Apodex Discovery: Reality Benchmarks and Environments for Evaluating and Building Discoverative Artificial Intelligence

Apollo did not reach the Moon merely because its engineers could solve difficult equations. It succeeded by turning a distant ambition into a mission architecture of explicit objectives, simulation, verification, and repeated correction. AI now faces a similar transition: frontier models can solve difficult tasks once the problem, tools, and success criteria are specified, yet consequential real-world challenges rarely arrive in an executable or verifiable form. We introduce Apodex Discovery, a framework for building and evaluating discoverative AI through the heavy-duty solver, a system comprising a foundation model, harness, tools, and control policies that pursues extended, stateful, verifiable investigations. It has three core components. First, a problem-scouting process surveyed 561 industries across 16 sectors, assembled 423 high-value real-world problems, and selected 20 for the initial release. Second, a common environment-task-episode abstraction provides data, tools, constraints, feedback, trajectory recording, and verification of intermediate artifacts and final submissions. Third, HDS6 evaluates Tools, Repair, Alternatives, Coherence, Evidence, and Scope independently of final-task success. In AAV capsid design, Apodex surpassed the published state of the art by 7% across viability, tropism, structure prediction, and generative design. In drug repurposing and reformulation, a task-specific biomedical environment improved the mean normalized prediction score of GPT-5.5 and GPT-5.6-sol by 2.5 and 7.6 points over the same closed-book backbone. Controlled ablations show that the fixed TRACES episode interface enables attribution of performance differences to specific solver components. Apodex Discovery moves AI evaluation beyond predefined benchmarks toward verifiable investigations aimed at genuine discovery.

Density-aware Hierarchical Clustering Based on Element-Categorized Connection Subgraphs

Clustering is a fundamental data mining technique for pattern recognition through unsupervised learning. Among various clustering methods, hierarchical clustering, density-based clustering, and graph clustering stand out as representative approaches. For hierarchical clustering, it can be categorized into agglomerative and divisive modes to construct clusters in a recursive manner. The key aspect of both modes is the calculation of inter-cluster similarity, which determines whether to merge the sub-clusters into one cluster or divide a current cluster into sub-clusters. Traditionally, the similarity is derived from pairwise distances, often overlooking density variations and structural connectivity in graphs. To address this, we propose a density-aware hierarchical clustering method based on element-categorized connection subgraphs (DHC-ECS), which effectively integrates the hierarchical clustering, density-based clustering, and graph clustering. Particularly, a novel inter-cluster similarity metric is introduced that considers not only distances but also the element categorization in the KNN connection subgraphs, kernel density estimation, and local connectivity within sub-clusters. Extensive evaluations on heterogeneous benchmark datasets demonstrate that DHC-ECS exhibits superior overall performance in terms of clustering accuracy and parameter robustness compared with the baseline methods (including AChameleon, RNN-DBSCAN, McDPC, and G-RMS). The work indicates the great potential of the proposed clustering algorithm for low-dimensional datasets by leveraging local density and graph-structured connectivity (i.e., the duality of vertices and edges), as well as the possibility to determine an intrinsic threshold, reducing the reliance on manual parameter tuning.

Sustainable Metal-Organic Framework Water Harvesters in the Artificial Intelligence Era

Metal-organic frameworks (MOFs) are excellent candidates for water harvesting due to their tunable pore environments, which can be precisely engineered to capture and release water in arid conditions. Integrating artificial intelligence (AI) into MOF discovery can further accelerate the design of high-performance sorbents by identifying structural features that enhance atmospheric water harvesting (AWH), stability, and cycling efficiency. In this Perspective, we examine key MOF design principles, including cooperative adsorption, operational relative humidity (RH), uptake capacity, hysteresis, and scalability. We highlight recent design advancements such as multivariate strategies and long-arm linker extension, and examine how these principles tune pore capacity and hydrophilicity, while preserving stability and crystallinity. Furthermore, we discuss how AI, large language models (LLMs), and data mining can accelerate the discovery process through predictive synthesis, inverse design, and elucidating synthesis-structure-property relationships for the next generation of MOF water harvesters.

SciCustom: A Framework for Custom Evaluation of Scientific Capabilities in Large Language Models

Large language models (LLMs) are increasingly applied to scientific research, yet existing evaluations often fail to reflect the fine-grained capabilities required in practice. Most benchmarks are manually curated or domain-generic, limiting scalability and alignment with real scientific use cases. In this paper, we propose a new framework named SciCustom to address the problem. It enables the custom construction of benchmarks from large-scale scientific data to evaluate application-specific scientific capabilities in LLMs. SciCustom first organizes scientific knowledge into ontology-grounded knowledge units with controlled granularity and trains a tagger to map large-scale data instances into this knowledge space. Given a custom requirement, relevant knowledge units are identified via voting-based multi-model consensus. These units enable relevance-aware benchmark retrieval via binary search, followed by proxy subset selection and data-grounded benchmark generation for efficient evaluation. Experiments in chemistry and healthcare demonstrate that SciCustom reveals fine-grained differences in LLM scientific capabilities that standard benchmarks overlook, while requiring neither expert annotation nor synthetic question generation. This work provides a scalable and application-aware foundation for benchmarking scientific capabilities in LLMs. The source code is available at https://github.com/yjwtheonly/SciCustom.

Predicting Scale-Up of Metal-Organic Framework Syntheses with Large Language Models

Scalable synthesis remains the gate between MOF discovery and industrial deployment, as scale-up know-how is fragmented across disparate reports. We introduce ESU-MOF, a literature-mined dataset and a positive-unlabeled learning strategy that fine-tunes large language models to predict scalability potential with 91.4% accuracy, enabling rapid data-driven triage for industrial MOF discovery.

Bridging the Skill Gap in Clinical CBCT Interpretation with CBCTRepD

Generative AI has advanced rapidly in medical report generation; however, its application to oral and maxillofacial CBCT reporting remains limited, largely because of the scarcity of high-quality paired CBCT-report data and the intrinsic complexity of volumetric CBCT interpretation. To address this, we introduce CBCTRepD, a bilingual oral and maxillofacial CBCT report-generation system designed for integration into routine radiologist-AI co-authoring workflows. We curated a large-scale, high-quality paired CBCT-report dataset comprising approximately 7,408 studies, covering 55 oral disease entities across diverse acquisition settings, and used it to develop the system. We further established a clinically grounded, multi-level evaluation framework that assesses both direct AI-generated drafts and radiologist-edited collaboration reports using automatic metrics together with radiologist- and clinician-centered evaluation. Using this framework, we show that CBCTRepD achieves superior report-generation performance and produces drafts with writing quality and standardization comparable to those of intermediate radiologists. More importantly, in radiologist-AI collaboration, CBCTRepD provides consistent and clinically meaningful benefits across experience levels: it helps novice radiologists improve toward intermediate-level reporting, enables intermediate radiologists to approach senior-level performance, and even assists senior radiologists by reducing omission-related errors, including clinically important missed lesions. By improving report structure, reducing omissions, and promoting attention to co-existing lesions across anatomical regions, CBCTRepD shows strong and reliable potential as a practical assistant for real-world CBCT reporting across multi-level care settings.

Mozi: Governed Autonomy for Drug Discovery LLM Agents

Tool-augmented large language model (LLM) agents promise to unify scientific reasoning with computation, yet their deployment in high-stakes domains like drug discovery is bottlenecked by two critical barriers: unconstrained tool-use governance and poor long-horizon reliability. In dependency-heavy pharmaceutical pipelines, autonomous agents often drift into irreproducible trajectories, where early-stage hallucinations multiplicatively compound into downstream failures. To overcome this, we present Mozi, a dual-layer architecture that bridges the flexibility of generative AI with the deterministic rigor of computational biology. Layer A (Control Plane) establishes a governed supervisor--worker hierarchy that enforces role-based tool isolation, limits execution to constrained action spaces, and drives reflection-based replanning. Layer B (Workflow Plane) operationalizes canonical drug discovery stages -- from Target Identification to Lead Optimization -- as stateful, composable skill graphs. This layer integrates strict data contracts and strategic human-in-the-loop (HITL) checkpoints to safeguard scientific validity at high-uncertainty decision boundaries. Operating on the design principle of ``free-form reasoning for safe tasks, structured execution for long-horizon pipelines,'' Mozi provides built-in robustness mechanisms and trace-level audibility to completely mitigate error accumulation. We evaluate Mozi on PharmaBench, a curated benchmark for biomedical agents, demonstrating superior orchestration accuracy over existing baselines. Furthermore, through end-to-end therapeutic case studies, we demonstrate Mozi's ability to navigate massive chemical spaces, enforce stringent toxicity filters, and generate highly competitive in silico candidates, effectively transforming the LLM from a fragile conversationalist into a reliable, governed co-scientist.

TriC-Motion: Tri-Domain Causal Modeling Grounded Text-to-Motion Generation

Text-to-motion generation, a rapidly evolving field in computer vision, aims to produce realistic and text-aligned motion sequences. Current methods primarily focus on spatial-temporal modeling or independent frequency domain analysis, lacking a unified framework for joint optimization across spatial, temporal, and frequency domains. This limitation hinders the model's ability to leverage information from all domains simultaneously, leading to suboptimal generation quality. Additionally, in motion generation frameworks, motion-irrelevant cues caused by noise are often entangled with features that contribute positively to generation, thereby leading to motion distortion. To address these issues, we propose Tri-Domain Causal Text-to-Motion Generation (TriC-Motion), a novel diffusion-based framework integrating spatial-temporal-frequency-domain modeling with causal intervention. TriC-Motion includes three core modeling modules for domain-specific modeling, namely Temporal Motion Encoding, Spatial Topology Modeling, and Hybrid Frequency Analysis. After comprehensive modeling, a Score-guided Tri-domain Fusion module integrates valuable information from the triple domains, simultaneously ensuring temporal consistency, spatial topology, motion trends, and dynamics. Moreover, the Causality-based Counterfactual Motion Disentangler is meticulously designed to expose motion-irrelevant cues to eliminate noise, disentangling the real modeling contributions of each domain for superior generation. Extensive experimental results validate that TriC-Motion achieves superior performance compared to state-of-the-art methods, attaining an outstanding R@1 of 0.612 on the HumanML3D dataset. These results demonstrate its capability to generate high-fidelity, coherent, diverse, and text-aligned motion sequences. Code is available at: https://caoyiyang1105.github.io/TriC-Motion/.

Human Identification at a Distance: Challenges, Methods and Results on the Competition HID 2025

Human identification at a distance (HID) is challenging because traditional biometric modalities such as face and fingerprints are often difficult to acquire in real-world scenarios. Gait recognition provides a practical alternative, as it can be captured reliably at a distance. To promote progress in gait recognition and provide a fair evaluation platform, the International Competition on Human Identification at a Distance (HID) has been organized annually since 2020. Since 2023, the competition has adopted the challenging SUSTech-Competition dataset, which features substantial variations in clothing, carried objects, and view angles. No dedicated training data are provided, requiring participants to train their models using external datasets. Each year, the competition applies a different random seed to generate distinct evaluation splits, which reduces the risk of overfitting and supports a fair assessment of cross-domain generalization. While HID 2023 and HID 2024 already used this dataset, HID 2025 explicitly examined whether algorithmic advances could surpass the accuracy limits observed previously. Despite the heightened difficulty, participants achieved further improvements, and the best-performing method reached 94.2% accuracy, setting a new benchmark on this dataset. We also analyze key technical trends and outline potential directions for future research in gait recognition.

Agentic reinforcement learning empowers next-generation chemical language models for molecular design and synthesis

Language models are revolutionizing the biochemistry domain, assisting scientists in drug design and chemical synthesis with high efficiency. Yet current approaches struggle between small language models prone to hallucination and limited knowledge retention, and large cloud-based language models plagued by privacy risks and high inference costs. To bridge this gap, we introduce ChemCRAFT, a novel framework leveraging agentic reinforcement learning to decouple chemical reasoning from knowledge storage. Instead of forcing the model to memorize vast chemical data, our approach empowers the language model to interact with a sandbox for precise information retrieval. This externalization of knowledge allows a locally deployable small model to achieve superior performance with minimal inference costs. To enable small language models for agent-calling ability, we build an agentic trajectory construction pipeline and a comprehensive chemical-agent sandbox. Based on sandbox interactions, we constructed ChemToolDataset, the first large-scale chemical tool trajectory dataset. Simultaneously, we propose SMILES-GRPO to build a dense chemical reward function, promoting the model's ability to call chemical agents. Evaluations across diverse aspects of drug design show that ChemCRAFT outperforms current cloud-based LLMs in molecular structure analysis, molecular optimization, and synthesis pathway prediction, demonstrating that scientific reasoning is not solely an emergent ability of model scale, but a learnable policy of tool orchestration. This work establishes a cost-effective and privacy-preserving paradigm for AI-aided chemistry, opening new avenues for accelerating molecular discovery with locally deployable agents.