Ongoing advances in force field and computer hardware development enable the use of molecular dynamics (MD) to simulate increasingly complex systems with the ultimate goal of reaching cellular complexity. At the same time, rational design by high-throughput (HT) simulations is another forefront of MD. In these areas, the Martini coarse-grained force field, especially the latest version (i.e. v3), is being actively explored because it offers enhanced spatial-temporal resolution. However, the automation tools for preparing simulations with the Martini force field, accompanying the previous version, were not designed for HT simulations or studies of complex cellular systems. Therefore, they become a major limiting factor. To address these shortcomings, we present the open-source vermouth python library. Vermouth is designed to become the unified framework for developing programs, which prepare, run, and analyze Martini simulations of complex systems. To demonstrate the power of the vermouth library, the martinize2 program is showcased as a generalization of the martinize script, originally aimed to set up simulations of proteins. In contrast to the previous version, martinize2 automatically handles protonation states in proteins and post-translation modifications, offers more options to fine-tune structural biases such as the elastic network, and can convert non-protein molecules such as ligands. Finally, martinize2 is used in two high-complexity benchmarks. The entire I-TASSER protein template database as well as a subset of 200,000 structures from the AlphaFold Protein Structure Database are converted to CG resolution and we illustrate how the checks on input structure quality can safeguard HT applications.
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3D semantic occupancy prediction aims to obtain 3D fine-grained geometry and semantics of the surrounding scene and is an important task for the robustness of vision-centric autonomous driving. Most existing methods employ dense grids such as voxels as scene representations, which ignore the sparsity of occupancy and the diversity of object scales and thus lead to unbalanced allocation of resources. To address this, we propose an object-centric representation to describe 3D scenes with sparse 3D semantic Gaussians where each Gaussian represents a flexible region of interest and its semantic features. We aggregate information from images through the attention mechanism and iteratively refine the properties of 3D Gaussians including position, covariance, and semantics. We then propose an efficient Gaussian-to-voxel splatting method to generate 3D occupancy predictions, which only aggregates the neighboring Gaussians for a certain position. We conduct extensive experiments on the widely adopted nuScenes and KITTI-360 datasets. Experimental results demonstrate that GaussianFormer achieves comparable performance with state-of-the-art methods with only 17.8% - 24.8% of their memory consumption. Code is available at: //github.com/huang-yh/GaussianFormer.
Detecting out-of-distribution (OOD) samples is important for deploying machine learning models in safety-critical applications such as autonomous driving and robot-assisted surgery. Existing research has mainly focused on unimodal scenarios on image data. However, real-world applications are inherently multimodal, which makes it essential to leverage information from multiple modalities to enhance the efficacy of OOD detection. To establish a foundation for more realistic Multimodal OOD Detection, we introduce the first-of-its-kind benchmark, MultiOOD, characterized by diverse dataset sizes and varying modality combinations. We first evaluate existing unimodal OOD detection algorithms on MultiOOD, observing that the mere inclusion of additional modalities yields substantial improvements. This underscores the importance of utilizing multiple modalities for OOD detection. Based on the observation of Modality Prediction Discrepancy between in-distribution (ID) and OOD data, and its strong correlation with OOD performance, we propose the Agree-to-Disagree (A2D) algorithm to encourage such discrepancy during training. Moreover, we introduce a novel outlier synthesis method, NP-Mix, which explores broader feature spaces by leveraging the information from nearest neighbor classes and complements A2D to strengthen OOD detection performance. Extensive experiments on MultiOOD demonstrate that training with A2D and NP-Mix improves existing OOD detection algorithms by a large margin. Our source code and MultiOOD benchmark are available at //github.com/donghao51/MultiOOD.
Group testing (GT) is the art of identifying binary signals and the marketplace for exchanging new ideas for related fields such as unique-element counting, compressed sensing, traitor tracing, and geno-typing. A GT scheme can be nonadaptive or adaptive; the latter is preferred when latency is ess of an issue. To construct adaptive GT schemes, a popular strategy is to spend the majority of tests in the first few rounds to gain as much information as possible, and uses later rounds to refine details. In this paper, we propose a transparent strategy called "isolate and then identify" (I@I). In the first few rounds, I@I divides the population into teams until every team contains at most one sick person. Then, in the last round, I@I identifies the sick person in each team. Performance-wise, I@I is the first GT scheme that achieves the optimal coefficient $1/$capacity$(Z)$ for the $k \log_2 (n/k)$ term in the number of tests when $Z$ is a generic channel corrupting the test outcomes. I@I follows a modular methodology whereby the isolating part and the identification part can be optimized separately.
High-resolution Large Multimodal Models (LMMs) encounter the challenges of excessive visual tokens and quadratic visual complexity. Current high-resolution LMMs address the quadratic complexity while still generating excessive visual tokens. However, the redundancy in visual tokens is the key problem as it leads to more substantial compute. To mitigate this issue, we propose ConvLLaVA, which employs ConvNeXt, a hierarchical backbone, as the visual encoder of LMM to replace Vision Transformer (ViT). ConvLLaVA compresses high-resolution images into information-rich visual features, effectively preventing the generation of excessive visual tokens. To enhance the capabilities of ConvLLaVA, we propose two critical optimizations. Since the low-resolution pretrained ConvNeXt underperforms when directly applied on high resolution, we update it to bridge the gap. Moreover, since ConvNeXt's original compression ratio is inadequate for much higher resolution inputs, we train a successive stage to further compress the visual tokens, thereby reducing redundancy. These optimizations enable ConvLLaVA to support inputs of 1536x1536 resolution generating only 576 visual tokens, capable of handling images of arbitrary aspect ratios. Experimental results demonstrate that our method achieves competitive performance with state-of-the-art models on mainstream benchmarks. The ConvLLaVA model series are publicly available at //github.com/alibaba/conv-llava.
Instruction tuning large language models (LLMs) remains a challenging task, owing to the complexity of hyperparameter selection and the difficulty involved in evaluating the tuned models. To determine the optimal hyperparameters, an automatic, robust, and reliable evaluation benchmark is essential. However, establishing such a benchmark is not a trivial task due to the challenges associated with evaluation accuracy and privacy protection. In response to these challenges, we introduce a judge large language model, named PandaLM, which is trained to distinguish the superior model given several LLMs. PandaLM's focus extends beyond just the objective correctness of responses, which is the main focus of traditional evaluation datasets. It addresses vital subjective factors such as relative conciseness, clarity, adherence to instructions, comprehensiveness, and formality. To ensure the reliability of PandaLM, we collect a diverse human-annotated test dataset, where all contexts are generated by humans and labels are aligned with human preferences. Our results indicate that PandaLM-7B achieves 93.75% of GPT-3.5's evaluation ability and 88.28% of GPT-4's in terms of F1-score on our test dataset. PandaLM enables the evaluation of LLM to be fairer but with less cost, evidenced by significant improvements achieved by models tuned through PandaLM compared to their counterparts trained with default Alpaca's hyperparameters. In addition, PandaLM does not depend on API-based evaluations, thus avoiding potential data leakage. All resources of PandaLM are released at //github.com/WeOpenML/PandaLM.
Neural implicit representations have recently demonstrated considerable potential in the field of visual simultaneous localization and mapping (SLAM). This is due to their inherent advantages, including low storage overhead and representation continuity. However, these methods necessitate the size of the scene as input, which is impractical for unknown scenes. Consequently, we propose NeB-SLAM, a neural block-based scalable RGB-D SLAM for unknown scenes. Specifically, we first propose a divide-and-conquer mapping strategy that represents the entire unknown scene as a set of sub-maps. These sub-maps are a set of neural blocks of fixed size. Then, we introduce an adaptive map growth strategy to achieve adaptive allocation of neural blocks during camera tracking and gradually cover the whole unknown scene. Finally, extensive evaluations on various datasets demonstrate that our method is competitive in both mapping and tracking when targeting unknown environments.
Mil2 pushes the performance of high-resolution cloth simulation, making the simulation interactive (in milliseconds) for models with one million degrees of freedom (DOFs) while keeping every triangle untangled. The guarantee of being penetration-free is inspired by the interior-point method, which converts the inequality constraints to barrier potentials. Nevertheless, we propose a major overhaul of this modality by defining a novel and simple barrier formulation which does not depend on the distance between mesh primitives. Such a non-distance barrier model allows a new way to integrate collision detection into the simulation pipeline. Another contributor to the performance boost comes from the so-called subspace reuse strategy. This is based on the observation that low-frequency strain vibrations are near orthogonal to the deformation induced by collisions or self-collisions, often of high frequency. Subspace reuse then takes care of low-frequency residuals, while high-frequency residuals can also be effectively smoothed by GPU-based iterative solvers. We show that our method outperforms existing fast cloth simulators by nearly one order while keeping the entire simulation penetration-free and producing high-equality animations of high-resolution models.
Automated driving systems are an integral part of the automotive industry. Tools such as Robot Operating System and simulators support their development. However, in the end, the developers must test their algorithms on a real vehicle. To better observe the difference between reality and simulation--the reality gap--digital twin technology offers real-time communication between the real vehicle and its model. We present low fidelity digital twin generator and describe situations where automatic generation is preferable to high fidelity simulation. We validated our approach of generating a virtual environment with a vehicle model by replaying the data recorded from the real vehicle.
The incredible development of federated learning (FL) has benefited various tasks in the domains of computer vision and natural language processing, and the existing frameworks such as TFF and FATE has made the deployment easy in real-world applications. However, federated graph learning (FGL), even though graph data are prevalent, has not been well supported due to its unique characteristics and requirements. The lack of FGL-related framework increases the efforts for accomplishing reproducible research and deploying in real-world applications. Motivated by such strong demand, in this paper, we first discuss the challenges in creating an easy-to-use FGL package and accordingly present our implemented package FederatedScope-GNN (FS-G), which provides (1) a unified view for modularizing and expressing FGL algorithms; (2) comprehensive DataZoo and ModelZoo for out-of-the-box FGL capability; (3) an efficient model auto-tuning component; and (4) off-the-shelf privacy attack and defense abilities. We validate the effectiveness of FS-G by conducting extensive experiments, which simultaneously gains many valuable insights about FGL for the community. Moreover, we employ FS-G to serve the FGL application in real-world E-commerce scenarios, where the attained improvements indicate great potential business benefits. We publicly release FS-G, as submodules of FederatedScope, at //github.com/alibaba/FederatedScope to promote FGL's research and enable broad applications that would otherwise be infeasible due to the lack of a dedicated package.
High spectral dimensionality and the shortage of annotations make hyperspectral image (HSI) classification a challenging problem. Recent studies suggest that convolutional neural networks can learn discriminative spatial features, which play a paramount role in HSI interpretation. However, most of these methods ignore the distinctive spectral-spatial characteristic of hyperspectral data. In addition, a large amount of unlabeled data remains an unexploited gold mine for efficient data use. Therefore, we proposed an integration of generative adversarial networks (GANs) and probabilistic graphical models for HSI classification. Specifically, we used a spectral-spatial generator and a discriminator to identify land cover categories of hyperspectral cubes. Moreover, to take advantage of a large amount of unlabeled data, we adopted a conditional random field to refine the preliminary classification results generated by GANs. Experimental results obtained using two commonly studied datasets demonstrate that the proposed framework achieved encouraging classification accuracy using a small number of data for training.
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