Conditional language models are predominantly trained with maximum likelihood estimation (MLE), giving probability mass to sparsely observed target sequences. While MLE trained models assign high probability to plausible sequences given the context, the model probabilities often do not accurately rank-order generated sequences by quality. This has been empirically observed in beam search decoding as output quality degrading with large beam sizes, and decoding strategies benefiting from heuristics such as length normalization and repetition-blocking. In this work, we introduce sequence likelihood calibration (SLiC) where the likelihood of model generated sequences are calibrated to better align with reference sequences in the model's latent space. With SLiC, decoding heuristics become unnecessary and decoding candidates' quality significantly improves regardless of the decoding method. Furthermore, SLiC shows no sign of diminishing returns with model scale, and presents alternative ways to improve quality with limited training and inference budgets. With SLiC, we exceed or match SOTA results on a wide range of generation tasks spanning abstractive summarization, question generation, abstractive question answering and data-to-text generation, even with modest-sized models.

Building models of human decision-making from observed behaviour is critical to better understand, diagnose and support real-world policies such as clinical care. As established policy learning approaches remain focused on imitation performance, they fall short of explaining the demonstrated decision-making process. Policy Extraction through decision Trees (POETREE) is a novel framework for interpretable policy learning, compatible with fully-offline and partially-observable clinical decision environments -- and builds probabilistic tree policies determining physician actions based on patients' observations and medical history. Fully-differentiable tree architectures are grown incrementally during optimization to adapt their complexity to the modelling task, and learn a representation of patient history through recurrence, resulting in decision tree policies that adapt over time with patient information. This policy learning method outperforms the state-of-the-art on real and synthetic medical datasets, both in terms of understanding, quantifying and evaluating observed behaviour as well as in accurately replicating it -- with potential to improve future decision support systems.

To discover new drugs is to seek and to prove causality. As an emerging approach leveraging human knowledge and creativity, data, and machine intelligence, causal inference holds the promise of reducing cognitive bias and improving decision making in drug discovery. While it has been applied across the value chain, the concepts and practice of causal inference remain obscure to many practitioners. This article offers a non-technical introduction to causal inference, reviews its recent applications, and discusses opportunities and challenges of adopting the causal language in drug discovery and development.

Sparse inversion and classification problems are ubiquitous in modern data science and imaging. They are often formulated as non-smooth minimisation problems. In sparse inversion, we minimise, e.g., the sum of a data fidelity term and an L1/LASSO regulariser. In classification, we consider, e.g., the sum of a data fidelity term and a non-smooth Ginzburg--Landau energy. Standard (sub)gradient descent methods have shown to be inefficient when approaching such problems. Splitting techniques are much more useful: here, the target function is partitioned into a sum of two subtarget functions -- each of which can be efficiently optimised. Splitting proceeds by performing optimisation steps alternately with respect to each of the two subtarget functions. In this work, we study splitting from a stochastic continuous-time perspective. Indeed, we define a differential inclusion that follows one of the two subtarget function's negative subdifferential at each point in time. The choice of the subtarget function is controlled by a binary continuous-time Markov process. The resulting dynamical system is a stochastic approximation of the underlying subgradient flow. We investigate this stochastic approximation for an L1-regularised sparse inversion flow and for a discrete Allen-Cahn equation minimising a Ginzburg--Landau energy. In both cases, we study the longtime behaviour of the stochastic dynamical system and its ability to approximate the underlying subgradient flow at any accuracy. We illustrate our theoretical findings in a simple sparse estimation problem and also in low- and high-dimensional classification problems.

In drug discovery, aqueous solubility is an important pharmacokinetic property which affects absorption and assay availability of drug. Thus, in silico prediction of solubility has been studied for its utility in virtual screening and lead optimization. Recently, machine learning (ML) methods using experimental data has been popular because physics-based methods like quantum mechanics and molecular dynamics are not suitable for high-throughput tasks due to its computational costs. However, ML method can exhibit over-fitting problem in a data-deficient condition, and this is the case for most chemical property datasets. In addition, ML methods are regarded as a black box function in that it is difficult to interpret contribution of hidden features to outputs, hindering analysis and modification of structure-activity relationship. To deal with mentioned issues, we developed Bayesian graph neural networks (GNNs) with the self-attention readout layer. Unlike most GNNs using self-attention in node updates, self-attention applied at readout layer enabled a model to improve prediction performance as well as to identify atom-wise importance, which can help lead optimization as exemplified for three FDA-approved drugs. Also, Bayesian inference enables us to separate more or less accurate results according to uncertainty in solubility prediction task We expect that our accurate, reliable and interpretable model can be used for more careful decision-making and various applications in the development of drugs.

Driven by the critical needs of biomanufacturing 4.0, we introduce a probabilistic knowledge graph hybrid model characterizing the risk- and science-based understanding of bioprocess mechanisms. It can faithfully capture the important properties, including nonlinear reactions, partially observed state, and nonstationary dynamics. Given very limited real process observations, we derive a posterior distribution quantifying model estimation uncertainty. To avoid the evaluation of intractable likelihoods, Approximate Bayesian Computation sampling with Sequential Monte Carlo (ABC-SMC) is utilized to approximate the posterior distribution. Under high stochastic and model uncertainties, it is computationally expensive to match output trajectories. Therefore, we create a linear Gaussian dynamic Bayesian network (LG-DBN) auxiliary likelihood-based ABC-SMC approach. Through matching the summary statistics driven through LG-DBN likelihood that can capture critical interactions and variations, the proposed algorithm can accelerate hybrid model inference, support process monitoring, and facilitate mechanism learning and robust control.

This paper is concerned with forecast error, particularly in relation to loss reserving. This is generally regarded as consisting of three components, namely parameter, process and model errors. The first two of these components, and their estimation, are well understood, but less so model error. Model error itself is considered in two parts: one part that is capable of estimation from past data (internal model error), and another part that is not (external model error). Attention is focused here on internal model error. Estimation of this error component is approached by means of Bayesian model averaging, using the Bayesian interpretation of the LASSO. This is used to generate a set of admissible models, each with its prior probability and the likelihood of observed data. A posterior on the model set, conditional on the data, results, and an estimate of model error (contained in a loss reserve) is obtained as the variance of the loss reserve according to this posterior. The population of models entering materially into the support of the posterior may turn out to be thinner than desired, and bootstrapping of the LASSO is used to gain bulk. This provides the bonus of an estimate of parameter error also. It turns out that the estimates of parameter and model errors are entangled, and dissociation of them is at least difficult, and possibly not even meaningful. These matters are discussed. The majority of the discussion applies to forecasting generally, but numerical illustration of the concepts is given in relation to insurance data and the problem of insurance loss reserving.

Learning causal structure from observational data is a fundamental challenge in machine learning. However, the majority of commonly used differentiable causal discovery methods are non-identifiable, turning this problem into a continuous optimization task prone to data biases. In many real-life situations, data is collected from different environments, in which the functional relations remain consistent across environments, while the distribution of additive noises may vary. This paper proposes Differentiable Invariant Causal Discovery (DICD), utilizing the multi-environment information based on a differentiable framework to avoid learning spurious edges and wrong causal directions. Specifically, DICD aims to discover the environment-invariant causation while removing the environment-dependent correlation. We further formulate the constraint that enforces the target structure equation model to maintain optimal across the environments. Theoretical guarantees for the identifiability of proposed DICD are provided under mild conditions with enough environments. Extensive experiments on synthetic and real-world datasets verify that DICD outperforms state-of-the-art causal discovery methods up to 36% in SHD. Our code will be open-sourced.

This research presents an examination of categorizing the severity states of patients based on their electronic health records during a certain time range using multiple machine learning and deep learning approaches. The suggested method uses an EHR dataset collected from an open-source platform to categorize severity. Some tools were used in this research, such as openRefine was used to pre-process, RapidMiner was used for implementing three algorithms (Fast Large Margin, Generalized Linear Model, Multi-layer Feed-forward Neural Network) and Tableau was used to visualize the data, for implementation of algorithms we used Google Colab. Here we implemented several supervised and unsupervised algorithms along with semi-supervised and deep learning algorithms. The experimental results reveal that hyperparameter-tuned Random Forest outperformed all the other supervised machine learning algorithms with 76% accuracy as well as Generalized Linear algorithm achieved the highest precision score 78%, whereas the hyperparameter-tuned Hierarchical Clustering with 86% precision score and Gaussian Mixture Model with 61% accuracy outperformed other unsupervised approaches. Dimensionality Reduction improved results a lot for most unsupervised techniques. For implementing Deep Learning we employed a feed-forward neural network (multi-layer) and the Fast Large Margin approach for semi-supervised learning. The Fast Large Margin performed really well with a recall score of 84% and an F1 score of 78%. Finally, the Multi-layer Feed-forward Neural Network performed admirably with 75% accuracy, 75% precision, 87% recall, 81% F1 score.

In this paper we present a world model, which learns causal features using the invariance principle. In particular, we use contrastive unsupervised learning to learn the invariant causal features, which enforces invariance across augmentations of irrelevant parts or styles of the observation. The world-model-based reinforcement learning methods independently optimize representation learning and the policy. Thus naive contrastive loss implementation collapses due to a lack of supervisory signals to the representation learning module. We propose an intervention invariant auxiliary task to mitigate this issue. Specifically, we utilize depth prediction to explicitly enforce the invariance and use data augmentation as style intervention on the RGB observation space. Our design leverages unsupervised representation learning to learn the world model with invariant causal features. Our proposed method significantly outperforms current state-of-the-art model-based and model-free reinforcement learning methods on out-of-distribution point navigation tasks on the iGibson dataset. Moreover, our proposed model excels at the sim-to-real transfer of our perception learning module. Finally, we evaluate our approach on the DeepMind control suite and enforce invariance only implicitly since depth is not available. Nevertheless, our proposed model performs on par with the state-of-the-art counterpart.