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  1. bioRxiv

    BLOOM turns sparse developmental atlases into a queryable virtual embryo, topping gene and cell correlation on all three mouse atlases

    BLOOM frames transcriptomic virtual-embryo modeling as conditional generation: given an observed window of cell populations, a requested developmental stage and cell-state information, it generates the expression distribution at that stage. Pseudo-trajectories link independently sampled populations, while developmental age, cell-identity hierarchy, anatomical context, gene programmes and transcription-factor–target networks condition both a Gaussian base and a flow-matching generator. Across prenatal, visual-cortex and multi-organ endothelial mouse single-cell atlases, BLOOM ranks first for stage-averaged gene and cell correlations against 22 time-series forecasting baselines.

  2. CovDiff-PaAno keeps PaAno's encoder and rewrites only the scoring: multivariate anomaly AUC-ROC rises from 0.7612 to 0.7843

    CovDiff-PaAno replaces cosine matching in patch-based time-series anomaly detection with regularized Mahalanobis scoring and adds raw, first-difference and second-difference views that share one frozen encoder while each keeps its own memory bank and covariance. In a ten-seed controlled comparison on TSB-AD-M, AUC-ROC rose from 0.7612 for reproduced PaAno to 0.7843 and Range-F1 from 0.4043 to 0.4384; on TSB-AD-U the corresponding scores rose from 0.8532 to 0.8626 and from 0.4822 to 0.4924. The encoder parameter count stays at about 0.397M, but inference time grows 3.47-fold and peak inference memory 10.01-fold.

  3. arXiv

    Beyond whether an image is AI: EviScene checks the depicted situation, reaching 52.26% evidence sufficiency

    Image factuality assessment no longer stops at whether a picture is AI-generated: the EviScene multimodal agent refines its own questions during investigation and reaches 79.05% balanced accuracy and 52.26% evidence sufficiency on 1,527 test images.

  4. bioRxiv

    Phage matching stops relying on one embedding: routing by query novelty lifts both-unseen AUPRC from 0.036 to 0.671

    Phage therapy needs a matching phage for each clinical bacterial isolate, and conventional experimental screening is slow and labor-intensive. PhageHost-GNN encodes phage receptor-binding proteins and bacterial K-locus proteins as sequence, structure and genomic-context embeddings, feeds them to a graph neural network, and automatically selects the embedding model best suited to how novel a query strain is relative to the training set. On the Spain-derived Beamud2023 data, with both hosts and phages unseen, the routed model reached an AUPRC of 0.671, while fixed-embedding models stayed at or below 0.036.

  5. arXiv

    Same object, new material prompt: PhysForge fits physics on contact and deformation windows

    PhysForge treats material-conditioned dynamics from a video diffusion model as references for fitting the physical parameters of 3D assets, so a user-specified material actually changes how an object contacts and deforms. Previously such parameters were largely inferred from appearance, making it hard to assign a material to the same object or to estimate properties from complex interactions between objects and semantic parts. On PhysAssets and Google Scanned Objects it reaches the best CLIP and physical controllability scores for both common and uncommon materials, with average physical controllability 4.3 versus 3.8 for the strongest baseline.

  6. arXiv

    APEX moves indirect prompt-injection defense to the execution boundary, cutting attack success to 0% on five of six benchmarks and 0.56% on the sixth

    The work presents APEX, which shifts indirect prompt-injection defense from recognizing attack patterns to checking each proposed effect at the execution boundary: before untrusted execution it compiles the user's authorization into a contract, WRAP admits an effect only when the contract and runtime evidence reconstruct its authorization, and PLANT places probes on the contract's endorsed dependencies so unendorsed use of runtime information reveals itself before commitment; across six benchmarks and 13 baselines APEX reaches 0% attack success on five benchmarks and 0.56% on the sixth, and holds 0% under three adaptive attacks spanning all three capability-unit types.

  7. arXiv

    CrashSim generates crash scenarios from real-world crash priors, builds the 4,000+ scenario nuCrash dataset, and widens measured safety gaps across five planners

    The authors present CrashSim, a human behavior-informed crash scenario generation framework that uses a vision-language model to interpret naturalistic driving scenes, hierarchically retrieves real-world crash priors, and converts their relative-motion patterns and behavior-stage timings into anchor guidance for a diffusion generator pretrained on nuScenes; results show CrashSim reproduces real-world pre-impact behavior, collision dynamics, collision geometry and crash-type distributions more closely than Strive and LD-scene, and it is used to build nuCrash, a dataset of over 4,000 crash and near-crash scenarios on which five planners show larger closed-loop performance differences than on nuScenes, with an LLM evaluation agent providing capability-level diagnoses and improvement guidance.

  8. arXiv

    Same bytes, two kinds of authority: splitting forged chat-template markers into ordinary subwords cuts injection success by 39 to 66 percentage points on Llama-3.1, GLM-4.5 and Seed-OSS-36B

    Holding bytes identical and changing only whether forged chat-template markers are encoded as reserved token ids or as ordinary subwords, this study measures the resulting gap in indirect prompt-injection success on LLM agents in InjecAgent, finding an identity gap of 39 to 66 percentage points on Llama-3.1, GLM-4.5 and Seed-OSS-36B while Qwen3-8B draws most of its attack from marker text, and further showing that the authority lives in the single learned input vector at the marker position and that the standard tokenizer-side mitigation misses the tool-protocol tokens that carry tool output.

  9. arXiv

    Under matched compute on Dream-7B and LLaDA-8B, ORM reranking beats deterministic PRM guidance by up to 82.71% versus 70.02%

    The work introduces a forward-pass-matched diagnostic protocol for reward-guided reasoning in discrete diffusion language models and shows, on Dream-7B and LLaDA-8B-Base, that deterministic top-k process-reward-model guidance trails independent sampling plus task-matched outcome-reward-model reranking on GSM8K, MATH, and MBPP, decomposing the gap into candidate-pool damage from guidance and terminal selection quality.

  10. arXiv

    SLCA-GRPO routes tool-segment and summary-segment advantages separately, raising tool-calling success by up to 10.03 points across three backbones

    The work splits tool-calling RL trajectories into a tool segment and a summary segment, argues that broadcasting a single trajectory-level advantage causes cross-segment credit misattribution, and proposes SLCA-GRPO, which normalizes the two segment rewards within the group and routes each only to its own tokens inside a single unified policy, paired with a Schema-Guided LLM Simulator and Hierarchical Rewards; across Qwen2.5-3B/7B-Instruct and Qwen3-8B-Base on Toucan-Test, BFCL V3 and τ²-Bench it reports higher means than matched GRPO, with 7B gaps of +2.53, +1.36 and +9.15 percentage points.

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