Determining the most informative features for predicting the overall survival of patients diagnosed with high-grade gastroenteropancreatic neuroendocrine neoplasms is crucial to improve individual treatment plans for patients, as well as the biological understanding of the disease. Recently developed ensemble feature selectors like the Repeated Elastic Net Technique for Feature Selection (RENT) and the User-Guided Bayesian Framework for Feature Selection (UBayFS) allow the user to identify such features in datasets with low sample sizes. While RENT is purely data-driven, UBayFS is capable of integrating expert knowledge a priori in the feature selection process. In this work we compare both feature selectors on a dataset comprising of 63 patients and 134 features from multiple sources, including basic patient characteristics, baseline blood values, tumor histology, imaging, and treatment information. Our experiments involve data-driven and expert-driven setups, as well as combinations of both. We use findings from clinical literature as a source of expert knowledge. Our results demonstrate that both feature selectors allow accurate predictions, and that expert knowledge has a stabilizing effect on the feature set, while the impact on predictive performance is limited. The features WHO Performance Status, Albumin, Platelets, Ki-67, Tumor Morphology, Total MTV, Total TLG, and SUVmax are the most stable and predictive features in our study.

The d-separation criterion detects the compatibility of a joint probability distribution with a directed acyclic graph through certain conditional independences. In this work, we study this problem in the context of categorical probability theory by introducing a categorical definition of causal models, a categorical notion of d-separation, and proving an abstract version of the d-separation criterion. This approach has two main benefits. First, categorical d-separation is a very intuitive criterion based on topological connectedness. Second, our results apply both to measure-theoretic probability (with standard Borel spaces) and beyond probability theory, including to deterministic and possibilistic networks. It therefore provides a clean proof of the equivalence of local and global Markov properties with causal compatibility for continuous and mixed random variables as well as deterministic and possibilistic variables.

Neuroscientific studies aim to find an accurate and reliable brain Effective Connectome (EC). Although current EC discovery methods have contributed to our understanding of brain organization, their performances are severely constrained by the short sample size and poor temporal resolution of fMRI data, and high dimensionality of the brain connectome. By leveraging the DTI data as prior knowledge, we introduce two Bayesian causal discovery frameworks -- the Bayesian GOLEM (BGOLEM) and Bayesian FGES (BFGES) methods -- that offer significantly more accurate and reliable ECs and address the shortcomings of the existing causal discovery methods in discovering ECs based on only fMRI data. Through a series of simulation studies on synthetic and hybrid (DTI of the Human Connectome Project (HCP) subjects and synthetic fMRI) data, we demonstrate the effectiveness of the proposed methods in discovering EC. To numerically assess the improvement in the accuracy of ECs with our method on empirical data, we first introduce the Pseudo False Discovery Rate (PFDR) as a new computational accuracy metric for causal discovery in the brain. We show that our Bayesian methods achieve higher accuracy than traditional methods on HCP data. Additionally, we measure the reliability of discovered ECs using the Rogers-Tanimoto index for test-retest data and show that our Bayesian methods provide significantly more reproducible ECs than traditional methods. Overall, our study's numerical and graphical results highlight the potential for these frameworks to advance our understanding of brain function and organization significantly.

We consider the general problem of recovering a high-dimensional signal from noisy quantized measurements. Quantization, especially coarse quantization such as 1-bit sign measurements, leads to severe information loss and thus a good prior knowledge of the unknown signal is helpful for accurate recovery. Motivated by the power of score-based generative models (SGM, also known as diffusion models) in capturing the rich structure of natural signals beyond simple sparsity, we propose an unsupervised data-driven approach called quantized compressed sensing with SGM (QCS-SGM), where the prior distribution is modeled by a pre-trained SGM. To perform posterior sampling, an annealed pseudo-likelihood score called noise perturbed pseudo-likelihood score is introduced and combined with the prior score of SGM. The proposed QCS-SGM applies to an arbitrary number of quantization bits. Experiments on a variety of baseline datasets demonstrate that the proposed QCS-SGM significantly outperforms existing state-of-the-art algorithms by a large margin for both in-distribution and out-of-distribution samples. Moreover, as a posterior sampling method, QCS-SGM can be easily used to obtain confidence intervals or uncertainty estimates of the reconstructed results. The code is available at https://github.com/mengxiangming/QCS-SGM.

While diffusion models have achieved great success in generating continuous signals such as images and audio, it remains elusive for diffusion models in learning discrete sequence data like natural languages. Although recent advances circumvent this challenge of discreteness by embedding discrete tokens as continuous surrogates, they still fall short of satisfactory generation quality. To understand this, we first dive deep into the denoised training protocol of diffusion-based sequence generative models and determine their three severe problems, i.e., 1) failing to learn, 2) lack of scalability, and 3) neglecting source conditions. We argue that these problems can be boiled down to the pitfall of the not completely eliminated discreteness in the embedding space, and the scale of noises is decisive herein. In this paper, we introduce DINOISER to facilitate diffusion models for sequence generation by manipulating noises. We propose to adaptively determine the range of sampled noise scales for counter-discreteness training; and encourage the proposed diffused sequence learner to leverage source conditions with amplified noise scales during inference. Experiments show that DINOISER enables consistent improvement over the baselines of previous diffusion-based sequence generative models on several conditional sequence modeling benchmarks thanks to both effective training and inference strategies. Analyses further verify that DINOISER can make better use of source conditions to govern its generative process.

We investigate the benefit of treating all the parameters in a Bayesian neural network stochastically and find compelling theoretical and empirical evidence that this standard construction may be unnecessary. To this end, we prove that expressive predictive distributions require only small amounts of stochasticity. In particular, partially stochastic networks with only $n$ stochastic biases are universal probabilistic predictors for $n$-dimensional predictive problems. In empirical investigations, we find no systematic benefit of full stochasticity across four different inference modalities and eight datasets; partially stochastic networks can match and sometimes even outperform fully stochastic networks, despite their reduced memory costs.

This paper develops a model-free sequential test for conditional independence. The proposed test allows researchers to analyze an incoming i.i.d. data stream with any arbitrary dependency structure, and safely conclude whether a feature is conditionally associated with the response under study. We allow the processing of data points online, as soon as they arrive, and stop data acquisition once significant results are detected, rigorously controlling the type-I error rate. Our test can work with any sophisticated machine learning algorithm to enhance data efficiency to the extent possible. The developed method is inspired by two statistical frameworks. The first is the model-X conditional randomization test, a test for conditional independence that is valid in offline settings where the sample size is fixed in advance. The second is testing by betting, a ``game-theoretic'' approach for sequential hypothesis testing. We conduct synthetic experiments to demonstrate the advantage of our test over out-of-the-box sequential tests that account for the multiplicity of tests in the time horizon, and demonstrate the practicality of our proposal by applying it to real-world tasks.

While machine learning models rapidly advance the state-of-the-art on various real-world tasks, out-of-domain (OOD) generalization remains a challenging problem given the vulnerability of these models to spurious correlations. We propose a balanced mini-batch sampling strategy to transform a biased data distribution into a spurious-free balanced distribution, based on the invariance of the underlying causal mechanisms for the data generation process. We argue that the Bayes optimal classifiers trained on such balanced distribution are minimax optimal across a diverse enough environment space. We also provide an identifiability guarantee of the latent variable model of the proposed data generation process, when utilizing enough train environments. Experiments are conducted on DomainBed, demonstrating empirically that our method obtains the best performance across 20 baselines reported on the benchmark.

Learning with noisy labels has become imperative in the Big Data era, which saves expensive human labors on accurate annotations. Previous noise-transition-based methods have achieved theoretically-grounded performance under the Class-Conditional Noise model (CCN). However, these approaches builds upon an ideal but impractical anchor set available to pre-estimate the noise transition. Even though subsequent works adapt the estimation as a neural layer, the ill-posed stochastic learning of its parameters in back-propagation easily falls into undesired local minimums. We solve this problem by introducing a Latent Class-Conditional Noise model (LCCN) to parameterize the noise transition under a Bayesian framework. By projecting the noise transition into the Dirichlet space, the learning is constrained on a simplex characterized by the complete dataset, instead of some ad-hoc parametric space wrapped by the neural layer. We then deduce a dynamic label regression method for LCCN, whose Gibbs sampler allows us efficiently infer the latent true labels to train the classifier and to model the noise. Our approach safeguards the stable update of the noise transition, which avoids previous arbitrarily tuning from a mini-batch of samples. We further generalize LCCN to different counterparts compatible with open-set noisy labels, semi-supervised learning as well as cross-model training. A range of experiments demonstrate the advantages of LCCN and its variants over the current state-of-the-art methods.

Unsupervised meta-learning aims to learn the meta knowledge from unlabeled data and rapidly adapt to novel tasks. However, existing approaches may be misled by the context-bias (e.g. background) from the training data. In this paper, we abstract the unsupervised meta-learning problem into a Structural Causal Model (SCM) and point out that such bias arises due to hidden confounders. To eliminate the confounders, we define the priors are \textit{conditionally} independent, learn the relationships between priors and intervene on them with casual factorization. Furthermore, we propose Causal Meta VAE (CMVAE) that encodes the priors into latent codes in the causal space and learns their relationships simultaneously to achieve the downstream few-shot image classification task. Results on toy datasets and three benchmark datasets demonstrate that our method can remove the context-bias and it outperforms other state-of-the-art unsupervised meta-learning algorithms because of bias-removal. Code is available at \url{https://github.com/GuodongQi/CMVAE}