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Linear regression adjustment is commonly used to analyse randomised controlled experiments due to its efficiency and robustness against model misspecification. Current testing and interval estimation procedures leverage the asymptotic distribution of such estimators to provide Type-I error and coverage guarantees that hold only at a single sample size. Here, we develop the theory for the anytime-valid analogues of such procedures, enabling linear regression adjustment in the sequential analysis of randomised experiments. We first provide sequential $F$-tests and confidence sequences for the parametric linear model, which provide time-uniform Type-I error and coverage guarantees that hold for all sample sizes. We then relax all linear model parametric assumptions in randomised designs and provide nonparametric model-free sequential tests and confidence sequences for treatment effects. This formally allows experiments to be continuously monitored for significance, stopped early, and safeguards against statistical malpractices in data collection. A particular feature of our results is their simplicity. Our test statistics and confidence sequences all emit closed-form expressions, which are functions of statistics directly available from a standard linear regression table. We illustrate our methodology with the sequential analysis of software A/B experiments at Netflix, performing regression adjustment with pre-treatment outcomes.

Hyperparameter optimization is critical in modern machine learning, requiring expert knowledge, numerous trials, and high computational and human resources. Despite the advancements in Automated Machine Learning (AutoML), challenges in terms of trial efficiency, setup complexity, and interoperability still persist. To address these issues, we introduce a novel paradigm leveraging Large Language Models (LLMs) to automate hyperparameter optimization across diverse machine learning tasks, which is named AgentHPO (short for LLM Agent-based Hyperparameter Optimization). Specifically, AgentHPO processes the task information autonomously, conducts experiments with specific hyperparameters (HPs), and iteratively optimizes them based on historical trials. This human-like optimization process largely reduces the number of required trials, simplifies the setup process, and enhances interpretability and user trust, compared to traditional AutoML methods. Extensive empirical experiments conducted on 12 representative machine-learning tasks indicate that AgentHPO not only matches but also often surpasses the best human trials in terms of performance while simultaneously providing explainable results. Further analysis sheds light on the strategies employed by the LLM in optimizing these tasks, highlighting its effectiveness and adaptability in various scenarios.

Optimal transport (OT) barycenters are a mathematically grounded way of averaging probability distributions while capturing their geometric properties. In short, the barycenter task is to take the average of a collection of probability distributions w.r.t. given OT discrepancies. We propose a novel algorithm for approximating the continuous Entropic OT (EOT) barycenter for arbitrary OT cost functions. Our approach is built upon the dual reformulation of the EOT problem based on weak OT, which has recently gained the attention of the ML community. Beyond its novelty, our method enjoys several advantageous properties: (i) we establish quality bounds for the recovered solution; (ii) this approach seemlessly interconnects with the Energy-Based Models (EBMs) learning procedure enabling the use of well-tuned algorithms for the problem of interest; (iii) it provides an intuitive optimization scheme avoiding min-max, reinforce and other intricate technical tricks. For validation, we consider several low-dimensional scenarios and image-space setups, including non-Euclidean cost functions. Furthermore, we investigate the practical task of learning the barycenter on an image manifold generated by a pretrained generative model, opening up new directions for real-world applications.

We propose a reinforcement learning (RL)-based system that would automatically prescribe a hypothetical patient medication that may help the patient with their mental health-related speech disfluency, and adjust the medication and the dosages in response to zero-cost frequent measurement of the fluency of the patient. We demonstrate the components of the system: a module that detects and evaluates speech disfluency on a large dataset we built, and an RL algorithm that automatically finds good combinations of medications. To support the two modules, we collect data on the effect of psychiatric medications for speech disfluency from the literature, and build a plausible patient simulation system. We demonstrate that the RL system is, under some circumstances, able to converge to a good medication regime. We collect and label a dataset of people with possible speech disfluency and demonstrate our methods using that dataset. Our work is a proof of concept: we show that there is promise in the idea of using automatic data collection to address speech disfluency.

Deep learning methods are transforming research, enabling new techniques, and ultimately leading to new discoveries. As the demand for more capable AI models continues to grow, we are now entering an era of Trillion Parameter Models (TPM), or models with more than a trillion parameters -- such as Huawei's PanGu-$\Sigma$. We describe a vision for the ecosystem of TPM users and providers that caters to the specific needs of the scientific community. We then outline the significant technical challenges and open problems in system design for serving TPMs to enable scientific research and discovery. Specifically, we describe the requirements of a comprehensive software stack and interfaces to support the diverse and flexible requirements of researchers.

We construct a randomized vector quantizer which has a smaller maximum error compared to all known lattice quantizers with the same entropy for dimensions 5, 6, ..., 48, and also has a smaller mean squared error compared to known lattice quantizers with the same entropy for dimensions 35, ..., 48, in the high resolution limit. Moreover, our randomized quantizer has a desirable property that the quantization error is always uniform over the ball and independent of the input. Our construction is based on applying rejection sampling on universal quantization, which allows us to shape the error distribution to be any continuous distribution, not only uniform distributions over basic cells of a lattice as in conventional dithered quantization. We also characterize the high SNR limit of one-shot channel simulation for any additive noise channel under a mild assumption (e.g., the AWGN channel), up to an additive constant of 1.45 bits.

Denoising diffusion probabilistic models (DDPMs) have recently taken the field of generative modeling by storm, pioneering new state-of-the-art results in disciplines such as computer vision and computational biology for diverse tasks ranging from text-guided image generation to structure-guided protein design. Along this latter line of research, methods have recently been proposed for generating 3D molecules using equivariant graph neural networks (GNNs) within a DDPM framework. However, such methods are unable to learn important geometric and physical properties of 3D molecules during molecular graph generation, as they adopt molecule-agnostic and non-geometric GNNs as their 3D graph denoising networks, which negatively impacts their ability to effectively scale to datasets of large 3D molecules. In this work, we address these gaps by introducing the Geometry-Complete Diffusion Model (GCDM) for 3D molecule generation, which outperforms existing 3D molecular diffusion models by significant margins across conditional and unconditional settings for the QM9 dataset as well as for the larger GEOM-Drugs dataset. Importantly, we demonstrate that the geometry-complete denoising process GCDM learns for 3D molecule generation allows the model to generate realistic and stable large molecules at the scale of GEOM-Drugs, whereas previous methods fail to do so with the features they learn. Additionally, we show that extensions of GCDM can not only effectively design 3D molecules for specific protein pockets but also that GCDM's geometric features can effectively be repurposed to directly optimize the geometry and chemical composition of existing 3D molecules for specific molecular properties, demonstrating new, real-world versatility of molecular diffusion models. Our source code and data are freely available at //github.com/BioinfoMachineLearning/Bio-Diffusion.

Graph Neural Networks (GNNs) are widely used for analyzing graph-structured data. Most GNN methods are highly sensitive to the quality of graph structures and usually require a perfect graph structure for learning informative embeddings. However, the pervasiveness of noise in graphs necessitates learning robust representations for real-world problems. To improve the robustness of GNN models, many studies have been proposed around the central concept of Graph Structure Learning (GSL), which aims to jointly learn an optimized graph structure and corresponding representations. Towards this end, in the presented survey, we broadly review recent progress of GSL methods for learning robust representations. Specifically, we first formulate a general paradigm of GSL, and then review state-of-the-art methods classified by how they model graph structures, followed by applications that incorporate the idea of GSL in other graph tasks. Finally, we point out some issues in current studies and discuss future directions.

Multi-relation Question Answering is a challenging task, due to the requirement of elaborated analysis on questions and reasoning over multiple fact triples in knowledge base. In this paper, we present a novel model called Interpretable Reasoning Network that employs an interpretable, hop-by-hop reasoning process for question answering. The model dynamically decides which part of an input question should be analyzed at each hop; predicts a relation that corresponds to the current parsed results; utilizes the predicted relation to update the question representation and the state of the reasoning process; and then drives the next-hop reasoning. Experiments show that our model yields state-of-the-art results on two datasets. More interestingly, the model can offer traceable and observable intermediate predictions for reasoning analysis and failure diagnosis, thereby allowing manual manipulation in predicting the final answer.

While existing machine learning models have achieved great success for sentiment classification, they typically do not explicitly capture sentiment-oriented word interaction, which can lead to poor results for fine-grained analysis at the snippet level (a phrase or sentence). Factorization Machine provides a possible approach to learning element-wise interaction for recommender systems, but they are not directly applicable to our task due to the inability to model contexts and word sequences. In this work, we develop two Position-aware Factorization Machines which consider word interaction, context and position information. Such information is jointly encoded in a set of sentiment-oriented word interaction vectors. Compared to traditional word embeddings, SWI vectors explicitly capture sentiment-oriented word interaction and simplify the parameter learning. Experimental results show that while they have comparable performance with state-of-the-art methods for document-level classification, they benefit the snippet/sentence-level sentiment analysis.