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Adverse drug events (ADEs) significantly impact clinical research, causing many clinical trial failures. ADE prediction is key for developing safer medications and enhancing patient outcomes. To support this effort, we introduce CT-ADE, a dataset for multilabel predictive modeling of ADEs in monopharmacy treatments. CT-ADE integrates data from 2,497 unique drugs, encompassing 168,984 drug-ADE pairs extracted from clinical trials, annotated with patient and contextual information, and comprehensive ADE concepts standardized across multiple levels of the MedDRA ontology. Preliminary analyses with large language models (LLMs) achieved F1-scores up to 55.90%. Models using patient and contextual information showed F1-score improvements of 21%-38% over models using only chemical structure data. Our results highlight the importance of target population and treatment regimens in the predictive modeling of ADEs, offering greater performance gains than LLM domain specialization and scaling. CT-ADE provides an essential tool for researchers aiming to leverage artificial intelligence and machine learning to enhance patient safety and minimize the impact of ADEs on pharmaceutical research and development. The dataset is publicly accessible at https://github.com/ds4dh/CT-ADE.

Adversarial attacks can mislead neural network classifiers. The defense against adversarial attacks is important for AI safety. Adversarial purification is a family of approaches that defend adversarial attacks with suitable pre-processing. Diffusion models have been shown to be effective for adversarial purification. Despite their success, many aspects of diffusion purification still remain unexplored. In this paper, we investigate and improve upon three limiting designs of diffusion purification: the use of an improved diffusion model, advanced numerical simulation techniques, and optimal control of randomness. Based on our findings, we propose Purify++, a new diffusion purification algorithm that is now the state-of-the-art purification method against several adversarial attacks. Our work presents a systematic exploration of the limits of diffusion purification methods.

Adversarial attacks have the potential to mislead deep neural network classifiers by introducing slight perturbations. Developing algorithms that can mitigate the effects of these attacks is crucial for ensuring the safe use of artificial intelligence. Recent studies have suggested that score-based diffusion models are effective in adversarial defenses. However, existing diffusion-based defenses rely on the sequential simulation of the reversed stochastic differential equations of diffusion models, which are computationally inefficient and yield suboptimal results. In this paper, we introduce a novel adversarial defense scheme named ScoreOpt, which optimizes adversarial samples at test-time, towards original clean data in the direction guided by score-based priors. We conduct comprehensive experiments on multiple datasets, including CIFAR10, CIFAR100 and ImageNet. Our experimental results demonstrate that our approach outperforms existing adversarial defenses in terms of both robustness performance and inference speed., Comment: NeurIPS 2023

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.

This paper describes the work of the Data Science for Digital Health (DS4DH) group at the TREC Health Misinformation Track 2021. The TREC Health Misinformation track focused on the development of retrieval methods that provide relevant, correct and credible information for health related searches on the Web. In our methodology, we used a two-step ranking approach that includes i) a standard retrieval phase, based on BM25 model, and ii) a re-ranking phase, with a pipeline of models focused on the usefulness, supportiveness and credibility dimensions of the retrieved documents. To estimate the usefulness, we classified the initial rank list using pre-trained language models based on the transformers architecture fine-tuned on the MS MARCO corpus. To assess the supportiveness, we utilized BERT-based models fine-tuned on scientific and Wikipedia corpora. Finally, to evaluate the credibility of the documents, we employed a random forest model trained on the Microsoft Credibility dataset combined with a list of credible sites. The resulting ranked lists were then combined using the Reciprocal Rank Fusion algorithm to obtain the final list of useful, supporting and credible documents. Our approach achieved competitive results, being top-2 in the compatibility measurement for the automatic runs. Our findings suggest that integrating automatic ranking models created for each information quality dimension with transfer learning can increase the effectiveness of health-related information retrieval.

Automated claim checking is the task of determining the veracity of a claim given evidence found in a knowledge base of trustworthy facts. While previous work has taken the knowledge base as given and optimized the claim-checking pipeline, we take the opposite approach - taking the pipeline as given, we explore the choice of knowledge base. Our first insight is that a claim-checking pipeline can be transferred to a new domain of claims with access to a knowledge base from the new domain. Second, we do not find a "universally best" knowledge base - higher domain overlap of a task dataset and a knowledge base tends to produce better label accuracy. Third, combining multiple knowledge bases does not tend to improve performance beyond using the closest-domain knowledge base. Finally, we show that the claim-checking pipeline's confidence score for selecting evidence can be used to assess whether a knowledge base will perform well for a new set of claims, even in the absence of ground-truth labels.

Delta smelt is an endangered fish species in the San Francisco estuary that have shown an overall population decline over the past 30 years. Researchers have developed a stochastic, agent-based simulator to virtualize the system, with the goal of understanding the relative contribution of natural and anthropogenic factors suggested as playing a role in their decline. However, the input configuration space is high-dimensional, running the simulator is time-consuming, and its noisy outputs change nonlinearly in both mean and variance. Getting enough runs to effectively learn input--output dynamics requires both a nimble modeling strategy and parallel supercomputer evaluation. Recent advances in heteroskedastic Gaussian process (HetGP) surrogate modeling helps, but little is known about how to appropriately plan experiments for highly distributed simulator evaluation. We propose a batch sequential design scheme, generalizing one-at-a-time variance-based active learning for HetGP surrogates, as a means of keeping multi-core cluster nodes fully engaged with expensive runs. Our acquisition strategy is carefully engineered to favor selection of replicates which boost statistical and computational efficiencies when training surrogates to isolate signal in high noise regions. Design and modeling performance is illustrated on a range of toy examples before embarking on a large-scale smelt simulation campaign and downstream high-fidelity input sensitivity analysis.