全原子和粗粒分子动力学是两个广泛使用的计算工具，用于研究蛋白质的构象状态。然而，这两种仿真方法遭受了这样的事实，即在没有获得超级计算资源的情况下，难以实现这些状态的时间和长度尺度。这种方法的一种替代方法是基于编码分子动力学的原子轨迹作为没有物理粒子的速记版本，然后学习通过使用人工智能来传播编码的轨迹。在这里，我们表明，作为Ramachandran盆地类的向量，分子动力学轨迹框架框架的简单文本表示保留了蛋白质在每个帧中的完整原子代表的大多数结构信息，并且可用于生成无原子轨迹适用于训练不同类型的生成神经网络。反过来，训练有素的生成模型可用于无限期地扩展无原子动力学，或在潜在的模型中从其表示中采样蛋白质的构象空间。我们将这种方法定义为没有分子的分子动力学，并表明它可以涵盖与传统分子动力学难以访问的蛋白质的物理相关状态。

Previous work has shown the potential of deep learning to predict renal obstruction using kidney ultrasound images. However, these image-based classifiers have been trained with the goal of single-visit inference in mind. We compare methods from video action recognition (i.e. convolutional pooling, LSTM, TSM) to adapt single-visit convolutional models to handle multiple visit inference. We demonstrate that incorporating images from a patient's past hospital visits provides only a small benefit for the prediction of obstructive hydronephrosis. Therefore, inclusion of prior ultrasounds is beneficial, but prediction based on the latest ultrasound is sufficient for patient risk stratification.

Applying deep learning concepts from image detection and graph theory has greatly advanced protein-ligand binding affinity prediction, a challenge with enormous ramifications for both drug discovery and protein engineering. We build upon these advances by designing a novel deep learning architecture consisting of a 3-dimensional convolutional neural network utilizing channel-wise attention and two graph convolutional networks utilizing attention-based aggregation of node features. HAC-Net (Hybrid Attention-Based Convolutional Neural Network) obtains state-of-the-art results on the PDBbind v.2016 core set, the most widely recognized benchmark in the field. We extensively assess the generalizability of our model using multiple train-test splits, each of which maximizes differences between either protein structures, protein sequences, or ligand extended-connectivity fingerprints. Furthermore, we perform 10-fold cross-validation with a similarity cutoff between SMILES strings of ligands in the training and test sets, and also evaluate the performance of HAC-Net on lower-quality data. We envision that this model can be extended to a broad range of supervised learning problems related to structure-based biomolecular property prediction. All of our software is available as open source at https://github.com/gregory-kyro/HAC-Net/.

In recent years several learning approaches to point goal navigation in previously unseen environments have been proposed. They vary in the representations of the environments, problem decomposition, and experimental evaluation. In this work, we compare the state-of-the-art Deep Reinforcement Learning based approaches with Partially Observable Markov Decision Process (POMDP) formulation of the point goal navigation problem. We adapt the (POMDP) sub-goal framework proposed by [1] and modify the component that estimates frontier properties by using partial semantic maps of indoor scenes built from images' semantic segmentation. In addition to the well-known completeness of the model-based approach, we demonstrate that it is robust and efficient in that it leverages informative, learned properties of the frontiers compared to an optimistic frontier-based planner. We also demonstrate its data efficiency compared to the end-to-end deep reinforcement learning approaches. We compare our results against an optimistic planner, ANS and DD-PPO on Matterport3D dataset using the Habitat Simulator. We show comparable, though slightly worse performance than the SOTA DD-PPO approach, yet with far fewer data.

It is known that neural networks have the problem of being over-confident when directly using the output label distribution to generate uncertainty measures. Existing methods mainly resolve this issue by retraining the entire model to impose the uncertainty quantification capability so that the learned model can achieve desired performance in accuracy and uncertainty prediction simultaneously. However, training the model from scratch is computationally expensive and may not be feasible in many situations. In this work, we consider a more practical post-hoc uncertainty learning setting, where a well-trained base model is given, and we focus on the uncertainty quantification task at the second stage of training. We propose a novel Bayesian meta-model to augment pre-trained models with better uncertainty quantification abilities, which is effective and computationally efficient. Our proposed method requires no additional training data and is flexible enough to quantify different uncertainties and easily adapt to different application settings, including out-of-domain data detection, misclassification detection, and trustworthy transfer learning. We demonstrate our proposed meta-model approach's flexibility and superior empirical performance on these applications over multiple representative image classification benchmarks.

Convolutional neural networks (CNNs) are currently among the most widely-used neural networks available and achieve state-of-the-art performance for many problems. While originally applied to computer vision tasks, CNNs work well with any data with a spatial relationship, besides images, and have been applied to different fields. However, recent works have highlighted how CNNs, like other deep learning models, are sensitive to noise injection which can jeopardise their performance. This paper quantifies the numerical uncertainty of the floating point arithmetic inaccuracies of the inference stage of DeepGOPlus, a CNN that predicts protein function, in order to determine its numerical stability. In addition, this paper investigates the possibility to use reduced-precision floating point formats for DeepGOPlus inference to reduce memory consumption and latency. This is achieved with Monte Carlo Arithmetic, a technique that experimentally quantifies floating point operation errors and VPREC, a tool that emulates results with customizable floating point precision formats. Focus is placed on the inference stage as it is the main deliverable of the DeepGOPlus model that will be used across environments and therefore most likely be subjected to the most amount of noise. Furthermore, studies have shown that the inference stage is the part of the model which is most disposed to being scaled down in terms of reduced precision. All in all, it has been found that the numerical uncertainty of the DeepGOPlus CNN is very low at its current numerical precision format, but the model cannot currently be reduced to a lower precision that might render it more lightweight.

In this work, we present a novel framework built to simplify 3D asset generation for amateur users. To enable interactive generation, our method supports a variety of input modalities that can be easily provided by a human, including images, text, partially observed shapes and combinations of these, further allowing to adjust the strength of each input. At the core of our approach is an encoder-decoder, compressing 3D shapes into a compact latent representation, upon which a diffusion model is learned. To enable a variety of multi-modal inputs, we employ task-specific encoders with dropout followed by a cross-attention mechanism. Due to its flexibility, our model naturally supports a variety of tasks, outperforming prior works on shape completion, image-based 3D reconstruction, and text-to-3D. Most interestingly, our model can combine all these tasks into one swiss-army-knife tool, enabling the user to perform shape generation using incomplete shapes, images, and textual descriptions at the same time, providing the relative weights for each input and facilitating interactivity. Despite our approach being shape-only, we further show an efficient method to texture the generated shape using large-scale text-to-image models.

With water quality management processes, identifying and interpreting relationships between features, such as location and weather variable tuples, and water quality variables, such as levels of bacteria, is key to gaining insights and identifying areas where interventions should be made. There is a need for a search process to identify the locations and types of phenomena that are influencing water quality and a need to explain why the quality is being affected and which factors are most relevant. This paper addresses both of these issues through the development of a process for collecting data for features that represent a variety of variables over a spatial region, which are used for training and inference, and analysing the performance of the features using the model and Shapley values. Shapley values originated in cooperative game theory and can be used to aid in the interpretation of machine learning results. Evaluations are performed using several machine learning algorithms and water quality data from the Dublin Grand Canal basin.

Oxidation states are the charges of atoms after their ionic approximation of their bonds, which have been widely used in charge-neutrality verification, crystal structure determination, and reaction estimation. Currently only heuristic rules exist for guessing the oxidation states of a given compound with many exceptions. Recent work has developed machine learning models based on heuristic structural features for predicting the oxidation states of metal ions. However, composition based oxidation state prediction still remains elusive so far, which is more important in new material discovery for which the structures are not even available. This work proposes a novel deep learning based BERT transformer language model BERTOS for predicting the oxidation states of all elements of inorganic compounds given only their chemical composition. Our model achieves 96.82\% accuracy for all-element oxidation states prediction benchmarked on the cleaned ICSD dataset and achieves 97.61\% accuracy for oxide materials. We also demonstrate how it can be used to conduct large-scale screening of hypothetical material compositions for materials discovery.

In this paper, hypernetworks are trained to generate behaviors across a range of unseen task conditions, via a novel TD-based training objective and data from a set of near-optimal RL solutions for training tasks. This work relates to meta RL, contextual RL, and transfer learning, with a particular focus on zero-shot performance at test time, enabled by knowledge of the task parameters (also known as context). Our technical approach is based upon viewing each RL algorithm as a mapping from the MDP specifics to the near-optimal value function and policy and seek to approximate it with a hypernetwork that can generate near-optimal value functions and policies, given the parameters of the MDP. We show that, under certain conditions, this mapping can be considered as a supervised learning problem. We empirically evaluate the effectiveness of our method for zero-shot transfer to new reward and transition dynamics on a series of continuous control tasks from DeepMind Control Suite. Our method demonstrates significant improvements over baselines from multitask and meta RL approaches.