Cell transplant across the tree of life hints at how animals emerged
Embryonic ‘organizer cells’ can tell embryos of various phyla what kind of body to build. Embryonic ‘organizer cells’ can tell embryos of various phyla what kind of body to build.
Academic Intelligence · Curated Daily
AcademicHub 汇聚顶级期刊与预印本平台的实时文献。定制您的专属科研雷达,利用大语言模型自动生成交叉领域文献分析简报。
Embryonic ‘organizer cells’ can tell embryos of various phyla what kind of body to build. Embryonic ‘organizer cells’ can tell embryos of various phyla what kind of body to build.
arXiv:2505.12369v2 Announce Type: replace Abstract: Multi-hop logical reasoning on knowledge graphs requires faithfully mapping the logical semantics to latent space. Current geometric embedding methods show to be useful on this task by mapping entities to geometric regions and logical operations to latent transformations. While a geometric embedding can provide a direct interpretability framework for query answering, current methods have only leveraged the geometric construction of entities, failing to map logical operations to pure geometric transformations and, instead, using neural components to learn these operations. On the other hand, purely neural-based methods outperform geometric methods, but they lack interpretability in the latent space. We introduce GeometrE, a geometric embedding method for multi-hop reasoning, that maps every logical operation to a purely geometric operation in the latent space. Additionally, we introduce a transitive loss function and show that, unlike existing methods, it can preserve the logical rule for all a,b,c: r(a,b) and r(b,c) -> r(a,c). Our experiments show that GeometrE outperforms current state-of-the-art geometric methods and remains competitive with existing neural-based methods on standard benchmark datasets.
arXiv:2606.15983v1 Announce Type: new Abstract: Recent theoretical progress has established conditions under which machine learning models can efficiently predict ground-state properties of gapped local Hamiltonians when trained on quantum-generated data. Previous experimental demonstrations in this paradigm, however, have largely been limited to small systems or highly structured states, due to the difficulty of preparing many-body ground states on quantum processors. In this work, we demonstrate learning from experimental quantum data generated from approximate ground states of the two-dimensional Heisenberg XXZ model with system sizes up to 115 qubits. We construct a dataset of single-site expectation values, two-point correlations, and 12-body loop correlations across the antiferromagnetic phase. We then train neural networks on this data and show that they can accurately predict spatially resolved observables for previously unseen Hamiltonian parameters, both within the training distribution and in an out-of-distribution regime approaching the phase boundary. Our results demonstrate the practical realization of learning from quantum data for an interacting two-dimensional many-body system at scale, motivating a path toward regimes where quantum processors could provide training data beyond the reach of classical approximation methods.
Solving mathematical reasoning problems requires not only accurate access to relevant knowledge but also careful, multi-step thinking. However, current retrieval-augmented models often rely on a single perspective, follow inflexible search strategies, and struggle to effectively combine information from multiple sources. We introduce SIGMA (Search-Augmented On-Demand Knowledge Integration for AGentic Mathematical reAsoning), a unified framework that orchestrates specialized agents to independently reason, perform targeted searches, and synthesize findings through a moderator mechanism. Each agent generates hypothetical passages to optimize retrieval for its analytic perspective, ensuring knowledge integration is both context-sensitive and computation-efficient. When evaluated on challenging benchmarks such as MATH500, AIME, and PhD-level science QA GPQA, SIGMA consistently outperforms both open- and closed-source systems, achieving an absolute performance improvement of 7.4%. Our results demonstrate that multi-agent, on-demand knowledge integration significantly enhances both reasoning accuracy and efficiency, offering a scalable approach for complex, knowledge-intensive problem-solving. We will release the code upon publication.
arXiv:2507.18623v4 Announce Type: replace-cross Abstract: The ability to adapt to physical actions and constraints in an environment is crucial for embodied agents (e.g., robots) to effectively collaborate with humans. Such physically grounded human-AI collaboration must account for the increased complexity of the continuous state-action space and constrained dynamics caused by physical constraints. However, most existing collaboration benchmarks are discrete or do not consider physical attributes and constraints. To address this, we introduce Moving Out, a human-AI collaboration benchmark that resembles a wide range of collaboration modes affected by physical attributes and constraints, such as moving heavy items together and coordinating actions to move an item around a corner. Moving Out consists of two challenges and human-human interaction data to comprehensively evaluate models' abilities to adapt to diverse human behaviors and unseen physical attributes. To give embodied agents the capability to collaborate with humans under physical attributes and constraints, we propose a novel method, BASS (Behavior Augmentation, Simulation, and Selection), to enhance the diversity of agents and their understanding of the outcome of actions. We systematically compare BASS and state-of-the-art models in AI-AI and human-AI experiments, showing that BASS can effectively collaborate with both unseen AI and humans. The project page is available at https://live-robotics-uva.github.io/movingout_ai/.
Accurate cell type annotation is essential for single-cell transcriptomics, directly shaping downstream analyses and biological interpretations. Yet, objective evaluation of annotation quality remains a major challenge. Here, we argue that a cell type or cell state label has practical utility only if it captures a molecular pattern that is reproducible across biological replicates. Based on this principle, we introduce inter-sample consistency (ISC), a quantitative framework to assess annotation quality in single-cell RNA-seq datasets. Unlike existing cluster validation approaches, ISC distinguishes annotations that generalize across samples and individuals from those driven by technical or unwanted variation, thereby providing principled criteria for annotation quality and transferability. When applied to published single-cell atlases, ISC reveals widespread reproducibility gaps and provides actionable guidance for repairing inconsistent annotations. Notably, ISC enables benchmarking of automated cell type annotation tools even when ground-truth labels are unavailable, providing interpretable metrics to guide their development and evaluation. Implemented as the scTypeEval Bioconductor package, this framework offers a broadly applicable resource for evaluating and improving cell type annotations in single-cell RNA-seq experiments.
arXiv:2606.19416v1 Announce Type: new Abstract: Loan origination is the process by which a lender creates a new loan, from application and underwriting through approval and funding. This process serves a critical role in evaluating the eligibility and level of risk posed by an applicant. Recently, firms have begun using mortgage loan agents to augment human loan officers, despite a lack of any public benchmark. To fill this gap, we present MortarBench, a loan origination agent benchmark. MortarBench uses a financial data synthesis and mutation pipeline to generate examples with broad edge case coverage that match real-world distributions and questions. We find that state-of-the-art large language models (LLMs) perform poorly, with closed-source models achieving at most 77.1\% exact match accuracy. We also discover systematic biases in LLM perception of foreignness related to non-English names. Noting these weaknesses, we introduce CRIT, a confidence calibration framework. Our method increases accuracy to 80.5\% while improving risk management steering and reducing bias.
arXiv:2606.16152v1 Announce Type: new Abstract: Knowledge distillation from powerful reasoning models is widely used to improve Small Language Models (SLMs) on mathematical reasoning, often assuming that traces with higher reward model scores provide more useful supervision. We identify a counterintuitive Quality-Utility Paradox in mathematical reasoning distillation. Data refined or synthesized by a stronger Oracle obtains higher perceived quality according to reward models, yet consistently underperforms traces generated by the SLM itself and selected through rejection sampling across Qwen2.5, LLaMA-3, and DeepSeek families. Our analysis shows that Oracle refinement couples logical repair with distributional drift away from the SLM's native reasoning distribution. This drift increases the learner's adaptation cost and can outweigh the benefit of improved reasoning logic. To test this mechanism, we introduce Style-Aligned Refinement, which preserves the native trajectory of the SLM while retaining logical repair from the Oracle. This intervention lowers adaptation cost and restores downstream utility. These findings suggest that effective mathematical reasoning distillation should jointly optimize perceived solution quality and learner-data compatibility, rather than relying solely on reward-model scores. The datasets and code are available at https://github.com/Dracoqhl/Quality-Utility-Paradox.
The abundance of pre-trained diffusion models provides an opportunity for composition. Combining several models, however, runs the risk of one model dominating or models disagreeing with each other. Here, we propose Divide-and-Denoise, a method for coordinating multiple pre-trained diffusion models during sampling. Much like managing a specialized workforce, our method creates a fair but efficient division of labor across models. Central to our method is the notion of an allocation which defines the responsibility of each model to every region of the noisy sample. At every timestep, we then denoise by (i) updating the allocation by solving a fair division game, where we divide the sample into regions that maximize total utility under fairness constraints, and (ii) aligning the models with this allocation, where we guide each model to denoise within its assigned region. This leads to a new composite denoising process that evolves in tandem with a division process. We evaluate Divide-and-Denoise on conditional image generation. Across several quality metrics, including the GenEval benchmark, our method outperforms baselines and resolves common failures including missing objects and mismatched attributes. Experiments show that Divide-and-Denoise utilizes each model's expertise without neglecting any other model.
arXiv:2510.02660v2 Announce Type: replace-cross Abstract: When researchers claim AI systems possess ToM or mental models, they are fundamentally discussing behavioral predictions and bias corrections rather than genuine mental states. This position paper argues that the current discourse conflates sophisticated pattern matching with authentic cognition, missing a crucial distinction between simulation and experience. While recent studies show LLMs achieving human-level performance on ToM laboratory tasks, these results are based only on behavioral mimicry. More importantly, the entire testing paradigm may be flawed in applying individual human cognitive tests to AI systems, but assessing human cognition directly in the moment of human-AI interaction. I suggest shifting focus toward mutual ToM frameworks that acknowledge the simultaneous contributions of human cognition and AI algorithms, emphasizing the interaction dynamics, instead of testing AI in isolation.
arXiv:2601.17634v2 Announce Type: replace Abstract: We study endpoint distributions of balanced affine weighted Motzkin paths. In the balanced case, the generating-function equation has Pearson-type characteristic geometry. We show that this geometry controls the terminal-height law globally: the characteristic escape time determines the limiting cumulant generating function, the large-deviation rate function, and the ray-scale asymptotics. Thus the usual Gaussian window is only the local quadratic approximation to a global Pearson-driven profile. For finite sizes, we prove a uniform Daniels saddlepoint approximation in the one-dominant-singularity regimes and identify the exceptional antipodal case requiring a lattice/interference correction.
In the Indian Ocean, a deep-sea area roughly 1,200 kilometres long and 7 kilometres deep was found to harbour an ecological landmark site of whale remains. In the Indian Ocean, a deep-sea area roughly 1,200 kilometres long and 7 kilometres deep was found to harbour an ecological landmark site of whale remains.
World Action Models (WAMs) offer a promising route for robot manipulation by using video generation models to model future scene evolution before producing control actions. However, our empirical observations reveal a phenomenon: generating plausible visual futures does not always guarantee the extraction of accurate actions. To diagnose this failure, we conduct action-head attention analysis and causal interventions. We find that the action decoder fails to focus on task-relevant interaction regions and remains sensitive to perturbations in task-irrelevant areas. This reveals a representation mismatch: hidden states optimized for visual reconstruction are not inherently organized in a form useful for low-level action control. In this paper, we propose AGRA, an Action-Grounded Representation Alignment objective that regularizes the world-action interface by aligning intermediate video diffusion features with spatially coherent semantic representations from a foundation visual encoder. We evaluate AGRA on real-world manipulation tasks. Experiments show that AGRA makes world model representations more action-grounded: by focusing the action decoder on the correct interaction regions, it improves object localization accuracy and affordance understanding, and makes the policy more robust to perturbations in task-irrelevant regions. As a result, AGRA consistently improves both in-distribution performance and out-of-distribution generalization over the baseline world action model.
arXiv:2512.10903v2 Announce Type: replace Abstract: Circuit discovery aims to identify minimal subnetworks that are responsible for specific behaviors in large language models (LLMs). Existing approaches primarily rely on iterative edge pruning, which is computationally expensive and limited to coarse-grained units such as attention heads or MLP blocks, overlooking finer structures like individual neurons. We propose a node-level pruning framework for circuit discovery that addresses both scalability and granularity limitations. Our method introduces learnable masks across multiple levels of granularity, from entire blocks to individual neurons, within a unified optimization objective. Granularity-specific sparsity penalties guide the pruning process, allowing a comprehensive compression in a single fine-tuning run. Empirically, our approach identifies circuits that are smaller in nodes than those discovered by prior methods; moreover, we demonstrate that many neurons deemed important by coarse methods are actually irrelevant, while still maintaining task performance. Furthermore, our method has a significantly lower memory footprint, 5-10x, as it does not require keeping intermediate activations in the memory to work.
arXiv:2511.14427v4 Announce Type: replace-cross Abstract: Effective contact-rich manipulation requires robots to synergistically leverage vision, force, and proprioception. However, Reinforcement Learning agents struggle to learn in such multisensory settings, especially amidst sensory noise and dynamic changes. We propose MultiSensory Dynamic Pretraining (MSDP), a novel framework for learning expressive multisensory representations tailored for task-oriented policy learning. MSDP is based on masked autoencoding and trains a transformer-based encoder by reconstructing multisensory observations from only a subset of sensor embeddings, leading to cross-modal prediction and sensor fusion. For downstream policy learning, we introduce a novel asymmetric architecture, where a cross-attention mechanism allows the critic to extract dynamic, task-specific features from the frozen embeddings, while the actor receives a stable pooled representation to guide its actions. Our method demonstrates accelerated learning and robust performance under diverse perturbations, including sensor noise, and changes in object dynamics. Evaluations in multiple challenging, contact-rich robot manipulation tasks in simulation and the real world showcase the effectiveness of MSDP. Our approach exhibits strong robustness to perturbations and achieves high success rates on the real robot with as few as 6,000 online interactions, offering a simple yet powerful solution for complex multisensory robotic control. Website: https://msdp-pearl.github.io/
arXiv:2603.18897v2 Announce Type: replace-cross Abstract: LLM-powered agents execute tasks through a sequential loop of model generation and tool execution. Today's serving systems serialize this loop, leaving tool latency exposed on the task critical path. This paper presents PASTE, a tool-aware agent-serving system that predicts concrete future tool invocations from recurring agent patterns and executes them speculatively while the LLM is still generating. PASTE isolates speculative results until confirmed by the LLM and jointly schedules tool execution and returning LLM sessions to avoid shifting bottlenecks to the GPU. Across deep research, coding, and scientific-agent workloads, PASTE reduces average task completion time by 43.5% and lowers observed tool latency by 1.8x.
arXiv:2606.14386v1 Announce Type: cross Abstract: Scientific discovery saturates when new hypotheses cease to provide independent information, even if the nominal hypothesis space remains large. We study hybrid discovery systems that combine structured local search with LLM-generated non-local proposals and pose the Search Compression Hypothesis: non-local exploration helps only when three geometric conditions co-occur: spectral compression, orthogonal escape from the explored span, and residual signal alignment with the target. We formalize these conditions, derive necessary conditions for hybrid advantage, and test the mechanism in controlled synthetic environments, large-scale A-share factor discovery, and symbolic-regression benchmarks; a public tabular operational sanity check tests the associated budget-allocation implication. Signal-planting and directed-versus-random experiments show that novelty alone is insufficient: random orthogonal jumps expand coverage but do not improve yield without predictive alignment. Across compression sweeps, real factor archives, and LLM-SRBench tasks, hybrid gains concentrate in weakly represented but target-bearing directions and vanish as the hypothesis space approaches full rank. The framework turns LLM-guided discovery from generic novelty search into a diagnostic procedure for deciding when directed non-local exploration is warranted.
Vision-language-action (VLA) models can describe scenes and reason about them in language, yet still struggle to ground their actions in the dense 3D world around them. Existing approaches either inject features from a frozen 3D foundation model without an objective that ensures the policy uses them, or constrain geometry with sparse box and map losses that provide no dense spatial signal. We introduce VLGA, the first vision-language-action model supervised to reconstruct the dense 3D world it drives through. VLGA introduces geometry as a fourth modality alongside vision, language, and action through a dedicated expert supervised by a per-pixel pointmap regression loss against LiDAR. Extensive experiments conducted on challenging nuScenes and Bench2Drive datasets for open-loop and closed-loop evaluations, respectively, show the superiority of VLGA over counterpart VLA methods. In particular, on open-loop nuScenes, VLGA sets a new state of the art among VLA methods without ego status, with the lowest L2 (0.50\,m average) and 3-second collision rate (0.18\%). On closed-loop Bench2Drive, VLGA attains the state-of-the-art driving score of 79.08, +0.71 over the strongest prior VLA, at comparable efficiency and comfort.
arXiv:2606.11537v1 Announce Type: new Abstract: Financial and tabular question answering requires more than fluent reasoning: answers must be grounded in the exact facts, formulas, units, signs, and scales that support them. A single misread cell or incorrect operation can silently produce a plausible but wrong result. We introduce \textsc{MOCA-Agent}, a market-of-claims code agent that replaces free-form multi-agent debate with claim-level verification. The system decomposes each question into typed atomic claims, asks specialist trader agents to buy or sell those claims, clears their orders into confidence-weighted accept/reject decisions, and synthesizes an executable Python program from market-supported evidence. A code-aware verifier then checks the program for execution, structural consistency, and common financial reasoning errors, with at most one market-aware repair round. Across ten public benchmarks spanning financial numerical reasoning, general tabular reasoning, ESG question answering, and multimodal chart reasoning, \textsc{MOCA-Agent} achieves strong performance using a fixed Qwen3.6-27B backbone, including $78.3\%$ on FinQA, $76.0\%$ on FinanceMath, $71.2\%$ on MultiHiertt, $86.9\%$ on ESGenius, and $85.6\%$ average on FinChart-Bench. These results show that aggregating evidence at the level of atomic claims, rather than whole answers, improves robustness in high-stakes numerical reasoning.\footnote{The code and data are available: https://github.com/UBC-NLP/MoCA-Agent.
Medical image classification faces a fundamental dilemma: while deep learning models achieve remarkable performance at scale, real-world clinical scenarios often suffer from severe data scarcity due to annotation costs, privacy constraints, and disease rarity. This challenge is particularly pronounced in pathological scar classification, where differentiating keloids from hypertrophic scars requires subtle expert knowledge and labeled images are extremely limited. We propose a novel paradigm that repositions large language models (LLMs) as knowledge-driven feature engineers rather than end-to-end classifiers. We call this framework ScaFE (Scar Feature Engineering). Our key insight is that LLMs encode rich medical knowledge that can be externalized as executable feature extraction code, enabling the transformation of high-dimensional images into low-dimensional, clinically interpretable representations. Specifically, we prompt an LLM with established scar assessment criteria to generate deterministic Python code that extracts features aligned with clinical scoring systems such as the Vancouver Scar Scale. Our approach offers three key advantages: (1) data efficiency, achieving robust performance with limited training samples by decoupling knowledge acquisition from statistical learning; (2) privacy preservation, as raw images are processed locally without exposure to external LLMs; and (3) interpretability, through explicit features grounded in clinical reasoning. Extensive experiments on scar classification demonstrate that our method consistently outperforms end-to-end deep learning baselines or using LLMs as black-box classifiers under limited data conditions, establishing a promising direction for integrating LLMs into data-efficient and clinically transparent medical AI systems.
Recent advances in spoken dialogue language models (SDLMs) reflect growing interest in shifting from turn-based to full-duplex systems, where the models continuously perceive user speech streams while generating responses. This simultaneous listening and speaking design enables real-time interaction and the agent can handle dynamic conversational behaviors like user barge-in. However, during the listening phase, existing systems keep the agent idle by repeatedly predicting the silence token, which departs from human behavior: we usually engage in lightweight thinking during conversation rather than remaining absent-minded. Inspired by this, we propose Chronological Thinking, an on-the-fly conversational thinking mechanism that aims to improve response quality in full-duplex SDLMs. Specifically, chronological thinking presents a paradigm shift from conventional LLM thinking approaches, such as Chain-of-Thought, purpose-built for streaming acoustic input. (1) Strictly causal: the agent reasons incrementally while listening, updating internal hypotheses only from past audio with no lookahead. (2) No additional latency: reasoning is amortized during the listening window; once the user stops speaking, the agent halts thinking and begins speaking without further delay. Experiments demonstrate the effectiveness of chronological thinking through both objective metrics and human evaluations show consistent improvements in response quality. Furthermore, chronological thinking robustly handles conversational dynamics and attains competitive performance on full-duplex interaction metrics.
arXiv:2602.00781v2 Announce Type: replace Abstract: Online reinforcement learning in non-episodic, finite-horizon MDPs remains underexplored and is challenged by the need to estimate returns to a fixed terminal time. Existing infinite-horizon methods, which often rely on discounted contraction, do not naturally account for this fixed-horizon structure. We introduce a modified Q-function: rather than targeting the full-horizon, we learn a K-step lookahead Q-function that truncates planning to the next K steps. To further improve sample efficiency, we introduce a thresholding mechanism: actions are selected only when their estimated K-step lookahead value exceeds a time-varying threshold. We provide an efficient tabular learning algorithm for this novel objective, proving it achieves fast finite-sample convergence: it achieves minimax optimal constant regret for $K=1$ and $\mathcal{O}(\max((K-1),C_{K-1})\sqrt{SAT\log(T)})$ regret for any $K \geq 2$. We numerically evaluate the performance of our algorithm under the objective of maximizing reward. Our implementation adaptively increases K over time, balancing lookahead depth against estimation variance. Empirical results demonstrate superior cumulative rewards over state-of-the-art tabular RL methods across synthetic MDPs and RL environments: JumpRiverswim, FrozenLake and AnyTrading. Code is provided on \href{https://github.com/jamie01713/K-Step-Lookahead}{github}.
arXiv:2606.01316v2 Announce Type: replace Abstract: Scientific discovery demands intelligence, perseverance, and serendipity across vast search spaces. Today, top scientific capabilities remain siloed–one AI system for biological analysis, another for clinical reasoning, mathematical derivation, or materials simulation–and no pre-designed team can anticipate every skill a question will need. Science Earth is a planet-scale scientific runtime in which any capability–a simulation cluster, a wet-lab robot, a proof engine, a single-cell pipeline–can connect to any other, with collaboration structure emerging from the question itself. Its underlying EACN protocol lets capabilities discover one another, negotiate task ownership, and adjudicate across incompatible evidentiary standards without prior knowledge of who will meet whom. This shifts the organizing challenge from workflow design to open-ended connectivity. Two runs validate this under structurally distinct conditions. In a trans-Pacific higher-order Kuramoto synchronization study, agents identified and corrected a closure-ratio assumption in Ott-Antonsen analytic theory that fails outside the Lorentzian limit, within thirty minutes. In an eight-agent single-cell run on the 4.88M-cell Kang 2024 pan-cancer atlas, heterogeneous capabilities coupled over a 64.9-hour window with one structural external instruction, producing three new result layers and anchoring findings against an independent wet-lab study on an adjacent CCR8- TIGIT+ Treg subset. These cases are a first empirical reading, not a benchmark sweep. They show that when AI capabilities are truly connectable and coordination emerges from the problem, scientific reasoning becomes a distributed, self-correcting process–a step towards scaling AI-native discovery to the planet.
arXiv:2402.02573v4 Announce Type: replace-cross Abstract: In the past two decades, extensive research has been conducted on the (co)homology of various models of random simplicial complexes. So far, it has always been examined merely as a list of groups. This paper expands upon this by describing both the ring structure and the Steenrod-algebra structure of the cohomology of the lower multiparametric model. We prove that the ring structure is always a.a.s trivial, while, for certain parameters, the Steenrod-algebra a.a.s acts non-trivially. This reveals that complex multi-dimensional topological structures appear as subcomplexes of this model.
Context: Log parsing is a critical standard operating procedure in software systems, enabling monitoring, anomaly detection, and failure diagnosis. However, automated log parsing remains challenging due to heterogeneous log formats, distribution shifts between training and deployment data, and the brittleness of rule-based approaches. Objectives: This study aims to systematically evaluate how sequence modelling architecture, representation choice, sequence length, and training data availability influence automated log parsing performance and computational cost. Methods: We conduct a controlled empirical study comparing four sequence modelling architectures: Transformer, Mamba state-space, monodirectional LSTM, and bidirectional LSTM models. In total, 396 models are trained across multiple dataset configurations and evaluated using relative Levenshtein edit distance with statistical significance testing. Results: Transformer achieves the lowest mean relative edit distance (0.111), followed by Mamba (0.145), mono-LSTM (0.186), and bi-LSTM (0.265), where lower values are better. Mamba provides competitive accuracy with substantially lower computational cost. Character-level tokenization generally improves performance, sequence length has negligible practical impact on Transformer accuracy, and both Mamba and Transformer demonstrate stronger sample efficiency than recurrent models. Conclusion: Overall, Transformers reduce parsing error by 23.4%, while Mamba is a strong alternative under data or compute constraints. These results also clarify the roles of representation choice, sequence length, and sample efficiency, providing practical guidance for researchers and practitioners.