RiboSphere: Learning Unified and Efficient Representations of RNA Structures

Accurate RNA structure modeling remains difficult because RNA backbones are highly flexible, non-canonical interactions are prevalent, and experimentally determined 3D structures are comparatively scarce. We introduce \emph{RiboSphere}, a framework that learns \emph{discrete} geometric representations of RNA by combining vector quantization with flow matching. Our design is motivated by the modular organization of RNA architecture: complex folds are composed from recurring structural motifs. RiboSphere uses a geometric transformer encoder to produce SE(3)-invariant (rotation/translation-invariant) features, which are discretized with finite scalar quantization (FSQ) into a finite vocabulary of latent codes. Conditioned on these discrete codes, a flow-matching decoder reconstructs atomic coordinates, enabling high-fidelity structure generation. We find that the learned code indices are enriched for specific RNA motifs, suggesting that the model captures motif-level compositional structure rather than acting as a purely compressive bottleneck. Across benchmarks, RiboSphere achieves strong performance in structure reconstruction (RMSD 1.25\,Å, TM-score 0.84), and its pretrained discrete representations transfer effectively to inverse folding and RNA--ligand binding prediction, with robust generalization in data-scarce regimes.

Co-Diffusion: An Affinity-Aware Two-Stage Latent Diffusion Framework for Generalizable Drug-Target Affinity Prediction

Predicting drug-target affinity is fundamental to virtual screening and lead optimization. However, existing deep models often suffer from representation collapse in stringent cold-start regimes, where the scarcity of labels and domain shifts prevent the learning of transferable pharmacophores and binding motifs. In this paper, we propose Co-Diffusion, a novel affinity-aware framework that redefines DTA prediction as a constrained latent denoising process to enhance generalization. Co-Diffusion employs a two-stage paradigm: Stage I establishes an affinity-steered latent manifold by aligning drug and target embeddings under an explicit supervised objective, ensuring that the latent space reflects the intrinsic binding landscape. Stage II introduces modality-specific latent diffusion as a stochastic perturb-and-denoise regularizer, forcing the model to recover consistent affinity semantics from noisy structural representations. This approach effectively mitigates the reconstruction-regression conflict common in generative DTA models. Theoretically, we show that Co-Diffusion maximizes a variational lower bound on the joint likelihood of drug structures, protein sequences, and binding strength. Extensive experiments across multiple benchmarks demonstrate that Co-Diffusion significantly outperforms state-of-the-art baselines, particularly yielding superior zero-shot generalization on unseen molecular scaffolds and novel protein families-paving a robust path for in silico drug prioritization in unexplored chemical spaces.

HarmonyCell: Automating Single-Cell Perturbation Modeling under Semantic and Distribution Shifts

Single-cell perturbation studies face dual heterogeneity bottlenecks: (i) semantic heterogeneity--identical biological concepts encoded under incompatible metadata schemas across datasets; and (ii) statistical heterogeneity--distribution shifts from biological variation demanding dataset-specific inductive biases. We propose HarmonyCell, an end-to-end agent framework resolving each challenge through a dedicated mechanism: an LLM-driven Semantic Unifier autonomously maps disparate metadata into a canonical interface without manual intervention; and an adaptive Monte Carlo Tree Search engine operates over a hierarchical action space to synthesize architectures with optimal statistical inductive biases for distribution shifts. Evaluated across diverse perturbation tasks under both semantic and distribution shifts, HarmonyCell achieves a 95% valid execution rate on heterogeneous input datasets (versus 0% for general agents) while matching or even exceeding expert-designed baselines in rigorous out-of-distribution evaluations. This dual-track orchestration enables scalable automatic virtual cell modeling without dataset-specific engineering.

How RL Unlocks the Aha Moment in Geometric Interleaved Reasoning

Solving complex geometric problems inherently requires interleaved reasoning: a tight alternation between constructing diagrams and performing logical deductions. Although recent Multimodal Large Language Models (MLLMs) have demonstrated strong capabilities in visual generation and plotting, we identify a counter-intuitive and underexplored phenomenon. Naively applying Supervised Fine-Tuning (SFT) on interleaved plot-solution data leads to a substantial degradation in reasoning performance compared to text-only baselines. We argue that this failure stems from a fundamental limitation of SFT, which primarily induces distributional alignment: the model learns to reproduce the surface format of interleaved plotting but fails to internalize the causal dependency between the generated plot and reasoning steps. To overcome this limitation, we propose Faire (Functional alignment for interleaved reasoning), a reinforcement learning framework that enforces three casual constraints to move beyond superficial imitation toward functional alignment. Extensive experiments show that Faire induces a qualitative shift in model behavior in which the plotting is effectively internalized, yielding competitive performance on challenging geometric reasoning benchmarks.

PointCoT: A Multi-modal Benchmark for Explicit 3D Geometric Reasoning

While Multimodal Large Language Models (MLLMs) demonstrate proficiency in 2D scenes, extending their perceptual intelligence to 3D point cloud understanding remains a significant challenge. Current approaches focus primarily on aligning 3D features with pre-trained models. However, they typically treat geometric reasoning as an implicit mapping process. These methods bypass intermediate logical steps and consequently suffer from geometric hallucinations. They confidently generate plausible responses that fail to ground in precise structural details. To bridge this gap, we present PointCoT, a novel framework that empowers MLLMs with explicit Chain-of-Thought (CoT) reasoning for 3D data. We advocate for a \textit{Look, Think, then Answer} paradigm. In this approach, the model is supervised to generate geometry-grounded rationales before predicting final answers. To facilitate this, we construct Point-Reason-Instruct, a large-scale benchmark comprising $\sim$86k instruction-tuning samples with hierarchical CoT annotations. By leveraging a dual-stream multi-modal architecture, our method synergizes semantic appearance with geometric truth. Extensive experiments demonstrate that PointCoT achieves state-of-the-art performance on complex reasoning tasks.

The Trinity of Consistency as a Defining Principle for General World Models

The construction of World Models capable of learning, simulating, and reasoning about objective physical laws constitutes a foundational challenge in the pursuit of Artificial General Intelligence. Recent advancements represented by video generation models like Sora have demonstrated the potential of data-driven scaling laws to approximate physical dynamics, while the emerging Unified Multimodal Model (UMM) offers a promising architectural paradigm for integrating perception, language, and reasoning. Despite these advances, the field still lacks a principled theoretical framework that defines the essential properties requisite for a General World Model. In this paper, we propose that a World Model must be grounded in the Trinity of Consistency: Modal Consistency as the semantic interface, Spatial Consistency as the geometric basis, and Temporal Consistency as the causal engine. Through this tripartite lens, we systematically review the evolution of multimodal learning, revealing a trajectory from loosely coupled specialized modules toward unified architectures that enable the synergistic emergence of internal world simulators. To complement this conceptual framework, we introduce CoW-Bench, a benchmark centered on multi-frame reasoning and generation scenarios. CoW-Bench evaluates both video generation models and UMMs under a unified evaluation protocol. Our work establishes a principled pathway toward general world models, clarifying both the limitations of current systems and the architectural requirements for future progress.

Thinking with Drafting: Optical Decompression via Logical Reconstruction

Existing multimodal large language models have achieved high-fidelity visual perception and exploratory visual generation. However, a precision paradox persists in complex reasoning tasks: optical perception systems transcribe symbols without capturing logical topology, while pixel-based generative models produce visual artifacts lacking mathematical exactness. To bridge this gap, we propose that reasoning over visual inputs be reconceptualized as optical decompression-the process of reconstructing latent logical structures from compressed visual tokens. Guided by the axiom that Parsing is Reasoning, we introduce Thinking with Drafting (TwD), which utilizes a minimalist Domain-Specific Language (DSL) as a grounding intermediate representation. Unlike standard approaches that hallucinate answers directly, TwD forces the model to draft its mental model into executable code, rendering deterministic visual proofs for self-verification. To validate this, we present VisAlg, a visual algebra benchmark. Experiments demonstrate that TwD serve as a superior cognitive scaffold. Our work establishes a closed-loop system where visual generation acts not as a creative output but as a logical verifier, offering a generalizable path for visual reasoning.

Dual Latent Memory for Visual Multi-agent System

While Visual Multi-Agent Systems (VMAS) promise to enhance comprehensive abilities through inter-agent collaboration, empirical evidence reveals a counter-intuitive "scaling wall": increasing agent turns often degrades performance while exponentially inflating token costs. We attribute this failure to the information bottleneck inherent in text-centric communication, where converting perceptual and thinking trajectories into discrete natural language inevitably induces semantic loss. To this end, we propose L$^{2}$-VMAS, a novel model-agnostic framework that enables inter-agent collaboration with dual latent memories. Furthermore, we decouple the perception and thinking while dynamically synthesizing dual latent memories. Additionally, we introduce an entropy-driven proactive triggering that replaces passive information transmission with efficient, on-demand memory access. Extensive experiments among backbones, sizes, and multi-agent structures demonstrate that our method effectively breaks the "scaling wall" with superb scalability, improving average accuracy by 2.7-5.4% while reducing token usage by 21.3-44.8%. Codes: https://github.com/YU-deep/L2-VMAS.

Chain-of-Thought Compression Should Not Be Blind: V-Skip for Efficient Multimodal Reasoning via Dual-Path Anchoring

While Chain-of-Thought (CoT) reasoning significantly enhances the performance of Multimodal Large Language Models (MLLMs), its autoregressive nature incurs prohibitive latency constraints. Current efforts to mitigate this via token compression often fail by blindly applying text-centric metrics to multimodal contexts. We identify a critical failure mode termed Visual Amnesia, where linguistically redundant tokens are erroneously pruned, leading to hallucinations. To address this, we introduce V-Skip that reformulates token pruning as a Visual-Anchored Information Bottleneck (VA-IB) optimization problem. V-Skip employs a dual-path gating mechanism that weighs token importance through both linguistic surprisal and cross-modal attention flow, effectively rescuing visually salient anchors. Extensive experiments on Qwen2-VL and Llama-3.2 families demonstrate that V-Skip achieves a $2.9\times$ speedup with negligible accuracy loss. Specifically, it preserves fine-grained visual details, outperforming other baselines over 30\% on the DocVQA.

SCP: Accelerating Discovery with a Global Web of Autonomous Scientific Agents

We introduce SCP: the Science Context Protocol, an open-source standard designed to accelerate discovery by enabling a global network of autonomous scientific agents. SCP is built on two foundational pillars: (1) Unified Resource Integration: At its core, SCP provides a universal specification for describing and invoking scientific resources, spanning software tools, models, datasets, and physical instruments. This protocol-level standardization enables AI agents and applications to discover, call, and compose capabilities seamlessly across disparate platforms and institutional boundaries. (2) Orchestrated Experiment Lifecycle Management: SCP complements the protocol with a secure service architecture, which comprises a centralized SCP Hub and federated SCP Servers. This architecture manages the complete experiment lifecycle (registration, planning, execution, monitoring, and archival), enforces fine-grained authentication and authorization, and orchestrates traceable, end-to-end workflows that bridge computational and physical laboratories. Based on SCP, we have constructed a scientific discovery platform that offers researchers and agents a large-scale ecosystem of more than 1,600 tool resources. Across diverse use cases, SCP facilitates secure, large-scale collaboration between heterogeneous AI systems and human researchers while significantly reducing integration overhead and enhancing reproducibility. By standardizing scientific context and tool orchestration at the protocol level, SCP establishes essential infrastructure for scalable, multi-institution, agent-driven science.