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Oct 5

FATE: A Formal Benchmark Series for Frontier Algebra of Multiple Difficulty Levels

Recent advances in large language models (LLMs) have demonstrated impressive capabilities in formal theorem proving, particularly on contest-based mathematical benchmarks like the IMO. However, these contests do not reflect the depth, breadth, and abstraction of modern mathematical research. To bridge this gap, we introduce FATE (Formal Algebra Theorem Evaluation), a new benchmark series in formal algebra designed to chart a course toward advanced mathematical reasoning. We present two new components, FATE-H and FATE-X, each with 100 problems in abstract and commutative algebra. The FATE series spans a difficulty spectrum from undergraduate exercises to problems exceeding PhD qualifying exams. Notably, FATE-X is the first formal benchmark to surpass both PhD-level exam difficulty and the coverage of the Mathlib library. Our evaluations of state-of-the-art LLM provers on this new benchmark reveal a stark performance gap compared to contest math: the best model achieves only 3% (pass@64) accuracy on FATE-H and 0% on FATE-X. Our two-stage evaluation reveals that models' natural-language reasoning is notably more accurate than their ability to formalize this reasoning. We systematically classify the common errors that arise during this formalization process. Furthermore, a comparative study shows that a specialized prover can exhibit less effective reflection than general-purpose models, reducing its accuracy at the natural-language stage. We believe FATE provides a robust and challenging benchmark that establishes essential checkpoints on the path toward research-level formal mathematical reasoning.

  • 11 authors
·
Mar 7

MathForm: Scaling Mathematical Autoformalization with Knowledge Retrieval and Verification-Guided Refinement

Autoformalization is commonly framed as translating natural-language mathematical statements into machine-verifiable formal languages such as Lean 4. However, faithful formalization requires more than translation. Models must map mathematical concepts to the complex hierarchy of types and definitions in formal libraries such as Mathlib, while ensuring that generated statements preserve the meaning of the source propositions. Existing approaches struggle because they rely heavily on the model's parametric memory for library-specific knowledge, while common data construction pipelines often resort to filtering single-pass outputs and lack mechanisms for feedback-driven revision. To address these challenges, we introduce MathForm, an autoformalization framework for constructing verified training data through Mathlib knowledge retrieval and verification-guided iterative refinement. Before generation, a retrieval planner gathers relevant definitions and existing formalizations from Mathlib to guide the formalization generator. Generated statements are then revised using compiler diagnostics and semantic-consistency feedback. Using this framework, we construct FormalVerse, a Lean 4 dataset containing approximately 367K verified examples across diverse mathematical domains and sources. We then train MathForm-8B through supervised fine-tuning followed by reinforcement learning. Across six benchmarks, MathForm-8B achieves average Pass@8 rates of 88.06% under Syntax Check (SC) and 72.37% under Consistency Check (CC), outperforming multiple specialized 32B autoformalizers. On the challenging FATE-H and FATE-X subsets, it attains CC pass rates of 63% and 37%, exceeding the strongest specialized baselines in both cases.

openbmb OpenBMB
·
Aug 14 6

From shape to fate: making bacterial swarming expansion predictable

Microbial swarming on mucosal surfaces reshapes microbial communities and influences mucosal healing and antibiotic tolerance. Yet even with time-lapse microscopy and deep learning, analyses of swarming colonies remain descriptive and cannot forecast how their fronts reorganize in time. This limitation is significant because the advancing edge determines access to nutrients, host tissue and competing microbes. We recast the expansion of Enterobacter sp. SM3 swarms as a problem of morphological forecasting, and assemble SwarmEvo, a time-lapse dataset represented as boundary-resolved segmentations. TexPol--Net, a texture- and geometry-aware segmentation model, sharpens diffuse edges and preserves fingered fronts, creating a stable substrate for dynamics. On this representation, we develop Morpher, an autoregressive forecasting network with a ``Morphon'' memory that links local curvature to long-range temporal dependencies. Morpher outperforms leading video-prediction models in maintaining front localization and anisotropic branching, and modest segmentation improvements yield noticeably more stable forecasts. Ablations across sequence models, inference strategies and observation ratios show that attention-based architectures with structural memory best preserve dense-finger propagation. By uniting geometry-aware segmentation with morphology-level forecasting, this framework turns swarming expansion into a predictive dynamical system, enabling quantitative interrogation and potential control of microbial collectives during mucosal repair and gut ecosystem engineering.

  • 8 authors
·
Feb 1

MIOFlow 2.0: A unified framework for inferring cellular stochastic dynamics from single cell and spatial transcriptomics data

Understanding cellular trajectories via time-resolved single-cell transcriptomics is vital for studying development, regeneration, and disease. A key challenge is inferring continuous trajectories from discrete snapshots. Biological complexity stems from stochastic cell fate decisions, temporal proliferation changes, and spatial environmental influences. Current methods often use deterministic interpolations treating cells in isolation, failing to capture the probabilistic branching, population shifts, and niche-dependent signaling driving real biological processes. We introduce Manifold Interpolating Optimal-Transport Flow (MIOFlow) 2.0. This framework learns biologically informed cellular trajectories by integrating manifold learning, optimal transport, and neural differential equations. It models three core processes: (1) stochasticity and branching via Neural Stochastic Differential Equations; (2) non-conservative population changes using a learned growth-rate model initialized with unbalanced optimal transport; and (3) environmental influence through a joint latent space unifying gene expression with spatial features like local cell type composition and signaling. By operating in a PHATE-distance matching autoencoder latent space, MIOFlow 2.0 ensures trajectories respect the data's intrinsic geometry. Empirical comparisons show expressive trajectory learning via neural differential equations outperforms existing generative models, including simulation-free flow matching. Validated on synthetic datasets, embryoid body differentiation, and spatially resolved axolotl brain regeneration, MIOFlow 2.0 improves trajectory accuracy and reveals hidden drivers of cellular transitions, like specific signaling niches. MIOFlow 2.0 thus bridges single-cell and spatial transcriptomics to uncover tissue-scale trajectories.

  • 14 authors
·
Apr 14

On-Policy Self-Evolution via Failure Trajectories for Agentic Safety Alignment

Tool-using LLM agents fail through trajectories rather than only final responses, as they may execute unsafe tool calls, follow injected instructions, comply with harmful requests, or over-refuse benign tasks despite producing a seemingly safe answer. Existing safety-alignment signals are largely response-level or off-policy, and often incur a safety-utility trade-off: improving agent safety comes at the cost of degraded task performance. Such sparse and single-objective rewards severely limit real-world usability. To bridge this gap, we propose FATE, an on-policy self-evolving framework that transforms verifier-scored failures into repair supervision without expert demonstrations. For each failure, the same policy proposes repair candidates, which are then re-scored by verifiers and filtered across security, utility, over-refusal control, and trajectory validity. This dense trajectory-level information is then used as a supervision signal for agent self-evolution. During this process, we further introduce Pareto-Front Policy Optimization (PFPO), combining supervised warmup with Pareto-aware policy optimization to preserve safety-utility trade-offs. Experiments on AgentDojo, AgentHarm, and ATBench show that FATE improves safety across different models and scales while preserving useful behavior. Compared with strong baselines, FATE reduces attack success rate by 33.5%, harmful compliance by 82.6%, and improves external trajectory-safety diagnosis by 6.5%. These results suggest that failed trajectories can provide structured repair supervision for safer self-evolving agents.

  • 3 authors
·
May 11

Online Unsupervised Video Object Segmentation via Contrastive Motion Clustering

Online unsupervised video object segmentation (UVOS) uses the previous frames as its input to automatically separate the primary object(s) from a streaming video without using any further manual annotation. A major challenge is that the model has no access to the future and must rely solely on the history, i.e., the segmentation mask is predicted from the current frame as soon as it is captured. In this work, a novel contrastive motion clustering algorithm with an optical flow as its input is proposed for the online UVOS by exploiting the common fate principle that visual elements tend to be perceived as a group if they possess the same motion pattern. We build a simple and effective auto-encoder to iteratively summarize non-learnable prototypical bases for the motion pattern, while the bases in turn help learn the representation of the embedding network. Further, a contrastive learning strategy based on a boundary prior is developed to improve foreground and background feature discrimination in the representation learning stage. The proposed algorithm can be optimized on arbitrarily-scale data i.e., frame, clip, dataset) and performed in an online fashion. Experiments on DAVIS_{16}, FBMS, and SegTrackV2 datasets show that the accuracy of our method surpasses the previous state-of-the-art (SoTA) online UVOS method by a margin of 0.8%, 2.9%, and 1.1%, respectively. Furthermore, by using an online deep subspace clustering to tackle the motion grouping, our method is able to achieve higher accuracy at 3times faster inference time compared to SoTA online UVOS method, and making a good trade-off between effectiveness and efficiency. Our code is available at https://github.com/xilin1991/ClusterNet.

  • 5 authors
·
Jun 21, 2023

Chreode: A Cell World Model for One-Step Temporal Dynamics and Perturbation Prediction

Predicting how a cell will change its transcriptional state under a developmental signal or a genetic perturbation is the computational core of in-silico biology and the AI Virtual Cell program. Existing approaches either fit static control-to-treated maps that discard time, or solve multi-step ODE / Schrödinger-bridge problems on each dataset independently. We introduce Chreode, a one-step cell world model that predicts action-conditioned cell-state transitions through a structured residual transition operator. It shifts distributional evolution from inference time to training time, enabling single-pass generation while preserving a Waddington-inspired decomposition into downhill landscape flow, rotational in-tangent dynamics, and stochastic spread. The model is pretrained with a shared scVI encoder and a DiT-based dynamics backbone on a 2.4M-cell mouse embryonic atlas spanning 7 datasets. As a fine-tuning initialization, Chreode improves per-target Sinkhorn distance on Weinreb hematopoiesis and Veres islet differentiation over matched scratch models, PI-SDE, and PRESCIENT. As a transferable gene-state embedding for GEARS, the pretrained dynamics representation reduces shared-vocabulary DE20 mean squared error on Norman Perturb-seq from 0.2121 to 0.1858, a 12.4% relative improvement, without changing the GEARS training procedure. We interpret this transfer to perturbation prediction as evidence that pretrained developmental-trajectory dynamics encode differentiation primitives transferable to CRISPR-induced state shifts, since both involve cell-state transitions in a shared latent geometry. The pretrained backbone additionally produces zero-shot clonal fate scores on Weinreb that are competitive with strong dynamic-OT baselines.

  • 7 authors
·
May 26