In computer-aided drug discovery (CADD), virtual screening (VS) is used for comparing a library of compounds against known active ligands to identify the drug candidates that are most likely to bind to a molecular target. Most VS methods to date have focused on using canonical compound representations (e.g., SMILES strings, Morgan fingerprints) or generating alternative fingerprints of the compounds by training progressively more complex variational autoencoders (VAEs) and graph neural networks (GNNs). Although VAEs and GNNs led to significant improvements in VS performance, these methods suffer from reduced performance when scaling to large virtual compound datasets. The performance of these methods has shown only incremental improvements in the past few years. To address this problem, we developed a novel method using multiparameter persistence (MP) homology that produces topological fingerprints of the compounds as multidimensional vectors. Our primary contribution is framing the VS process as a new topology-based graph ranking problem by partitioning a compound into chemical substructures informed by the periodic properties of its atoms and extracting their persistent homology features at multiple resolution levels. We show that the margin loss fine-tuning of pretrained Triplet networks attains highly competitive results in differentiating between compounds in the embedding space and ranking their likelihood of becoming effective drug candidates. We further establish theoretical guarantees for the stability properties of our proposed MP signatures, and demonstrate that our models, enhanced by the MP signatures, outperform state-of-the-art methods on benchmark datasets by a wide and highly statistically significant margin (e.g., 93\% gain for Cleves-Jain and 54\% gain for DUD-E Diverse dataset).

Search-based methods for hard combinatorial optimization are often guided by heuristics. Tuning heuristics in various conditions and situations is often time-consuming. In this paper, we propose NeuRewriter that learns a policy to pick heuristics and rewrite the local components of the current solution to iteratively improve it until convergence. The policy factorizes into a region-picking and a rule-picking component, each parameterized by a neural network trained with actor-critic methods in reinforcement learning. NeuRewriter captures the general structure of combinatorial problems and shows strong performance in three versatile tasks: expression simplification, online job scheduling and vehicle routing problems. NeuRewriter outperforms the expression simplification component in Z3; outperforms DeepRM and Google OR-tools in online job scheduling; and outperforms recent neural baselines and Google OR-tools in vehicle routing problems.

A longstanding goal of the field of AI is a method for learning a highly capable, generalist agent from diverse experience. In the subfields of vision and language, this was largely achieved by scaling up transformer-based models and training them on large, diverse datasets. Motivated by this progress, we investigate whether the same strategy can be used to produce generalist reinforcement learning agents. Specifically, we show that a single transformer-based model - with a single set of weights - trained purely offline can play a suite of up to 46 Atari games simultaneously at close-to-human performance. When trained and evaluated appropriately, we find that the same trends observed in language and vision hold, including scaling of performance with model size and rapid adaptation to new games via fine-tuning. We compare several approaches in this multi-game setting, such as online and offline RL methods and behavioral cloning, and find that our Multi-Game Decision Transformer models offer the best scalability and performance. We release the pre-trained models and code to encourage further research in this direction.

We introduce a simple yet effective framework for improving the robustness of learning algorithms against image corruptions for autonomous driving. These corruptions can occur due to both internal (e.g., sensor noises and hardware abnormalities) and external factors (e.g., lighting, weather, visibility, and other environmental effects). Using sensitivity analysis with FID-based parameterization, we propose a novel algorithm exploiting basis perturbations to improve the overall performance of autonomous steering and other image processing tasks, such as classification and detection, for self-driving cars. Our model not only improves the performance on the original dataset, but also achieves significant performance improvement on datasets with multiple and unseen perturbations, up to 87% and 77%, respectively. A comparison between our approach and other SOTA techniques confirms the effectiveness of our technique in improving the robustness of neural network training for learning-based steering and other image processing tasks.

AI-empowered drug recommendation has become an important task in healthcare research areas, which offers an additional perspective to assist human doctors with more accurate and more efficient drug prescriptions. Generally, drug recommendation is based on patients' diagnosis results in the electronic health records. We assume that there are three key factors to be addressed in drug recommendation: 1) elimination of recommendation bias due to limitations of observable information, 2) better utilization of historical health condition and 3) coordination of multiple drugs to control safety. To this end, we propose DrugRec, a causal inference based drug recommendation model. The causal graphical model can identify and deconfound the recommendation bias with front-door adjustment. Meanwhile, we model the multi-visit in the causal graph to characterize a patient's historical health conditions. Finally, we model the drug-drug interactions (DDIs) as the propositional satisfiability (SAT) problem, and solving the SAT problem can help better coordinate the recommendation. Comprehensive experiment results show that our proposed model achieves state-of-the-art performance on the widely used datasets MIMIC-III and MIMIC-IV, demonstrating the effectiveness and safety of our method.

Quantum neural networks (QNNs) have emerged as a leading strategy to establish applications in machine learning, chemistry, and optimization. While the applications of QNN have been widely investigated, its theoretical foundation remains less understood. In this paper, we formulate a theoretical framework for the expressive ability of data re-uploading quantum neural networks that consist of interleaved encoding circuit blocks and trainable circuit blocks. First, we prove that single-qubit quantum neural networks can approximate any univariate function by mapping the model to a partial Fourier series. We in particular establish the exact correlations between the parameters of the trainable gates and the Fourier coefficients, resolving an open problem on the universal approximation property of QNN. Second, we discuss the limitations of single-qubit native QNNs on approximating multivariate functions by analyzing the frequency spectrum and the flexibility of Fourier coefficients. We further demonstrate the expressivity and limitations of single-qubit native QNNs via numerical experiments. We believe these results would improve our understanding of QNNs and provide a helpful guideline for designing powerful QNNs for machine learning tasks.

While previous heuristic or learning-based works achieve decent solutions on small problem instances, their performance deteriorates in large problems. This article presents a novel learning-augmented local search framework to solve large-scale VRP. The method iteratively improves the solution by identifying appropriate subproblems and $delegating$ their improvement to a black box subsolver. At each step, we leverage spatial locality to consider only a linear number of subproblems, rather than exponential. We frame subproblem selection as regression and train a Transformer on a generated training set of problem instances. Our method accelerates state-of-the-art VRP solvers by 10x to 100x while achieving competitive solution qualities for VRPs with sizes ranging from 500 to 3000. Learned subproblem selection offers a 1.5x to 2x speedup over heuristic or random selection. Our results generalize to a variety of VRP distributions, variants, and solvers.

Consider making a prediction over new test data without any opportunity to learn from a training set of labelled data - instead given access to a set of expert models and their predictions alongside some limited information about the dataset used to train them. In scenarios from finance to the medical sciences, and even consumer practice, stakeholders have developed models on private data they either cannot, or do not want to, share. Given the value and legislation surrounding personal information, it is not surprising that only the models, and not the data, will be released - the pertinent question becoming: how best to use these models? Previous work has focused on global model selection or ensembling, with the result of a single final model across the feature space. Machine learning models perform notoriously poorly on data outside their training domain however, and so we argue that when ensembling models the weightings for individual instances must reflect their respective domains - in other words models that are more likely to have seen information on that instance should have more attention paid to them. We introduce a method for such an instance-wise ensembling of models, including a novel representation learning step for handling sparse high-dimensional domains. Finally, we demonstrate the need and generalisability of our method on classical machine learning tasks as well as highlighting a real world use case in the pharmacological setting of vancomycin precision dosing.

Images, captured by a camera, play a critical role in training Deep Neural Networks (DNNs). Usually, we assume the images acquired by cameras are consistent with the ones perceived by human eyes. However, due to the different physical mechanisms between human-vision and computer-vision systems, the final perceived images could be very different in some cases, for example shooting on digital monitors. In this paper, we find a special phenomenon in digital image processing, the moiré effect, that could cause unnoticed security threats to DNNs. Based on it, we propose a Moiré Attack (MA) that generates the physical-world moiré pattern adding to the images by mimicking the shooting process of digital devices. Extensive experiments demonstrate that our proposed digital Moiré Attack (MA) is a perfect camouflage for attackers to tamper with DNNs with a high success rate ($100.0\%$

For a self-driving car to operate reliably, its perceptual system must generalize to the end-user's environment --- ideally without additional annotation efforts. One potential solution is to leverage unlabeled data (e.g., unlabeled LiDAR point clouds) collected from the end-users' environments (i.e.