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In drug discovery, it is vital to confirm the predictions of pharmaceutical properties from computational models using costly wet-lab experiments. Hence, obtaining reliable uncertainty estimates is crucial for prioritizing drug molecules for subsequent experimental validation. Conformal Prediction (CP) is a promising tool for creating such prediction sets for molecular properties with a coverage guarantee. However, the exchangeability assumption of CP is often challenged with covariate shift in drug discovery tasks: Most datasets contain limited labeled data, which may not be representative of the vast chemical space from which molecules are drawn. To address this limitation, we propose a method called CoDrug that employs an energy-based model leveraging both training data and unlabelled data, and Kernel Density Estimation (KDE) to assess the densities of a molecule set. The estimated densities are then used to weigh the molecule samples while building prediction sets and rectifying for distribution shift. In extensive experiments involving realistic distribution drifts in various small-molecule drug discovery tasks, we demonstrate the ability of CoDrug to provide valid prediction sets and its utility in addressing the distribution shift arising from de novo drug design models. On average, using CoDrug can reduce the coverage gap by over 35% when compared to conformal prediction sets not adjusted for covariate shift.

Medical image fusion combines the complementary information of multimodal medical images to assist medical professionals in the clinical diagnosis of patients' disorders and provide guidance during preoperative and intra-operative procedures. Deep learning (DL) models have achieved end-to-end image fusion with highly robust and accurate fusion performance. However, most DL-based fusion models perform down-sampling on the input images to minimize the number of learnable parameters and computations. During this process, salient features of the source images become irretrievable leading to the loss of crucial diagnostic edge details and contrast of various brain tissues. In this paper, we propose a new multimodal medical image fusion model is proposed that is based on integrated Laplacian-Gaussian concatenation with attention pooling (LGCA). We prove that our model preserves effectively complementary information and important tissue structures.

Solving ill-posed inverse problems requires careful formulation of prior beliefs over the signals of interest and an accurate description of their manifestation into noisy measurements. Handcrafted signal priors based on e.g. sparsity are increasingly replaced by data-driven deep generative models, and several groups have recently shown that state-of-the-art score-based diffusion models yield particularly strong performance and flexibility. In this paper, we show that the powerful paradigm of posterior sampling with diffusion models can be extended to include rich, structured, noise models. To that end, we propose a joint conditional reverse diffusion process with learned scores for the noise and signal-generating distribution. We demonstrate strong performance gains across various inverse problems with structured noise, outperforming competitive baselines that use normalizing flows and adversarial networks. This opens up new opportunities and relevant practical applications of diffusion modeling for inverse problems in the context of non-Gaussian measurement models.

Estimating treatment effects over time is relevant in many real-world applications, such as precision medicine, epidemiology, economy, and marketing. Many state-of-the-art methods either assume the observations of all confounders or seek to infer the unobserved ones. We take a different perspective by assuming unobserved risk factors, i.e., adjustment variables that affect only the sequence of outcomes. Under unconfoundedness, we target the Individual Treatment Effect (ITE) estimation with unobserved heterogeneity in the treatment response due to missing risk factors. We address the challenges posed by time-varying effects and unobserved adjustment variables. Led by theoretical results over the validity of the learned adjustment variables and generalization bounds over the treatment effect, we devise Causal DVAE (CDVAE). This model combines a Dynamic Variational Autoencoder (DVAE) framework with a weighting strategy using propensity scores to estimate counterfactual responses. The CDVAE model allows for accurate estimation of ITE and captures the underlying heterogeneity in longitudinal data. Evaluations of our model show superior performance over state-of-the-art models.

Longitudinal analysis in medical imaging is crucial to investigate the progressive changes in anatomical structures or disease progression over time. In recent years, a novel class of algorithms has emerged with the goal of learning disease progression in a self-supervised manner, using either pairs of consecutive images or time series of images. By capturing temporal patterns without external labels or supervision, longitudinal self-supervised learning (LSSL) has become a promising avenue. To better understand this core method, we explore in this paper the LSSL algorithm under different scenarios. The original LSSL is embedded in an auto-encoder (AE) structure. However, conventional self-supervised strategies are usually implemented in a Siamese-like manner. Therefore, (as a first novelty) in this study, we explore the use of Siamese-like LSSL. Another new core framework named neural ordinary differential equation (NODE). NODE is a neural network architecture that learns the dynamics of ordinary differential equations (ODE) through the use of neural networks. Many temporal systems can be described by ODE, including modeling disease progression. We believe that there is an interesting connection to make between LSSL and NODE. This paper aims at providing a better understanding of those core algorithms for learning the disease progression with the mentioned change. In our different experiments, we employ a longitudinal dataset, named OPHDIAT, targeting diabetic retinopathy (DR) follow-up. Our results demonstrate the application of LSSL without including a reconstruction term, as well as the potential of incorporating NODE in conjunction with LSSL.

There is a wide availability of methods for testing normality under the assumption of independent and identically distributed data. When data are dependent in space and/or time, however, assessing and testing the marginal behavior is considerably more challenging, as the marginal behavior is impacted by the degree of dependence. We propose a new approach to assess normality for dependent data by non-linearly incorporating existing statistics from normality tests as well as sample moments such as skewness and kurtosis through a neural network. We calibrate (deep) neural networks by simulated normal and non-normal data with a wide range of dependence structures and we determine the probability of rejecting the null hypothesis. We compare several approaches for normality tests and demonstrate the superiority of our method in terms of statistical power through an extensive simulation study. A real world application to global temperature data further demonstrates how the degree of spatio-temporal aggregation affects the marginal normality in the data.

With increasing interest in adaptive clinical trial designs, challenges are present to drug supply chain management which may offset the benefit of adaptive designs. Thus, it is necessary to develop an optimization tool to facilitate the decision making and analysis of drug supply chain planning. The challenges include the uncertainty of maximum drug supply needed, the shifting of supply requirement, and rapid availability of new supply at decision points. In this paper, statistical simulations are designed to optimize the pre-study medication supply strategy and monitor ongoing drug supply using real-time data collected with the progress of study. Particle swarm algorithm is applied when performing optimization, where feature extraction is implemented to reduce dimensionality and save computational cost.

Triple extraction is an essential task in information extraction for natural language processing and knowledge graph construction. In this paper, we revisit the end-to-end triple extraction task for sequence generation. Since generative triple extraction may struggle to capture long-term dependencies and generate unfaithful triples, we introduce a novel model, contrastive triple extraction with a generative transformer. Specifically, we introduce a single shared transformer module for encoder-decoder-based generation. To generate faithful results, we propose a novel triplet contrastive training object. Moreover, we introduce two mechanisms to further improve model performance (i.e., batch-wise dynamic attention-masking and triple-wise calibration). Experimental results on three datasets (i.e., NYT, WebNLG, and MIE) show that our approach achieves better performance than that of baselines.

Human doctors with well-structured medical knowledge can diagnose a disease merely via a few conversations with patients about symptoms. In contrast, existing knowledge-grounded dialogue systems often require a large number of dialogue instances to learn as they fail to capture the correlations between different diseases and neglect the diagnostic experience shared among them. To address this issue, we propose a more natural and practical paradigm, i.e., low-resource medical dialogue generation, which can transfer the diagnostic experience from source diseases to target ones with a handful of data for adaptation. It is capitalized on a commonsense knowledge graph to characterize the prior disease-symptom relations. Besides, we develop a Graph-Evolving Meta-Learning (GEML) framework that learns to evolve the commonsense graph for reasoning disease-symptom correlations in a new disease, which effectively alleviates the needs of a large number of dialogues. More importantly, by dynamically evolving disease-symptom graphs, GEML also well addresses the real-world challenges that the disease-symptom correlations of each disease may vary or evolve along with more diagnostic cases. Extensive experiment results on the CMDD dataset and our newly-collected Chunyu dataset testify the superiority of our approach over state-of-the-art approaches. Besides, our GEML can generate an enriched dialogue-sensitive knowledge graph in an online manner, which could benefit other tasks grounded on knowledge graph.

Aspect based sentiment analysis (ABSA) can provide more detailed information than general sentiment analysis, because it aims to predict the sentiment polarities of the given aspects or entities in text. We summarize previous approaches into two subtasks: aspect-category sentiment analysis (ACSA) and aspect-term sentiment analysis (ATSA). Most previous approaches employ long short-term memory and attention mechanisms to predict the sentiment polarity of the concerned targets, which are often complicated and need more training time. We propose a model based on convolutional neural networks and gating mechanisms, which is more accurate and efficient. First, the novel Gated Tanh-ReLU Units can selectively output the sentiment features according to the given aspect or entity. The architecture is much simpler than attention layer used in the existing models. Second, the computations of our model could be easily parallelized during training, because convolutional layers do not have time dependency as in LSTM layers, and gating units also work independently. The experiments on SemEval datasets demonstrate the efficiency and effectiveness of our models.