The goal of Causal Discovery is to find automated search methods for learning causal structures from observational data. In some cases all variables of the interested causal mechanism are measured, and the task is to predict the effects one measured variable has on another. In contrast, sometimes the variables of primary interest are not directly observable but instead inferred from their manifestations in the data. These are referred to as latent variables. One commonly known example is the psychological construct of intelligence, which cannot directly measured so researchers try to assess through various indicators such as IQ tests. In this case, casual discovery algorithms can uncover underlying patterns and structures to reveal the causal connections between the latent variables and between the latent and observed variables. This thesis focuses on two questions in causal discovery: providing an alternative definition of k-Triangle Faithfulness that (i) is weaker than strong faithfulness when applied to the Gaussian family of distributions, (ii) can be applied to non-Gaussian families of distributions, and (iii) under the assumption that the modified version of Strong Faithfulness holds, can be used to show the uniform consistency of a modified causal discovery algorithm; relaxing the sufficiency assumption to learn causal structures with latent variables. Given the importance of inferring cause-and-effect relationships for understanding and forecasting complex systems, the work in this thesis of relaxing various simplification assumptions is expected to extend the causal discovery method to be applicable in a wider range with diversified causal mechanism and statistical phenomena.

The Laplace approximation provides a closed-form model selection objective for neural networks (NN). Online variants, which optimise NN parameters jointly with hyperparameters, like weight decay strength, have seen renewed interest in the Bayesian deep learning community. However, these methods violate Laplace's method's critical assumption that the approximation is performed around a mode of the loss, calling into question their soundness. This work re-derives online Laplace methods, showing them to target a variational bound on a mode-corrected variant of the Laplace evidence which does not make stationarity assumptions. Online Laplace and its mode-corrected counterpart share stationary points where 1. the NN parameters are a maximum a posteriori, satisfying the Laplace method's assumption, and 2. the hyperparameters maximise the Laplace evidence, motivating online methods. We demonstrate that these optima are roughly attained in practise by online algorithms using full-batch gradient descent on UCI regression datasets. The optimised hyperparameters prevent overfitting and outperform validation-based early stopping.

In this manuscript, we present various proposed methods estimate the prevalence of disease, a critical prerequisite for the adequate interpretation of screening tests. To address the limitations of these approaches, which revolve primarily around their a posteriori nature, we introduce a novel method to estimate the pretest probability of disease, a priori, utilizing the Logit function from the logistic regression model. This approach is a modification of McGee's heuristic, originally designed for estimating the posttest probability of disease. In a patient presenting with $n_\theta$ signs or symptoms, the minimal bound of the pretest probability, $\phi$, can be approximated by: $\phi \approx \frac{1}{5}{ln\left[\displaystyle\prod_{\theta=1}^{i}\kappa_\theta\right]}$ where $ln$ is the natural logarithm, and $\kappa_\theta$ is the likelihood ratio associated with the sign or symptom in question.

In practical compressed sensing (CS), the obtained measurements typically necessitate quantization to a limited number of bits prior to transmission or storage. This nonlinear quantization process poses significant recovery challenges, particularly with extreme coarse quantization such as 1-bit. Recently, an efficient algorithm called QCS-SGM was proposed for quantized CS (QCS) which utilizes score-based generative models (SGM) as an implicit prior. Due to the adeptness of SGM in capturing the intricate structures of natural signals, QCS-SGM substantially outperforms previous QCS methods. However, QCS-SGM is constrained to (approximately) row-orthogonal sensing matrices as the computation of the likelihood score becomes intractable otherwise. To address this limitation, we introduce an advanced variant of QCS-SGM, termed QCS-SGM+, capable of handling general matrices effectively. The key idea is a Bayesian inference perspective on the likelihood score computation, wherein expectation propagation is employed for its approximate computation. Extensive experiments are conducted, demonstrating the substantial superiority of QCS-SGM+ over QCS-SGM for general sensing matrices beyond mere row-orthogonality.

Language models are often trained on text alone, without additional grounding. There is debate as to how much of natural language semantics can be inferred from such a procedure. We prove that entailment judgments between sentences can be extracted from an ideal language model that has perfectly learned its target distribution, assuming the training sentences are generated by Gricean agents, i.e., agents who follow fundamental principles of communication from the linguistic theory of pragmatics. We also show entailment judgments can be decoded from the predictions of a language model trained on such Gricean data. Our results reveal a pathway for understanding the semantic information encoded in unlabeled linguistic data and a potential framework for extracting semantics from language models.

We introduce a new mean-field ODE and corresponding interacting particle systems for sampling from an unnormalized target density or Bayesian posterior. The interacting particle systems are gradient-free, available in closed form, and only require the ability to sample from the reference density and compute the (unnormalized) target-to-reference density ratio. The mean-field ODE is obtained by solving a Poisson equation for a velocity field that transports samples along the geometric mixture of the two densities, which is the path of a particular Fisher-Rao gradient flow. We employ a reproducing kernel Hilbert space ansatz for the velocity field, which makes the Poisson equation tractable and enables us to discretize the resulting mean-field ODE over finite samples, as a simple interacting particle system. The mean-field ODE can be additionally be derived from a discrete-time perspective as the limit of successive linearizations of the Monge-Amp\`ere equations within a framework known as sample-driven optimal transport. We demonstrate empirically that our interacting particle systems can produce high-quality samples from distributions with varying characteristics.

Gaussian process state-space models (GPSSMs) are a versatile and principled family of nonlinear dynamical system models. However, existing variational learning and inference methods for GPSSMs often necessitate optimizing a substantial number of variational parameters, leading to inadequate performance and efficiency. To overcome this issue, we propose incorporating the ensemble Kalman filter (EnKF), a well-established model-based filtering technique, into the variational inference framework to approximate the posterior distribution of latent states. This utilization of EnKF can effectively exploit the dependencies between latent states and GP dynamics, while eliminating the need for parameterizing the variational distribution, thereby significantly reducing the number of variational parameters. Moreover, we show that our proposed algorithm allows straightforward evaluation of an approximated evidence lower bound (ELBO) in variational inference via simply summating multiple terms with readily available closed-form solutions. Leveraging automatic differentiation tools, we hence can maximize the ELBO and train the GPSSM efficiently. We also extend the proposed algorithm to accommodate an online setting and provide detailed algorithmic analyses and insights. Extensive evaluation on diverse real and synthetic datasets demonstrates the superiority of our EnKF-aided variational inference algorithms in terms of learning and inference performance compared to existing methods.

The secondary structure of a ribonucleic acid (RNA) is higher order structure over the primary sequence of the molecule. Nucleotides on the sequence physically come close to each other through hydrogen bonds between bases, forming canonical Watson-Crick pairs (A-U and G-C), and the wobble pair (G-U) as the fundamental components of the structure. The secondary structure is the intermediate, to a great extent the scaffold for higher order interactions between nucleotides to generate RNA tertiary, i.e., 3-dimensional, structure [7, 17]. The latter determines important RNA functions in biological processes, not only as a genetic information carrier but also playing catalytic, scaffolding, structural, and regulatory roles [12, 4]. There has been abundant interest in understanding the detailed process and dynamics of how RNA folds into its structure [3]. Computational prediction of RNA secondary structure directly from its primary sequence is a very desirable step toward the prediction of RNA 3D structure. This is evident by the RNA Puzzles, an annual competition to predict RNA 3D structures, in which most of the used methods by participants are proceeded by a phase for secondary structure prediction [24, 22, 23]. These authors contributed equally to this work.

Due to the expanding scope of machine learning (ML) to the fields of sensor networking, cooperative robotics and many other multi-agent systems, distributed deployment of inference algorithms has received a lot of attention. These algorithms involve collaboratively learning unknown parameters from dispersed data collected by multiple agents. There are two competing aspects in such algorithms, namely, intra-agent computation and inter-agent communication. Traditionally, algorithms are designed to perform both synchronously. However, certain circumstances need frugal use of communication channels as they are either unreliable, time-consuming, or resource-expensive. In this paper, we propose gossip-based asynchronous communication to leverage fast computations and reduce communication overhead simultaneously. We analyze the effects of multiple (local) intra-agent computations by the active agents between successive inter-agent communications. For local computations, Bayesian sampling via unadjusted Langevin algorithm (ULA) MCMC is utilized. The communication is assumed to be over a connected graph (e.g., as in decentralized learning), however, the results can be extended to coordinated communication where there is a central server (e.g., federated learning). We theoretically quantify the convergence rates in the process. To demonstrate the efficacy of the proposed algorithm, we present simulations on a toy problem as well as on real world data sets to train ML models to perform classification tasks. We observe faster initial convergence and improved performance accuracy, especially in the low data range. We achieve on average 78% and over 90% classification accuracy respectively on the Gamma Telescope and mHealth data sets from the UCI ML repository.

This manuscript is technical memoir about my work at Stanford and Microsoft Research. Included are fundamental concepts central to machine learning and artificial intelligence, applications of these concepts, and stories behind their creation.