Data transformations are essential for broad applicability of parametric regression models. However, for Bayesian analysis, joint inference of the transformation and model parameters typically involves restrictive parametric transformations or nonparametric representations that are computationally inefficient and cumbersome for implementation and theoretical analysis, which limits their usability in practice. This paper introduces a simple, general, and efficient strategy for joint posterior inference of an unknown transformation and all regression model parameters. The proposed approach directly targets the posterior distribution of the transformation by linking it with the marginal distributions of the independent and dependent variables, and then deploys a Bayesian nonparametric model via the Bayesian bootstrap. Crucially, this approach delivers (1) joint posterior consistency under general conditions, including multiple model misspecifications, and (2) efficient Monte Carlo (not Markov chain Monte Carlo) inference for the transformation and all parameters for important special cases. These tools apply across a variety of data domains, including real-valued, integer-valued, compactly-supported, and positive data. Simulation studies and an empirical application demonstrate the effectiveness and efficiency of this strategy for semiparametric Bayesian analysis with linear models, quantile regression, and Gaussian processes.

In this paper, our aim is to briefly survey and articulate the logical and philosophical foundations of using (first-order) logic to represent (probabilistic) knowledge in a non-technical fashion. Our motivation is three fold. First, for machine learning researchers unaware of why the research community cares about relational representations, this article can serve as a gentle introduction. Second, for logical experts who are newcomers to the learning area, such an article can help in navigating the differences between finite vs infinite, and subjective probabilities vs random-world semantics. Finally, for researchers from statistical relational learning and neuro-symbolic AI, who are usually embedded in finite worlds with subjective probabilities, appreciating what infinite domains and random-world semantics brings to the table is of utmost theoretical import.

We resolve difficulties in training and sampling from a discrete generative model by learning a smoothed energy function, sampling from the smoothed data manifold with Langevin Markov chain Monte Carlo (MCMC), and projecting back to the true data manifold with one-step denoising. Our Discrete Walk-Jump Sampling formalism combines the maximum likelihood training of an energy-based model and improved sample quality of a score-based model, while simplifying training and sampling by requiring only a single noise level. We evaluate the robustness of our approach on generative modeling of antibody proteins and introduce the distributional conformity score to benchmark protein generative models. By optimizing and sampling from our models for the proposed distributional conformity score, 97-100% of generated samples are successfully expressed and purified and 35% of functional designs show equal or improved binding affinity compared to known functional antibodies on the first attempt in a single round of laboratory experiments. We also report the first demonstration of long-run fast-mixing MCMC chains where diverse antibody protein classes are visited in a single MCMC chain.

Over-generalization is a thorny issue in cognitive science, where people may become overly cautious due to past experiences. Agents in multi-agent reinforcement learning (MARL) also have been found to suffer relative over-generalization (RO) as people do and stuck to sub-optimal cooperation. Recent methods have shown that assigning reasoning ability to agents can mitigate RO algorithmically and empirically, but there has been a lack of theoretical understanding of RO, let alone designing provably RO-free methods. This paper first proves that RO can be avoided when the MARL method satisfies a consistent reasoning requirement under certain conditions. Then we introduce a novel reasoning framework, called negotiated reasoning, that first builds the connection between reasoning and RO with theoretical justifications. After that, we propose an instantiated algorithm, Stein variational negotiated reasoning (SVNR), which uses Stein variational gradient descent to derive a negotiation policy that provably avoids RO in MARL under maximum entropy policy iteration. The method is further parameterized with neural networks for amortized learning, making computation efficient. Numerical experiments on many RO-challenged environments demonstrate the superiority and efficiency of SVNR compared to state-of-the-art methods in addressing RO.

Efficiently sampling from un-normalized target distributions is a fundamental problem in scientific computing and machine learning. Traditional approaches like Markov Chain Monte Carlo (MCMC) guarantee asymptotically unbiased samples from such distributions but suffer from computational inefficiency, particularly when dealing with high-dimensional targets, as they require numerous iterations to generate a batch of samples. In this paper, we propose an efficient and scalable neural implicit sampler that overcomes these limitations. Our sampler can generate large batches of samples with low computational costs by leveraging a neural transformation that directly maps easily sampled latent vectors to target samples without the need for iterative procedures. To train the neural implicit sampler, we introduce two novel methods: the KL training method and the Fisher training method. The former minimizes the Kullback-Leibler divergence, while the latter minimizes the Fisher divergence. By employing these training methods, we effectively optimize the neural implicit sampler to capture the desired target distribution. To demonstrate the effectiveness, efficiency, and scalability of our proposed samplers, we evaluate them on three sampling benchmarks with different scales. These benchmarks include sampling from 2D targets, Bayesian inference, and sampling from high-dimensional energy-based models (EBMs). Notably, in the experiment involving high-dimensional EBMs, our sampler produces samples that are comparable to those generated by MCMC-based methods while being more than 100 times more efficient, showcasing the efficiency of our neural sampler. We believe that the theoretical and empirical contributions presented in this work will stimulate further research on developing efficient samplers for various applications beyond the ones explored in this study.

The Origin-Destination~(OD) networks provide an estimation of the flow of people from every region to others in the city, which is an important research topic in transportation, urban simulation, etc. Given structural regional urban features, generating the OD network has become increasingly appealing to many researchers from diverse domains. However, existing works are limited in independent generation of each OD pair, i.e., flow of people from one region to another, overlooking the relations within the overall network. In this paper, we instead propose to generate the OD network, and design a graph denoising diffusion method to learn the conditional joint probability distribution of the nodes and edges within the OD network given city characteristics at region level. To overcome the learning difficulty of the OD networks covering over thousands of regions, we decompose the original one-shot generative modeling of the diffusion model into two cascaded stages, corresponding to the generation of network topology and the weights of edges, respectively. To further reproduce important network properties contained in the city-wide OD network, we design an elaborated graph denoising network structure including a node property augmentation module and a graph transformer backbone. Empirical experiments on data collected in three large US cities have verified that our method can generate OD matrices for new cities with network statistics remarkably similar with the ground truth, further achieving superior outperformance over competitive baselines in terms of the generation realism.

Large language models generate fluent texts and can follow natural language instructions to solve a wide range of tasks without task-specific training. Nevertheless, it is notoriously difficult to control their generation to satisfy the various constraints required by different applications. In this work, we present InstructCTG, a controlled text generation framework that incorporates different constraints by conditioning on natural language descriptions and demonstrations of the constraints. In particular, we first extract the underlying constraints of natural texts through a combination of off-the-shelf NLP tools and simple heuristics. We then verbalize the constraints into natural language instructions to form weakly supervised training data. By prepending natural language descriptions of the constraints and a few demonstrations, we fine-tune a pre-trained language model to incorporate various types of constraints. Compared to existing search-based or score-based methods, InstructCTG is more flexible to different constraint types and has a much smaller impact on the generation quality and speed because it does not modify the decoding procedure. Additionally, InstructCTG allows the model to adapt to new constraints without re-training through the use of few-shot task generalization and in-context learning abilities of instruction-tuned language models.

We study the causal bandit problem when the causal graph is unknown and develop an efficient algorithm for finding the parent node of the reward node using atomic interventions. We derive the exact equation for the expected number of interventions performed by the algorithm and show that under certain graphical conditions it could perform either logarithmically fast or, under more general assumptions, slower but still sublinearly in the number of variables. We formally show that our algorithm is optimal as it meets the universal lower bound we establish for any algorithm that performs atomic interventions. Finally, we extend our algorithm to the case when the reward node has multiple parents. Using this algorithm together with a standard algorithm from bandit literature leads to improved regret bounds.

We consider the problem of estimating (diagonally dominant) M-matrices as precision matrices in Gaussian graphical models. These models exhibit intriguing properties, such as the existence of the maximum likelihood estimator with merely two observations for M-matrices \citep{lauritzen2019maximum,slawski2015estimation} and even one observation for diagonally dominant M-matrices \citep{truell2021maximum}. We propose an adaptive multiple-stage estimation method that refines the estimate by solving a weighted $\ell_1$-regularized problem at each stage. Furthermore, we develop a unified framework based on the gradient projection method to solve the regularized problem, incorporating distinct projections to handle the constraints of M-matrices and diagonally dominant M-matrices. A theoretical analysis of the estimation error is provided. Our method outperforms state-of-the-art methods in precision matrix estimation and graph edge identification, as evidenced by synthetic and financial time-series data sets.

Normalizing flows (NF) are a class of powerful generative models that have gained popularity in recent years due to their ability to model complex distributions with high flexibility and expressiveness. In this work, we introduce a new type of normalizing flow that is tailored for modeling positions and orientations of multiple objects in three-dimensional space, such as molecules in a crystal. Our approach is based on two key ideas: first, we define smooth and expressive flows on the group of unit quaternions, which allows us to capture the continuous rotational motion of rigid bodies; second, we use the double cover property of unit quaternions to define a proper density on the rotation group. This ensures that our model can be trained using standard likelihood-based methods or variational inference with respect to a thermodynamic target density. We evaluate the method by training Boltzmann generators for two molecular examples, namely the multi-modal density of a tetrahedral system in an external field and the ice XI phase in the TIP4P water model. Our flows can be combined with flows operating on the internal degrees of freedom of molecules and constitute an important step towards the modeling of distributions of many interacting molecules.