Structure-based drug design (SBDD) aims to discover drug candidates by finding molecules (ligands) that bind tightly to a disease-related protein (targets), which is the primary approach to computer-aided drug discovery. Recently, applying deep generative models for three-dimensional (3D) molecular design conditioned on protein pockets to solve SBDD has attracted much attention, but their formulation as probabilistic modeling often leads to unsatisfactory optimization performance. On the other hand, traditional combinatorial optimization methods such as genetic algorithms (GA) have demonstrated state-of-the-art performance in various molecular optimization tasks. However, they do not utilize protein target structure to inform design steps but rely on a random-walk-like exploration, which leads to unstable performance and no knowledge transfer between different tasks despite the similar binding physics. To achieve a more stable and efficient SBDD, we propose Reinforced Genetic Algorithm (RGA) that uses neural models to prioritize the profitable design steps and suppress random-walk behavior. The neural models take the 3D structure of the targets and ligands as inputs and are pre-trained using native complex structures to utilize the knowledge of the shared binding physics from different targets and then fine-tuned during optimization. We conduct thorough empirical studies on optimizing binding affinity to various disease targets and show that RGA outperforms the baselines in terms of docking scores and is more robust to random initializations. The ablation study also indicates that the training on different targets helps improve the performance by leveraging the shared underlying physics of the binding processes.

We consider the problem of online classification under a privacy constraint. In this setting a learner observes sequentially a stream of labelled examples $(x_t, y_t)$, for $1 \leq t \leq T$, and returns at each iteration $t$ a hypothesis $h_t$ which is used to predict the label of each new example $x_t$. The learner's performance is measured by her regret against a known hypothesis class $\mathcal{H}$. We require that the algorithm satisfies the following privacy constraint: the sequence $h_1, \ldots, h_T$ of hypotheses output by the algorithm needs to be an $(\epsilon, \delta)$-differentially private function of the whole input sequence $(x_1, y_1), \ldots, (x_T, y_T)$.We provide the first non-trivial regret bound for the realizable setting. Specifically, we show that if the class $\mathcal{H}$ has constant Littlestone dimension then, given an oblivious sequence of labelled examples, there is a private learner that makes in expectation at most $O(\log T)$ mistakes -- comparable to the optimal mistake bound in the non-private case, up to a logarithmic factor. Moreover, for general values of the Littlestone dimension $d$, the same mistake bound holds but with a doubly-exponential in $d$ factor. A recent line of work has demonstrated a strong connection between classes that are online learnable and those that are differentially-private learnable. Our results strengthen this connection and show that an online learning algorithm can in fact be directly privatized (in the realizable setting).We also discuss an adaptive setting and provide a sublinear regret bound of $O(\sqrt{T})$.

One of the most important AI research questions is to trade off computation versus performance since ``perfect rationality exists in theory but is impossible to achieve in practice. Recently, Monte-Carlo tree search (MCTS) has attracted considerable attention due to the significant performance improvement in various challenging domains. However, the expensive time cost during search severely restricts its scope for applications. This paper proposes the Virtual MCTS (V-MCTS), a variant of MCTS that spends more search time on harder states and less search time on simpler states adaptively. We give theoretical bounds of the proposed method and evaluate the performance and computations on $9 \times 9$ Go board games and Atari games. Experiments show that our method can achieve comparable performances to the original search algorithm while requiring less than $50\%$ search time on average. We believe that this approach is a viable alternative for tasks under limited time and resources.

Modeling a system's temporal behaviour in reaction to external stimuli is a fundamental problem in many areas. Pure Machine Learning (ML) approaches often fail in the small sample regime and cannot provide actionable insights beyond predictions. A promising modification has been to incorporate expert domain knowledge into ML models. The application we consider is predicting the patient health status and disease progression over time, where a wealth of domain knowledge is available from pharmacology. Pharmacological models describe the dynamics of carefully-chosen medically meaningful variables in terms of systems of Ordinary Differential Equations (ODEs). However, these models only describe a limited collection of variables, and these variables are often not observable in clinical environments. To close this gap, we propose the latent hybridisation model (LHM) that integrates a system of expert-designed ODEs with machine-learned Neural ODEs to fully describe the dynamics of the system and to link the expert and latent variables to observable quantities. We evaluated LHM on synthetic data as well as real-world intensive care data of COVID-19 patients. LHM consistently outperforms previous works, especially when few training samples are available such as at the beginning of the pandemic.

Neural networks have been shown effective in deep steganography for hiding a full image in another. However, the reason for its success remains not fully clear. Under the existing cover ($C$) dependent deep hiding (DDH) pipeline, it is challenging to analyze how the secret ($S$) image is encoded since the encoded message cannot be analyzed independently. We propose a novel universal deep hiding (UDH) meta-architecture to disentangle the encoding of $S$ from $C$. We perform extensive analysis and demonstrate that the success of deep steganography can be attributed to a frequency discrepancy between $C$ and the encoded secret image.

Clustering is a ubiquitous task in data science. Compared to the commonly used k-means clustering, k-medoids clustering requires the cluster centers to be actual data points and supports arbitrary distance metrics, which permits greater interpretability and the clustering of structured objects. Current state-of-the-art k-medoids clustering algorithms, such as Partitioning Around Medoids (PAM), are iterative and are quadratic in the dataset size n for each iteration, being prohibitively expensive for large datasets. We propose BanditPAM, a randomized algorithm inspired by techniques from multi-armed bandits, that reduces the complexity of each PAM iteration from O(n^2) to O(nlogn) and returns the same results with high probability, under assumptions on the data that often hold in practice. As such, BanditPAM matches state-of-the-art clustering loss while reaching solutions much faster.

We study online learning for optimal allocation when the resource to be allocated is time. An agent receives task proposals sequentially according to a Poisson process and can either accept or reject a proposed task. If she accepts the proposal, she is busy for the duration of the task and obtains a reward that depends on the task duration. If she rejects it, she remains on hold until a new task proposal arrives. We study the regret incurred by the agent first when she knows her reward function but does not know the distribution of the task duration, and then when she does not know her reward function, either. Faster rates are finally obtained by adding structural assumptions on the distribution of rides or on the reward function. This natural setting bears similarities with contextual (one-armed) bandits, but with the crucial difference that the normalized reward associated to a context depends on the whole distribution of contexts.

Collaborations among multiple organizations, such as financial institutions, medical centers, and retail markets in decentralized settings are crucial to providing improved service and performance. However, the underlying organizations may have little interest in sharing their local data, models, and objective functions. These requirements have created new challenges for multi-organization collaboration. In this work, we propose Gradient Assisted Learning (GAL), a new method for multiple organizations to assist each other in supervised learning tasks without sharing local data, models, and objective functions. In this framework, all participants collaboratively optimize the aggregate of local loss functions, and each participant autonomously builds its own model by iteratively fitting the gradients of the overarching objective function. We also provide asymptotic convergence analysis and practical case studies of GAL. Experimental studies demonstrate that GAL can achieve performance close to centralized learning when all data, models, and objective functions are fully disclosed.

Recently, Transformer has become a prevailing deep architecture for solving vehicle routing problems (VRPs). However, it is less effective in learning improvement models for VRP because its positional encoding (PE) method is not suitable in representing VRP solutions. This paper presents a novel Dual-Aspect Collaborative Transformer (DACT) to learn embeddings for the node and positional features separately, instead of fusing them together as done in existing ones, so as to avoid potential noises and incompatible correlations. Moreover, the positional features are embedded through a novel cyclic positional encoding (CPE) method to allow Transformer to effectively capture the circularity and symmetry of VRP solutions (i.e., cyclic sequences). We train DACT using Proximal Policy Optimization and design a curriculum learning strategy for better sample efficiency. We apply DACT to solve the traveling salesman problem (TSP) and capacitated vehicle routing problem (CVRP). Results show that our DACT outperforms existing Transformer based improvement models, and exhibits much better generalization performance across different problem sizes on synthetic and benchmark instances, respectively.

Multi-agent reinforcement learning has recently shown great promise as an approach to networked system control. Arguably, one of the most difficult and important tasks for which large scale networked system control is applicable is common-pool resource management. Crucial common-pool resources include arable land, fresh water, wetlands, wildlife, fish stock, forests and the atmosphere, of which proper management is related to some of society's greatest challenges such as food security, inequality and climate change. Here we take inspiration from a recent research program investigating the game-theoretic incentives of humans in social dilemma situations such as the well-known \textit{tragedy of the commons}. However, instead of focusing on biologically evolved human-like agents, our concern is rather to better understand the learning and operating behaviour of engineered networked systems comprising general-purpose reinforcement learning agents, subject only to nonbiological constraints such as memory, computation and communication bandwidth. Harnessing tools from empirical game-theoretic analysis, we analyse the differences in resulting solution concepts that stem from employing different information structures in the design of networked multi-agent systems. These information structures pertain to the type of information shared between agents as well as the employed communication protocol and network topology. Our analysis contributes new insights into the consequences associated with certain design choices and provides an additional dimension of comparison between systems beyond efficiency, robustness, scalability and mean control performance.