Bifunctional enzyme provides absolute concentration robustness in multisite covalent modification networks

Biochemical covalent modification networks exhibit a remarkable suite of steady state and dynamical properties such as multistationarity, oscillations, ultrasensitivity and absolute concentration robustness. This paper focuses on conditions required for a network to have a species with absolute concentration robustness. We find that the robustness in a substrate is endowed by its interaction with a bifunctional enzyme, which is an enzyme that has different roles when isolated versus when bound as a substrate-enzyme complex. When isolated, the bifunctional enzyme promotes production of more molecules of the robust species while when bound, the same enzyme facilitates degradation of the robust species. These dual actions produce robustness in the large class of covalent modification networks. For each network of this type, we find the network conditions for the presence of robustness, the species that has robustness, and its robustness value. The unified approach of simultaneously analyzing a large class of networks for a single property, i.e. absolute concentration robustness, reveals the underlying mechanism of the action of bifunctional enzyme while simultaneously providing a precise mathematical description of bifunctionality.Comment: 28 page

Sample-efficient Reinforcement Learning Representation Learning with Curiosity Contrastive Forward Dynamics Model

Developing an agent in reinforcement learning (RL) that is capable of performing complex control tasks directly from high-dimensional observation such as raw pixels is yet a challenge as efforts are made towards improving sample efficiency and generalization. This paper considers a learning framework for Curiosity Contrastive Forward Dynamics Model (CCFDM) in achieving a more sample-efficient RL based directly on raw pixels. CCFDM incorporates a forward dynamics model (FDM) and performs contrastive learning to train its deep convolutional neural network-based image encoder (IE) to extract conducive spatial and temporal information for achieving a more sample efficiency for RL. In addition, during training, CCFDM provides intrinsic rewards, produced based on FDM prediction error, encourages the curiosity of the RL agent to improve exploration. The diverge and less-repetitive observations provide by both our exploration strategy and data augmentation available in contrastive learning improve not only the sample efficiency but also the generalization. Performance of existing model-free RL methods such as Soft Actor-Critic built on top of CCFDM outperforms prior state-of-the-art pixel-based RL methods on the DeepMind Control Suite benchmark

A Cosine Similarity-based Method for Out-of-Distribution Detection

The ability to detect OOD data is a crucial aspect of practical machine learning applications. In this work, we show that cosine similarity between the test feature and the typical ID feature is a good indicator of OOD data. We propose Class Typical Matching (CTM), a post hoc OOD detection algorithm that uses a cosine similarity scoring function. Extensive experiments on multiple benchmarks show that CTM outperforms existing post hoc OOD detection methods.Comment: Accepted paper at ICML 2023 Workshop on Spurious Correlations, Invariance, and Stability. 10 pages (4 main + appendix

SoftGroup++: Scalable 3D Instance Segmentation with Octree Pyramid Grouping

Existing state-of-the-art 3D point cloud instance segmentation methods rely on a grouping-based approach that groups points to obtain object instances. Despite improvement in producing accurate segmentation results, these methods lack scalability and commonly require dividing large input into multiple parts. To process a scene with millions of points, the existing fastest method SoftGroup \cite{vu2022softgroup} requires tens of seconds, which is under satisfaction. Our finding is that $k$-Nearest Neighbor ($k$-NN), which serves as the prerequisite of grouping, is a computational bottleneck. This bottleneck severely worsens the inference time in the scene with a large number of points. This paper proposes SoftGroup++ to address this computational bottleneck and further optimize the inference speed of the whole network. SoftGroup++ is built upon SoftGroup, which differs in three important aspects: (1) performs octree $k$-NN instead of vanilla $k$-NN to reduce time complexity from $\mathcal{O}(n^2)$ to $\mathcal{O}(n \log n)$, (2) performs pyramid scaling that adaptively downsamples backbone outputs to reduce search space for $k$-NN and grouping, and (3) performs late devoxelization that delays the conversion from voxels to points towards the end of the model such that intermediate components operate at a low computational cost. Extensive experiments on various indoor and outdoor datasets demonstrate the efficacy of the proposed SoftGroup++. Notably, SoftGroup++ processes large scenes of millions of points by a single forward without dividing the input into multiple parts, thus enriching contextual information. Especially, SoftGroup++ achieves 2.4 points AP$_{50}$ improvement while nearly $6\times$ faster than the existing fastest method on S3DIS dataset. The code and trained models will be made publicly available.Comment: Technical repor