Prior-Guided Multi-Omic Transformers for Single-Cell Gene Regulatory Network Inference

Gene regulatory networks (GRNs) capture transcription factor-target interactions and are central to understanding cell-state regulation and disease. Reconstructing GRNs from paired single-cell transcriptomic and chromatin accessibility data is promising but challenging: scATAC is extremely sparse, and most methods rely on fixed peak-to-gene links and weak supervision. We present EpiAwareNet, a prior-guided multi-omic Transformer framework that reconstructs GRNs from paired single-cell data using only lightweight biological priors. In Stage 1, EpiAwareNet learns joint gene-peak representations with a gene-peak cross-attention module, enabling data-driven, gene-specific aggregation of accessibility signals rather than hard-coded peak-to-gene assignments. In Stage 2, EpiAwareNet incorporates a bulk-derived GRN prior as noisy positive edges to provide weak supervision under label scarcity, refining regulatory scores while remaining robust to prior noise. In our experiments, EpiAwareNet improves GRN reconstruction over representative single- and multi-omic baselines and yields GRNs with greater biological plausibility, such as improved recovery of known regulatory interactions, suggesting that lightweight biological priors from bulk data can effectively guide single-cell GRN inference when combined with adaptive cross-modal representation learning. Code and data will be available at https://github.com/tianyang-x/EpiAwareNet_pub.

Do Proactive Agents Really Need an LLM to Decide When to Wake and What to Anchor?

Proactive agents read user activity as text and call an LLM on every event to decide whether to act. But user activity is not natively text: it is a structured event stream of (actor, verb, object, timestamp) tuples that the operating system already maintains in graph form. Rendering the structure as text and asking an LLM to recover it is a round-trip the system never had to take. We treat the always-on signal as graph updates rather than text and use a small temporal-graph-learning (TGL) model as the encoder: one forward pass yields a per-event trigger probability and a per-entity routing score, and only the downstream agent (turning a small structured handoff into a fluent user-facing sentence) is an LLM call, invoked only when the trigger fires. TGL improves F1 on each of 14 backbones (mean +16.7, up to +46.0); in trigger-architecture comparisons, one TGL checkpoint gives the strongest trigger AUCs and the most stable deployed threshold. It runs at 11.13 ms per event on a GPU server and 13.99 ms on a consumer laptop, approximately 4--7x and 12--83x faster than every single-forward LLM-as-trigger configuration tested in each regime, with an approximately 220 MiB BF16 resident footprint deployable on-device alongside the privacy-sensitive activity stream it consumes.

Uncovering Latent Pathological Signatures in Pulmonary CT via Cross-Window Knowledge Distillation

Multi-window CT imaging captures complementary pathological information across anatomical structures of differing densities, yet existing deep learning methods fuse representations only at later stages, missing cross-density interactions. We propose a cross-window knowledge distillation framework in which student encoders learn latent clinical priors from a teacher trained on the most informative window. Evaluated retrospectively on three cohorts - COPD-CT-DF (n=719), RSNA PE (n=1,433), and an in-house CTEPD dataset (n=161) - distillation improved per-window AUC by 10.1-16.5 percentage points on COPD-CT-DF (0.75-0.81 to 0.90-0.94; all P<0.001), with ensemble AUC reaching 0.9960. Similar gains were observed on RSNA PE (0.80-0.83 to 0.90-0.92) and CTEPD (AUC 0.7481 vs. 0.6264). Cross-window distillation internalises pathological signatures invisible to supervised approaches, offering a generalisable solution for multi-window pulmonary CT analysis.

LegalDrill: Diagnosis-Driven Synthesis for Legal Reasoning in Small Language Models

Small language models (SLMs) are promising for real-world deployment due to their efficiency and low operational cost. However, their limited capacity struggles with high-stakes legal reasoning tasks that require coherent statute interpretation and logically consistent deduction. Furthermore, training SLMs for such tasks demands high-quality, concise reasoning trajectories, which are prohibitively expensive to manually collect and difficult to curate via standard rejection sampling, lacking granularity beyond final verdicts. To address these challenges, we propose {LegalDrill}, a diagnosis-driven synthesis framework that extracts and iteratively refines reasoning trajectories from a capable teacher via fine-grained prompting, then a self-reflective verification is employed to adaptively select the most effective data for the SLM student. The resulting data empower SLM training through supervised fine-tuning and direct preference optimization. Extensive experiments on several legal benchmarks demonstrate that {LegalDrill} significantly bolsters the legal reasoning capabilities of representative SLMs while bypassing the need for scarce expert annotations, paving a scalable path toward practical legal reasoning systems.

Bridging MARL to SARL: An Order-Independent Multi-Agent Transformer via Latent Consensus

Cooperative multi-agent reinforcement learning (MARL) is widely used to address large joint observation and action spaces by decomposing a centralized control problem into multiple interacting agents. However, such decomposition often introduces additional challenges, including non-stationarity, unstable training, weak coordination, and limited theoretical guarantees. In this paper, we propose the Consensus Multi-Agent Transformer (CMAT), a centralized framework that bridges cooperative MARL to a hierarchical single-agent reinforcement learning (SARL) formulation. CMAT treats all agents as a unified entity and employs a Transformer encoder to process the large joint observation space. To handle the extensive joint action space, we introduce a hierarchical decision-making mechanism in which a Transformer decoder autoregressively generates a high-level consensus vector, simulating the process by which agents reach agreement on their strategies in latent space. Conditioned on this consensus, all agents generate their actions simultaneously, enabling order-independent joint decision making and avoiding the sensitivity to action-generation order in conventional Multi-Agent Transformers (MAT). This factorization allows the joint policy to be optimized using single-agent PPO while preserving expressive coordination through the latent consensus. To evaluate the proposed method, we conduct experiments on benchmark tasks from StarCraft II, Multi-Agent MuJoCo, and Google Research Football. The results show that CMAT achieves superior performance over recent centralized solutions, sequential MARL methods, and conventional MARL baselines. The code for this paper is available at:https://github.com/RS2002/CMAT .

The Vision Wormhole: Latent-Space Communication in Heterogeneous Multi-Agent Systems

Multi-Agent Systems (MAS) powered by Large Language Models have unlocked advanced collaborative reasoning, yet they remain shackled by the inefficiency of discrete text communication, which imposes significant runtime overhead and information quantization loss. While latent state transfer offers a high-bandwidth alternative, existing approaches either assume homogeneous sender-receiver architectures or rely on pair-specific learned translators, limiting scalability and modularity across diverse model families with disjoint manifolds. In this work, we propose the Vision Wormhole, a novel framework that repurposes the visual interface of Vision-Language Models (VLMs) to enable model-agnostic, text-free communication. By introducing a Universal Visual Codec, we map heterogeneous reasoning traces into a shared continuous latent space and inject them directly into the receiver's visual pathway, effectively treating the vision encoder as a universal port for inter-agent telepathy. Our framework adopts a hub-and-spoke topology to reduce pairwise alignment complexity from O(N^2) to O(N) and leverages a label-free, teacher-student distillation objective to align the high-speed visual channel with the robust reasoning patterns of the text pathway. Extensive experiments across heterogeneous model families (e.g., Qwen-VL, Gemma) demonstrate that the Vision Wormhole reduces end-to-end wall-clock time in controlled comparisons while maintaining reasoning fidelity comparable to standard text-based MAS. Code is available at https://github.com/xz-liu/heterogeneous-latent-mas

The Trojan in the Vocabulary: Stealthy Sabotage of LLM Composition

The open-weight LLM ecosystem is increasingly defined by model composition techniques (such as weight merging, speculative decoding, and vocabulary expansion) that remix capabilities from diverse sources. A critical prerequisite for applying these methods across different model families is tokenizer transplant, which aligns incompatible vocabularies to a shared embedding space. We demonstrate that this essential interoperability step introduces a supply-chain vulnerability: we engineer a single "breaker token" that is functionally inert in a donor model yet reliably reconstructs into a high-salience malicious feature after transplant into a base model. By exploiting the geometry of coefficient reuse, our attack creates an asymmetric realizability gap that sabotages the base model's generation while leaving the donor's utility statistically indistinguishable from nominal behavior. We formalize this as a dual-objective optimization problem and instantiate the attack using a sparse solver. Empirically, the attack is training-free and achieves spectral mimicry to evade outlier detection, while demonstrating structural persistence against fine-tuning and weight merging, highlighting a hidden risk in the pipeline of modular AI composition. Code is available at https://github.com/xz-liu/tokenforge

Bohrium + SciMaster: Building the Infrastructure and Ecosystem for Agentic Science at Scale

AI agents are emerging as a practical way to run multi-step scientific workflows that interleave reasoning with tool use and verification, pointing to a shift from isolated AI-assisted steps toward \emph{agentic science at scale}. This shift is increasingly feasible, as scientific tools and models can be invoked through stable interfaces and verified with recorded execution traces, and increasingly necessary, as AI accelerates scientific output and stresses the peer-review and publication pipeline, raising the bar for traceability and credible evaluation. However, scaling agentic science remains difficult: workflows are hard to observe and reproduce; many tools and laboratory systems are not agent-ready; execution is hard to trace and govern; and prototype AI Scientist systems are often bespoke, limiting reuse and systematic improvement from real workflow signals. We argue that scaling agentic science requires an infrastructure-and-ecosystem approach, instantiated in Bohrium+SciMaster. Bohrium acts as a managed, traceable hub for AI4S assets -- akin to a HuggingFace of AI for Science -- that turns diverse scientific data, software, compute, and laboratory systems into agent-ready capabilities. SciMaster orchestrates these capabilities into long-horizon scientific workflows, on which scientific agents can be composed and executed. Between infrastructure and orchestration, a \emph{scientific intelligence substrate} organizes reusable models, knowledge, and components into executable building blocks for workflow reasoning and action, enabling composition, auditability, and improvement through use. We demonstrate this stack with eleven representative master agents in real workflows, achieving orders-of-magnitude reductions in end-to-end scientific cycle time and generating execution-grounded signals from real workloads at multi-million scale.

ChiMDQA: Towards Comprehensive Chinese Document QA with Fine-grained Evaluation

With the rapid advancement of natural language processing (NLP) technologies, the demand for high-quality Chinese document question-answering datasets is steadily growing. To address this issue, we present the Chinese Multi-Document Question Answering Dataset(ChiMDQA), specifically designed for downstream business scenarios across prevalent domains including academic, education, finance, law, medical treatment, and news. ChiMDQA encompasses long-form documents from six distinct fields, consisting of 6,068 rigorously curated, high-quality question-answer (QA) pairs further classified into ten fine-grained categories. Through meticulous document screening and a systematic question-design methodology, the dataset guarantees both diversity and high quality, rendering it applicable to various NLP tasks such as document comprehension, knowledge extraction, and intelligent QA systems. Additionally, this paper offers a comprehensive overview of the dataset's design objectives, construction methodologies, and fine-grained evaluation system, supplying a substantial foundation for future research and practical applications in Chinese QA. The code and data are available at: https://anonymous.4open.science/r/Foxit-CHiMDQA/.

PORTool: Tool-Use LLM Training with Rewarded Tree

Current tool-use large language models (LLMs) are trained on static datasets, enabling them to interact with external tools and perform multi-step, tool-integrated reasoning, which produces tool-call trajectories. However, these models imitate how a query is resolved in a generic tool-call routine, thereby failing to explore possible solutions and demonstrating limited performance in an evolved, dynamic tool-call environment. In this work, we propose PORTool, a reinforcement learning (RL) method that encourages a tool-use LLM to explore various trajectories yielding the correct answer. Specifically, this method starts with generating multiple rollouts for a given query, and some of them share the first few tool-call steps, thereby forming a tree-like structure. Next, we assign rewards to each step, based on its ability to produce a correct answer and make successful tool calls. A shared step across different trajectories receives the same reward, while different steps under the same fork receive different rewards. Finally, these step-wise rewards are used to calculate fork-relative advantages, blended with trajectory-relative advantages, to train the LLM for tool use. The experiments utilize 17 tools to address user queries, covering both time-sensitive and time-invariant topics. We conduct ablation studies to systematically justify the necessity and the design robustness of step-wise rewards. Furthermore, we compare the proposed PORTool with other training approaches and demonstrate significant improvements in final accuracy and the number of tool-call steps.