A clinical trial is an essential step in drug development, which is often costly and time-consuming. In silico trials are clinical trials conducted digitally through simulation and modeling as an alternative to traditional clinical trials. AI-enabled in silico trials can increase the case group size by creating virtual cohorts as controls. In addition, it also enables automation and optimization of trial design and predicts the trial success rate. This article systematically reviews papers under three main topics: clinical simulation, individualized predictive modeling, and computer-aided trial design. We focus on how machine learning (ML) may be applied in these applications. In particular, we present the machine learning problem formulation and available data sources for each task. We end with discussing the challenges and opportunities of AI for in silico trials in real-world applications.

Recently there is a large amount of work devoted to the study of Markov chain stochastic gradient methods (MC-SGMs) which mainly focus on their convergence analysis for solving minimization problems. In this paper, we provide a comprehensive generalization analysis of MC-SGMs for both minimization and minimax problems through the lens of algorithmic stability in the framework of statistical learning theory. For empirical risk minimization (ERM) problems, we establish the optimal excess population risk bounds for both smooth and non-smooth cases by introducing on-average argument stability. For minimax problems, we develop a quantitative connection between on-average argument stability and generalization error which extends the existing results for uniform stability \cite{lei2021stability}. We further develop the first nearly optimal convergence rates for convex-concave problems both in expectation and with high probability, which, combined with our stability results, show that the optimal generalization bounds can be attained for both smooth and non-smooth cases. To the best of our knowledge, this is the first generalization analysis of SGMs when the gradients are sampled from a Markov process.

Training deep neural networks often forces users to work in a distributed or outsourced setting, accompanied with privacy concerns. Split learning aims to address this concern by distributing the model among a client and a server. The scheme supposedly provides privacy, since the server cannot see the clients' models and inputs. We show that this is not true via two novel attacks. (1) We show that an honest-but-curious split learning server, equipped only with the knowledge of the client neural network architecture, can recover the input samples and obtain a functionally similar model to the client model, without being detected. (2) We show that if the client keeps hidden only the output layer of the model to "protect" the private labels, the honest-but-curious server can infer the labels with perfect accuracy. We test our attacks using various benchmark datasets and against proposed privacy-enhancing extensions to split learning. Our results show that plaintext split learning can pose serious risks, ranging from data (input) privacy to intellectual property (model parameters), and provide no more than a false sense of security.

We apply methods of machine-learning, such as neural networks, manifold learning and image processing, in order to study 2-dimensional amoebae in algebraic geometry and string theory. With the help of embedding manifold projection, we recover complicated conditions obtained from so-called lopsidedness. For certain cases it could even reach $\sim99\%$ accuracy, in particular for the lopsided amoeba of $F_0$ with positive coefficients which we place primary focus. Using weights and biases, we also find good approximations to determine the genus for an amoeba at lower computational cost. In general, the models could easily predict the genus with over $90\%$ accuracies. With similar techniques, we also investigate the membership problem, and image processing of the amoebae directly.

The thin-file borrowers are customers for whom a creditworthiness assessment is uncertain due to their lack of credit history; many researchers have used borrowers' relationships and interactions networks in the form of graphs as an alternative data source to address this. Incorporating network data is traditionally made by hand-crafted feature engineering, and lately, the graph neural network has emerged as an alternative, but it still does not improve over the traditional method's performance. Here we introduce a framework to improve credit scoring models by blending several Graph Representation Learning methods: feature engineering, graph embeddings, and graph neural networks. We stacked their outputs to produce a single score in this approach. We validated this framework using a unique multi-source dataset that characterizes the relationships and credit history for the entire population of a Latin American country, applying it to credit risk models, application, and behavior, targeting both individuals and companies. Our results show that the graph representation learning methods should be used as complements, and these should not be seen as self-sufficient methods as is currently done. In terms of AUC and KS, we enhance the statistical performance, outperforming traditional methods. In Corporate lending, where the gain is much higher, it confirms that evaluating an unbanked company cannot solely consider its features. The business ecosystem where these firms interact with their owners, suppliers, customers, and other companies provides novel knowledge that enables financial institutions to enhance their creditworthiness assessment. Our results let us know when and which group to use graph data and what effects on performance to expect. They also show the enormous value of graph data on the unbanked credit scoring problem, principally to help companies' banking.

Machine learning is a set of tools that, broadly speaking, allow us to "teach" computers how to perform tasks by providing examples of how they should be done. For example, suppose we wish to write a program to distinguish between valid email messages and unwanted spam. We could try to write a set of simple rules, for example, flagging messages that contain certain features (such as the word "viagra" or obviously-fake headers). However, writing rules to accurately distinguish which text is valid can actually be quite difficult to do well, resulting either in many missed spam messages, or, worse, many lost emails. Worse, the spammers will actively adjust the way they send spam in order to trick these strategies (e.g., writing "vi@gr@"). Writing effective rules -- and keeping them up to date -- quickly becomes an insurmountable task. Fortunately, machine learning has provided a solution. Modern spam filters are "learned" from Examples: we provide the learning algorithm with example emails which we have manually labelled as "ham" (valid email) or "spam" (unwanted email), and the algorithms learn to distinguish between them automatically.

Some company managers or stakeholders are pessimistic about machine learning model predictions. Therefore, it is data scientists' reasonability to convince them that the model prediction is credible and also understandable to humans. Therefore, we need to focus not only on creating powerful machine learning/deep learning models, but also make the models interpretable by humans. Interpretability helps in many ways, such as helping us to understand how a model makes a decision, it justifies model prediction and gaining insights, building trust in the model, and it helps us improve the model. There are two types of ML model interpretation -- global and local. Good Examples of inherently explainable models are linear regression and decision trees.

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We study the asymmetric matrix factorization problem under a natural nonconvex formulation with arbitrary overparametrization. The model-free setting is considered, with minimal assumption on the rank or singular values of the observed matrix, where the global optima provably overfit. We show that vanilla gradient descent with small random initialization sequentially recovers the principal components of the observed matrix. Consequently, when equipped with proper early stopping, gradient descent produces the best low-rank approximation of the observed matrix without explicit regularization. We provide a sharp characterization of the relationship between the approximation error, iteration complexity, initialization size and stepsize. Our complexity bound is almost dimension-free and depends logarithmically on the approximation error, with significantly more lenient requirements on the stepsize and initialization compared to prior work. Our theoretical results provide accurate prediction for the behavior gradient descent, showing good agreement with numerical experiments.

Learning pair interactions from experimental or simulation data is of great interest for molecular simulations. We propose a general stochastic method for learning pair interactions from data using differentiable simulations (DiffSim). DiffSim defines a loss function based on structural observables, such as the radial distribution function, through molecular dynamics (MD) simulations. The interaction potentials are then learned directly by stochastic gradient descent, using backpropagation to calculate the gradient of the structural loss metric with respect to the interaction potential through the MD simulation. This gradient-based method is flexible and can be configured to simulate and optimize multiple systems simultaneously. For example, it is possible to simultaneously learn potentials for different temperatures or for different compositions. We demonstrate the approach by recovering simple pair potentials, such as Lennard-Jones systems, from radial distribution functions. We find that DiffSim can be used to probe a wider functional space of pair potentials compared to traditional methods like Iterative Boltzmann Inversion. We show that our methods can be used to simultaneously fit potentials for simulations at different compositions and temperatures to improve the transferability of the learned potentials.