, all without extended thinking. These results position Kimi K2 as one of the most capable open-source large language models to date, particularly in software engineering and agentic tasks. We release our base and post-trained model checkpoints to facilitate future research and applications of agentic intelligence.

A Unified RCS Modeling of Typical Targets for 3GPP ISAC Channel Standardization and Experimental Analysis

Accurate radar cross section (RCS) modeling is crucial for characterizing target scattering and improving the precision of Integrated Sensing and Communication (ISAC) channel modeling. Existing RCS models are typically designed for specific target types, leading to increased complexity and lack of generalization. This makes it difficult to standardize RCS models for 3GPP ISAC channels, which need to account for multiple typical target types simultaneously. Furthermore, 3GPP models must support both system-level and link-level simulations, requiring the integration of large-scale and small-scale scattering characteristics. To address these challenges, this paper proposes a unified RCS modeling framework that consolidates these two aspects. The model decomposes RCS into three components: (1) a large-scale power factor representing overall scattering strength, (2) a small-scale angular-dependent component describing directional scattering, and (3) a random component accounting for variations across target instances. We validate the model through mono-static RCS measurements for UAV, human, and vehicle targets across five frequency bands. The results demonstrate that the proposed model can effectively capture RCS variations for different target types. Finally, the model is incorporated into an ISAC channel simulation platform to assess the impact of target RCS characteristics on path loss, delay spread, and angular spread, providing valuable insights for future ISAC system design.

Q${}^2$Forge: Minting Competency Questions and SPARQL Queries for Question-Answering Over Knowledge Graphs

The SPARQL query language is the standard method to access knowledge graphs (KGs). However, formulating SPARQL queries is a significant challenge for non-expert users, and remains time-consuming for the experienced ones. Best practices recommend to document KGs with competency questions and example queries to contextualise the knowledge they contain and illustrate their potential applications. In practice, however, this is either not the case or the examples are provided in limited numbers. Large Language Models (LLMs) are being used in conversational agents and are proving to be an attractive solution with a wide range of applications, from simple question-answering about common knowledge to generating code in a targeted programming language. However, training and testing these models to produce high quality SPARQL queries from natural language questions requires substantial datasets of question-query pairs. In this paper, we present Q${}^2$Forge that addresses the challenge of generating new competency questions for a KG and corresponding SPARQL queries. It iteratively validates those queries with human feedback and LLM as a judge. Q${}^2$Forge is open source, generic, extensible and modular, meaning that the different modules of the application (CQ generation, query generation and query refinement) can be used separately, as an integrated pipeline, or replaced by alternative services. The result is a complete pipeline from competency question formulation to query evaluation, supporting the creation of reference query sets for any target KG.

A Unified Deterministic Channel Model for Multi-Type RIS with Reflective, Transmissive, and Polarization Operations

Reconfigurable Intelligent Surface (RIS) technologies have been considered as a promising enabler for 6G, enabling advantageous control of electromagnetic (EM) propagation. RIS can be categorized into multiple types based on their reflective/transmissive modes and polarization control capabilities, all of which are expected to be widely deployed in practical environments. A reliable RIS channel model is essential for the design and development of RIS communication systems. While deterministic modeling approaches such as ray-tracing (RT) offer significant benefits, a unified model that accommodates all RIS types is still lacking. This paper addresses this gap by developing a high-precision deterministic channel model based on RT, supporting multiple RIS types: reflective, transmissive, hybrid, and three polarization operation modes. To achieve this, a unified EM response model for the aforementioned RIS types is developed. The reflection and transmission coefficients of RIS elements are derived using a tensor-based equivalent impedance approach, followed by calculating the scattered fields of the RIS to establish an EM response model. The performance of different RIS types is compared through simulations in typical scenarios. During this process, passive and lossless constraints on the reflection and transmission coefficients are incorporated to ensure fairness in the performance evaluation. Simulation results validate the framework's accuracy in characterizing the RIS channel, and specific cases tailored for dual-polarization independent control and polarization rotating RISs are highlighted as insights for their future deployment. This work can be helpful for the evaluation and optimization of RIS-enabled wireless communication systems.

CreoPep: A Universal Deep Learning Framework for Target-Specific Peptide Design and Optimization

Target-specific peptides, such as conotoxins, exhibit exceptional binding affinity and selectivity toward ion channels and receptors. However, their therapeutic potential remains underutilized due to the limited diversity of natural variants and the labor-intensive nature of traditional optimization strategies. Here, we present CreoPep, a deep learning-based conditional generative framework that integrates masked language modeling with a progressive masking scheme to design high-affinity peptide mutants while uncovering novel structural motifs. CreoPep employs an integrative augmentation pipeline, combining FoldX-based energy screening with temperature-controlled multinomial sampling, to generate structurally and functionally diverse peptides that retain key pharmacological properties. We validate this approach by designing conotoxin inhibitors targeting the $\alpha$7 nicotinic acetylcholine receptor, achieving submicromolar potency in electrophysiological assays. Structural analysis reveals that CreoPep-generated variants engage in both conserved and novel binding modes, including disulfide-deficient forms, thus expanding beyond conventional design paradigms. Overall, CreoPep offers a robust and generalizable platform that bridges computational peptide design with experimental validation, accelerating the discovery of next-generation peptide therapeutics.

Research and Experimental Validation for 3GPP ISAC Channel Modeling Standardization

Integrated Sensing and Communication (ISAC) is considered a key technology in 6G networks. An accurate sensing channel model is crucial for the design and sensing performance evaluation of ISAC systems. The widely used Geometry-Based Stochastic Model (GBSM), typically applied in standardized channel modeling, mainly focuses on the statistical fading characteristics of the channel. However, it fails to capture the characteristics of targets in ISAC systems, such as their positions and velocities, as well as the impact of the targets on the background. To address this issue, this paper proposes an extended GBSM (E-GBSM) sensing channel model that incorporates newly discovered channel characteristics into a unified modeling framework. In this framework, the sensing channel is divided into target and background channels. For the target channel, the model introduces a concatenated modeling approach, while for the background channel, a parameter called the power control factor is introduced to assess impact of the target on the background channel, making the modeling framework applicable to both mono-static and bi-static sensing modes. To validate the proposed model's effectiveness, measurements of target and background channels are conducted in both indoor and outdoor scenarios, covering various sensing targets such as metal plates, reconfigurable intelligent surfaces, human bodies, UAVs, and vehicles. The experimental results provide important theoretical support and empirical data for the standardization of ISAC channel modeling.

Advanced Codebook Design for SCMA-aided NTNs With Randomly Distributed Users

In this letter, a novel class of sparse codebooks is proposed for sparse code multiple access (SCMA) aided non-terrestrial networks (NTN) with randomly distributed users characterized by Rician fading channels. Specifically, we first exploit the upper bound of bit error probability (BEP) of an SCMA-aided NTN with large-scale fading of different users under Rician fading channels. Then, the codebook is designed by employing pulse-amplitude modulation constellation, user-specific rotation and power factors. To further reduce the optimization complexity while maintaining the power diversity of different users, an orthogonal layer-assisted joint layer and power assignment strategy is proposed. Finally, unlike existing SCMA codebook designs that treat all users as one super-user, we propose to minimize the BEP of the worst user to ensure user fairness. The simulation results show that the proposed scheme is capable of providing a substantial performance gain over conventional codebooks.