We propose a Bayesian approach for both medical inquiry and disease inference, the two major phases in differential diagnosis. Unlike previous work that simulates data from given probabilities and uses ML algorithms on them, we directly use the Quick Medical Reference (QMR) belief network, and apply Bayesian inference in the inference phase and Bayesian experimental design in the inquiry phase. Moreover, we improve the inquiry phase by extending the Bayesian experimental design framework from one-step search to multi-step search. Our approach has some practical advantages as it is interpretable, free of costly training, and able to adapt to new changes without any additional effort. Our experiments show that our approach achieves new state-of-the-art results on two simulated datasets, SymCAT and HPO, and competitive results on two diagnosis dialogue datasets, Muzhi and Dxy.

The growth of machine learning as a field has been accelerating with increasing interest and publications across fields, including statistics, but predominantly in computer science. How can we parse this vast literature for developments that exemplify the necessary rigor? How many of these manuscripts incorporate foundational theory to allow for statistical inference? Which advances have the greatest potential for impact in practice? One could posit many answers to these queries. Here, we assert that one essential idea is for machine learning to integrate maximum likelihood for estimation of functional parameters, such as prediction functions and conditional densities.

Recent studies have empirically investigated different methods to train a stochastic classifier by optimising a PAC-Bayesian bound via stochastic gradient descent. Most of these procedures need to replace the misclassification error with a surrogate loss, leading to a mismatch between the optimisation objective and the actual generalisation bound. The present paper proposes a novel training algorithm that optimises the PAC-Bayesian bound, without relying on any surrogate loss. Empirical results show that the bounds obtained with this approach are tighter than those found in the literature.

In vitro cellular experimentation with genetic interventions, using for example CRISPR technologies, is an essential step in early-stage drug discovery and target validation that serves to assess initial hypotheses about causal associations between biological mechanisms and disease pathologies. With billions of potential hypotheses to test, the experimental design space for in vitro genetic experiments is extremely vast, and the available experimental capacity - even at the largest research institutions in the world - pales in relation to the size of this biological hypothesis space. Machine learning methods, such as active and reinforcement learning, could aid in optimally exploring the vast biological space by integrating prior knowledge from various information sources as well as extrapolating to yet unexplored areas of the experimental design space based on available data. However, there exist no standardised benchmarks and data sets for this challenging task and little research has been conducted in this area to date. Here, we introduce GeneDisco, a benchmark suite for evaluating active learning algorithms for experimental design in drug discovery. GeneDisco contains a curated set of multiple publicly available experimental data sets as well as open-source implementations of state-of-the-art active learning policies for experimental design and exploration.

The recursive and hierarchical structure of full rooted trees is applicable to represent statistical models in various areas, such as data compression, image processing, and machine learning. In most of these cases, the full rooted tree is not a random variable; as such, model selection to avoid overfitting becomes problematic. A method to solve this problem is to assume a prior distribution on the full rooted trees. This enables overfitting to be avoided based on the Bayes decision theory. For example, by assigning a low prior probability to a complex model, the maximum a posteriori estimator prevents overfitting. Furthermore, overfitting can be avoided by averaging all the models weighted by their posteriors. In this paper, we propose a probability distribution on a set of full rooted trees. Its parametric representation is suitable for calculating the properties of our distribution using recursive functions, such as the mode, expectation, and posterior distribution. Although such distributions have been proposed in previous studies, they are only applicable to specific applications. Therefore, we extract their mathematically essential components and derive new generalized methods to calculate the expectation, posterior distribution, etc.

Out-of-distribution (OOD) detection is critical to ensuring the reliability and safety of machine learning systems. For instance, in autonomous driving, we would like the driving system to issue an alert and hand over the control to humans when it detects unusual scenes or objects that it has never seen before and cannot make a safe decision. This problem first emerged in 2017 and since then has received increasing attention from the research community, leading to a plethora of methods developed, ranging from classification-based to density-based to distance-based ones. Meanwhile, several other problems are closely related to OOD detection in terms of motivation and methodology. These include anomaly detection (AD), novelty detection (ND), open set recognition (OSR), and outlier detection (OD). Despite having different definitions and problem settings, these problems often confuse readers and practitioners, and as a result, some existing studies misuse terms. In this survey, we first present a generic framework called generalized OOD detection, which encompasses the five aforementioned problems, i.e., AD, ND, OSR, OOD detection, and OD. Under our framework, these five problems can be seen as special cases or sub-tasks, and are easier to distinguish. Then, we conduct a thorough review of each of the five areas by summarizing their recent technical developments. We conclude this survey with open challenges and potential research directions.

We study adaptive sensing of Cox point processes, a widely used model from spatial statistics. We introduce three tasks: maximization of captured events, search for the maximum of the intensity function and learning level sets of the intensity function. We model the intensity function as a sample from a truncated Gaussian process, represented in a specially constructed positive basis. In this basis, the positivity constraint on the intensity function has a simple form. We show how an minimal description positive basis can be adapted to the covariance kernel, non-stationarity and make connections to common positive bases from prior works. Our adaptive sensing algorithms use Langevin dynamics and are based on posterior sampling (\textsc{Cox-Thompson}) and top-two posterior sampling (\textsc{Top2}) principles. With latter, the difference between samples serves as a surrogate to the uncertainty. We demonstrate the approach using examples from environmental monitoring and crime rate modeling, and compare it to the classical Bayesian experimental design approach.

Computational level explanations based on optimal feedback control with signal-dependent noise have been able to account for a vast array of phenomena in human sensorimotor behavior. However, commonly a cost function needs to be assumed for a task and the optimality of human behavior is evaluated by comparing observed and predicted trajectories. Here, we introduce inverse optimal control with signal-dependent noise, which allows inferring the cost function from observed behavior. To do so, we formalize the problem as a partially observable Markov decision process and distinguish between the agent's and the experimenter's inference problems. Specifically, we derive a probabilistic formulation of the evolution of states and belief states and an approximation to the propagation equation in the linear-quadratic Gaussian problem with signal-dependent noise. We extend the model to the case of partial observability of state variables from the point of view of the experimenter. We show the feasibility of the approach through validation on synthetic data and application to experimental data. Our approach enables recovering the costs and benefits implicit in human sequential sensorimotor behavior, thereby reconciling normative and descriptive approaches in a computational framework.

The recent phenomenal success of language models has reinvigorated machine learning research, and large sequence models such as transformers are being applied to a variety of domains. One important problem class that has remained relatively elusive however is purposeful adaptive behavior. Currently there is a common perception that sequence models "lack the understanding of the cause and effect of their actions" leading them to draw incorrect inferences due to auto-suggestive delusions. In this report we explain where this mismatch originates, and show that it can be resolved by treating actions as causal interventions. Finally, we show that in supervised learning, one can teach a system to condition or intervene on data by training with factual and counterfactual error signals respectively.

A wide variety of methods have been developed to enable lifelong learning in conventional deep neural networks. However, to succeed, these methods require a `batch' of samples to be available and visited multiple times during training. While this works well in a static setting, these methods continue to suffer in a more realistic situation where data arrives in \emph{online streaming manner}. We empirically demonstrate that the performance of current approaches degrades if the input is obtained as a stream of data with the following restrictions: $(i)$ each instance comes one at a time and can be seen only once, and $(ii)$ the input data violates the i.i.d assumption, i.e., there can be a class-based correlation. We propose a novel approach (CIOSL) for the class-incremental learning in an \emph{online streaming setting} to address these challenges. The proposed approach leverages implicit and explicit dual weight regularization and experience replay. The implicit regularization is leveraged via the knowledge distillation, while the explicit regularization incorporates a novel approach for parameter regularization by learning the joint distribution of the buffer replay and the current sample. Also, we propose an efficient online memory replay and replacement buffer strategy that significantly boosts the model's performance. Extensive experiments and ablation on challenging datasets show the efficacy of the proposed method.