Construction of a scaffold structure that supports a desired motif, conferring protein function, shows promise for the design of vaccines and enzymes. But a general solution to this motif-scaffolding problem remains open. Current machine-learning techniques for scaffold design are either limited to unrealistically small scaffolds (up to length 20) or struggle to produce multiple diverse scaffolds. We propose to learn a distribution over diverse and longer protein backbone structures via an E(3)-equivariant graph neural network. We develop SMCDiff to efficiently sample scaffolds from this distribution conditioned on a given motif; our algorithm is the first to theoretically guarantee conditional samples from a diffusion model in the large-compute limit. We evaluate our designed backbones by how well they align with AlphaFold2-predicted structures. We show that our method can (1) sample scaffolds up to 80 residues and (2) achieve structurally diverse scaffolds for a fixed motif.
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Minimum Spanning Trees are a well-studied subset of graph problems. While classical algorithms have existed to solve these problems for decades, new variations and application areas are constantly being discovered. When dealing with large graph problems, however, memory constraints can often be limiting, especially when using these classical methods in memory restricted environments. In this work, we propose an augmentation of Prim's algorithm that can be empirically shown to solve MST problems with a reduction in auxiliary memory usage of over 90%, and a margin of error of less than 0.3%.
Over the past decade, 3D graphics have become highly detailed to mimic the real world, exploding their size and complexity. Certain applications and device constraints necessitate their simplification and/or lossy compression, which can degrade their visual quality. Thus, to ensure the best Quality of Experience (QoE), it is important to evaluate the visual quality to accurately drive the compression and find the right compromise between visual quality and data size. In this work, we focus on subjective and objective quality assessment of textured 3D meshes. We first establish a large-scale dataset, which includes 55 source models quantitatively characterized in terms of geometric, color, and semantic complexity, and corrupted by combinations of 5 types of compression-based distortions applied on the geometry, texture mapping and texture image of the meshes. This dataset contains over 343k distorted stimuli. We propose an approach to select a challenging subset of 3000 stimuli for which we collected 148929 quality judgments from over 4500 participants in a large-scale crowdsourced subjective experiment. Leveraging our subject-rated dataset, a learning-based quality metric for 3D graphics was proposed. Our metric demonstrates state-of-the-art results on our dataset of textured meshes and on a dataset of distorted meshes with vertex colors. Finally, we present an application of our metric and dataset to explore the influence of distortion interactions and content characteristics on the perceived quality of compressed textured meshes.
Accurate estimation of nuclear masses and their prediction beyond the experimentally explored domains of the nuclear landscape are crucial to an understanding of the fundamental origin of nuclear properties and to many applications of nuclear science, most notably in quantifying the $r$-process of stellar nucleosynthesis. Neural networks have been applied with some success to the prediction of nuclear masses, but they are known to have shortcomings in application to extrapolation tasks. In this work, we propose and explore a novel type of neural network for mass prediction in which the usual neuron-like processing units are replaced by complex-valued product units that permit multiplicative couplings of inputs to be learned from the input data. This generalized network model is tested on both interpolation and extrapolation data sets drawn from the Atomic Mass Evaluation. Its performance is compared with that of several neural-network architectures, substantiating its suitability for nuclear mass prediction. Additionally, a prediction-uncertainty measure for such complex-valued networks is proposed that serves to identify regions of expected low prediction error.
We give a simple characterization of which functions can be computed deterministically by anonymous processes in dynamic networks, depending on the number of leaders in the network. In addition, we provide efficient distributed algorithms for computing all such functions assuming minimal or no knowledge about the network. Each of our algorithms comes in two versions: one that terminates with the correct output and a faster one that stabilizes on the correct output without explicit termination. Notably, these are the first deterministic algorithms whose running times scale linearly with both the number of processes and a parameter of the network which we call "dynamic disconnectivity" (meaning that our dynamic networks do not necessarily have to be connected at all times). We also provide matching lower bounds, showing that all our algorithms are asymptotically optimal for any fixed number of leaders. While most of the existing literature on anonymous dynamic networks relies on classical mass-distribution techniques, our work makes use of a recently introduced combinatorial structure called "history tree", also developing its theory in new directions. Among other contributions, our results make definitive progress on two popular fundamental problems for anonymous dynamic networks: leaderless Average Consensus (i.e., computing the mean value of input numbers distributed among the processes) and multi-leader Counting (i.e., determining the exact number of processes in the network). In fact, our approach unifies and improves upon several independent lines of research on anonymous networks, including Nedic et al., IEEE Trans. Automat. Contr. 2009; Olshevsky, SIAM J. Control Optim. 2017; Kowalski-Mosteiro, ICALP 2019, SPAA 2021; Di Luna-Viglietta, FOCS 2022.
In the field of antibody engineering, an essential task is to design a novel antibody whose paratopes bind to a specific antigen with correct epitopes. Understanding antibody structure and its paratope can facilitate a mechanistic understanding of its function. Therefore, antibody structure prediction from its sequence alone has always been a highly valuable problem for de novo antibody design. AlphaFold2, a breakthrough in the field of structural biology, provides a solution to predict protein structure based on protein sequences and computationally expensive coevolutionary multiple sequence alignments (MSAs). However, the computational efficiency and undesirable prediction accuracy of antibodies, especially on the complementarity-determining regions (CDRs) of antibodies limit their applications in the industrially high-throughput drug design. To learn an informative representation of antibodies, we employed a deep antibody language model (ALM) on curated sequences from the observed antibody space database via a transformer model. We also developed a novel model named xTrimoABFold to predict antibody structure from antibody sequence based on the pretrained ALM as well as efficient evoformers and structural modules. The model was trained end-to-end on the antibody structures in PDB by minimizing the ensemble loss of domain-specific focal loss on CDR and the frame-aligned point loss. xTrimoABFold outperforms AlphaFold2 and other protein language model based SOTAs, e.g., OmegaFold, HelixFold-Single, and IgFold with a large significant margin (30+\% improvement on RMSD) while performing 151 times faster than AlphaFold2. To the best of our knowledge, xTrimoABFold achieved state-of-the-art antibody structure prediction. Its improvement in both accuracy and efficiency makes it a valuable tool for de novo antibody design and could make further improvements in immuno-theory.
Existing data-to-text generation efforts mainly focus on generating a coherent text from non-linguistic input data, such as tables and attribute-value pairs, but overlook that different application scenarios may require texts of different styles. Inspired by this, we define a new task, namely stylized data-to-text generation, whose aim is to generate coherent text for the given non-linguistic data according to a specific style. This task is non-trivial, due to three challenges: the logic of the generated text, unstructured style reference, and biased training samples. To address these challenges, we propose a novel stylized data-to-text generation model, named StyleD2T, comprising three components: logic planning-enhanced data embedding, mask-based style embedding, and unbiased stylized text generation. In the first component, we introduce a graph-guided logic planner for attribute organization to ensure the logic of generated text. In the second component, we devise feature-level mask-based style embedding to extract the essential style signal from the given unstructured style reference. In the last one, pseudo triplet augmentation is utilized to achieve unbiased text generation, and a multi-condition based confidence assignment function is designed to ensure the quality of pseudo samples. Extensive experiments on a newly collected dataset from Taobao have been conducted, and the results show the superiority of our model over existing methods.
Graph neural networks (GNNs) have been demonstrated to be a powerful algorithmic model in broad application fields for their effectiveness in learning over graphs. To scale GNN training up for large-scale and ever-growing graphs, the most promising solution is distributed training which distributes the workload of training across multiple computing nodes. However, the workflows, computational patterns, communication patterns, and optimization techniques of distributed GNN training remain preliminarily understood. In this paper, we provide a comprehensive survey of distributed GNN training by investigating various optimization techniques used in distributed GNN training. First, distributed GNN training is classified into several categories according to their workflows. In addition, their computational patterns and communication patterns, as well as the optimization techniques proposed by recent work are introduced. Second, the software frameworks and hardware platforms of distributed GNN training are also introduced for a deeper understanding. Third, distributed GNN training is compared with distributed training of deep neural networks, emphasizing the uniqueness of distributed GNN training. Finally, interesting issues and opportunities in this field are discussed.
Spectral clustering (SC) is a popular clustering technique to find strongly connected communities on a graph. SC can be used in Graph Neural Networks (GNNs) to implement pooling operations that aggregate nodes belonging to the same cluster. However, the eigendecomposition of the Laplacian is expensive and, since clustering results are graph-specific, pooling methods based on SC must perform a new optimization for each new sample. In this paper, we propose a graph clustering approach that addresses these limitations of SC. We formulate a continuous relaxation of the normalized minCUT problem and train a GNN to compute cluster assignments that minimize this objective. Our GNN-based implementation is differentiable, does not require to compute the spectral decomposition, and learns a clustering function that can be quickly evaluated on out-of-sample graphs. From the proposed clustering method, we design a graph pooling operator that overcomes some important limitations of state-of-the-art graph pooling techniques and achieves the best performance in several supervised and unsupervised tasks.
This paper aims at revisiting Graph Convolutional Neural Networks by bridging the gap between spectral and spatial design of graph convolutions. We theoretically demonstrate some equivalence of the graph convolution process regardless it is designed in the spatial or the spectral domain. The obtained general framework allows to lead a spectral analysis of the most popular ConvGNNs, explaining their performance and showing their limits. Moreover, the proposed framework is used to design new convolutions in spectral domain with a custom frequency profile while applying them in the spatial domain. We also propose a generalization of the depthwise separable convolution framework for graph convolutional networks, what allows to decrease the total number of trainable parameters by keeping the capacity of the model. To the best of our knowledge, such a framework has never been used in the GNNs literature. Our proposals are evaluated on both transductive and inductive graph learning problems. Obtained results show the relevance of the proposed method and provide one of the first experimental evidence of transferability of spectral filter coefficients from one graph to another. Our source codes are publicly available at: //github.com/balcilar/Spectral-Designed-Graph-Convolutions
Recent years have witnessed the emerging success of graph neural networks (GNNs) for modeling structured data. However, most GNNs are designed for homogeneous graphs, in which all nodes and edges belong to the same types, making them infeasible to represent heterogeneous structures. In this paper, we present the Heterogeneous Graph Transformer (HGT) architecture for modeling Web-scale heterogeneous graphs. To model heterogeneity, we design node- and edge-type dependent parameters to characterize the heterogeneous attention over each edge, empowering HGT to maintain dedicated representations for different types of nodes and edges. To handle dynamic heterogeneous graphs, we introduce the relative temporal encoding technique into HGT, which is able to capture the dynamic structural dependency with arbitrary durations. To handle Web-scale graph data, we design the heterogeneous mini-batch graph sampling algorithm---HGSampling---for efficient and scalable training. Extensive experiments on the Open Academic Graph of 179 million nodes and 2 billion edges show that the proposed HGT model consistently outperforms all the state-of-the-art GNN baselines by 9%--21% on various downstream tasks.
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