Zhenming Liu

Bo Qiang, Yiran Zhou, Yuheng Ding et al.

Chemical reactions are the fundamental building blocks of drug design and organic chemistry research. In recent years, there has been a growing need for a large-scale deep-learning framework that can efficiently capture the basic rules of chemical reactions. In this paper, we have proposed a unified framework that addresses both the reaction representation learning and molecule generation tasks, which allows for a more holistic approach. Inspired by the organic chemistry mechanism, we develop a novel pretraining framework that enables us to incorporate inductive biases into the model. Our framework achieves state-of-the-art results on challenging downstream tasks. By possessing chemical knowledge, our generative framework overcome the limitations of current molecule generation models that rely on a small number of reaction templates. In the extensive experiments, our model generates synthesizable drug-like structures of high quality. Overall, our work presents a significant step toward a large-scale deep-learning framework for a variety of reaction-based applications.

Qiong Wu, Jian Li, Zhenming Liu et al.

This paper revisits building machine learning algorithms that involve interactions between entities, such as those between financial assets in an actively managed portfolio, or interactions between users in a social network. Our goal is to forecast the future evolution of ensembles of multivariate time series in such applications (e.g., the future return of a financial asset or the future popularity of a Twitter account). Designing ML algorithms for such systems requires addressing the challenges of high-dimensional interactions and non-linearity. Existing approaches usually adopt an ad-hoc approach to integrating high-dimensional techniques into non-linear models and recent studies have shown these approaches have questionable efficacy in time-evolving interacting systems. To this end, we propose a novel framework, which we dub as the additive influence model. Under our modeling assumption, we show that it is possible to decouple the learning of high-dimensional interactions from the learning of non-linear feature interactions. To learn the high-dimensional interactions, we leverage kernel-based techniques, with provable guarantees, to embed the entities in a low-dimensional latent space. To learn the non-linear feature-response interactions, we generalize prominent machine learning techniques, including designing a new statistically sound non-parametric method and an ensemble learning algorithm optimized for vector regressions. Extensive experiments on two common applications demonstrate that our new algorithms deliver significantly stronger forecasting power compared to standard and recently proposed methods.

Ningfeng Liu, Jie Yu, Siyu Xiu et al.

Molecular generation, an essential method for identifying new drug structures, has been supported by advancements in machine learning and computational technology. However, challenges remain in multi-objective generation, model adaptability, and practical application in drug discovery. In this study, we developed a versatile 'plug-in' molecular generation model that incorporates multiple objectives related to target affinity, drug-likeness, and synthesizability, facilitating its application in various drug development contexts. We improved the Particle Swarm Optimization (PSO) in the context of drug discoveries, and identified PSO-ENP as the optimal variant for multi-objective molecular generation and optimization through comparative experiments. The model also incorporates a novel target-ligand affinity predictor, enhancing the model's utility by supporting three-dimensional information and improving synthetic feasibility. Case studies focused on generating and optimizing drug-like big marine natural products were performed, underscoring PSO-ENP's effectiveness and demonstrating its considerable potential for practical drug discovery applications.

Yibo Li, Jianxing Hu, Yanxing Wang et al.

The ultimate goal of drug design is to find novel compounds with desirable pharmacological properties. Designing molecules retaining particular scaffolds as the core structures of the molecules is one of the efficient ways to obtain potential drug candidates with desirable properties. We proposed a scaffold-based molecular generative model for scaffold-based drug discovery, which performs molecule generation based on a wide spectrum of scaffold definitions, including BM-scaffolds, cyclic skeletons, as well as scaffolds with specifications on side-chain properties. The model can generalize the learned chemical rules of adding atoms and bonds to a given scaffold. Furthermore, the generated compounds were evaluated by molecular docking in DRD2 targets and the results demonstrated that this approach can be effectively applied to solve several drug design problems, including the generation of compounds containing a given scaffold and de novo drug design of potential drug candidates with specific docking scores. Finally, a command line interface is created.

Yibo Li, Liangren Zhang, Zhenming Liu

Recently, deep generative models have revealed itself as a promising way of performing de novo molecule design. However, previous research has focused mainly on generating SMILES strings instead of molecular graphs. Although current graph generative models are available, they are often too general and computationally expensive, which restricts their application to molecules with small sizes. In this work, a new de novo molecular design framework is proposed based on a type sequential graph generators that do not use atom level recurrent units. Compared with previous graph generative models, the proposed method is much more tuned for molecule generation and have been scaled up to cover significantly larger molecules in the ChEMBL database. It is shown that the graph-based model outperforms SMILES based models in a variety of metrics, especially in the rate of valid outputs. For the application of drug design tasks, conditional graph generative model is employed. This method offers higher flexibility compared to previous fine-tuning based approach and is suitable for generation based on multiple objectives. This approach is applied to solve several drug design problems, including the generation of compounds containing a given scaffold, generation of compounds with specific drug-likeness and synthetic accessibility requirements, as well as generating dual inhibitors against JNK3 and GSK3$β$. Results show high enrichment rates for outputs satisfying the given requirements.

Henry Lam, Zhenming Liu

We consider a non-stochastic online learning approach to price financial options by modeling the market dynamic as a repeated game between the nature (adversary) and the investor. We demonstrate that such framework yields analogous structure as the Black-Scholes model, the widely popular option pricing model in stochastic finance, for both European and American options with convex payoffs. In the case of non-convex options, we construct approximate pricing algorithms, and demonstrate that their efficiency can be analyzed through the introduction of an artificial probability measure, in parallel to the so-called risk-neutral measure in the finance literature, even though our framework is completely adversarial. Continuous-time convergence results and extensions to incorporate price jumps are also presented.

Kai-Min Chung, Zhenming Liu, Rafael Pass

We demonstrate a simple, statistically secure, ORAM with computational overhead $\tilde{O}(\log^2 n)$; previous ORAM protocols achieve only computational security (under computational assumptions) or require $\tildeΩ(\log^3 n)$ overheard. An additional benefit of our ORAM is its conceptual simplicity, which makes it easy to implement in both software and (commercially available) hardware. Our construction is based on recent ORAM constructions due to Shi, Chan, Stefanov, and Li (Asiacrypt 2011) and Stefanov and Shi (ArXiv 2012), but with some crucial modifications in the algorithm that simplifies the ORAM and enable our analysis. A central component in our analysis is reducing the analysis of our algorithm to a "supermarket" problem; of independent interest (and of importance to our analysis,) we provide an upper bound on the rate of "upset" customers in the "supermarket" problem.