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Aug 10

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

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