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We proposed a new Convolution Neural Network implementation optimized for sparse 3D data inference. This implementation uses NanoVDB as the data structure to store the sparse tensor. It leaves a relatively small memory footprint while maintaining high performance. We demonstrate that this architecture is around 20 times faster than the state-of-the-art dense CNN model on a high-resolution 3D object classification network.

The prominent success of neural networks, mainly in computer vision tasks, is increasingly shadowed by their sensitivity to small, barely perceivable adversarial perturbations in image input. In this work, we aim at explaining this vulnerability through the framework of sparsity. We show the connection between adversarial attacks and sparse representations, with a focus on explaining the universality and transferability of adversarial examples in neural networks. To this end, we show that sparse coding algorithms, and the neural network-based learned iterative shrinkage thresholding algorithm (LISTA) among them, suffer from this sensitivity, and that common attacks on neural networks can be expressed as attacks on the sparse representation of the input image. The phenomenon that we observe holds true also when the network is agnostic to the sparse representation and dictionary, and thus can provide a possible explanation for the universality and transferability of adversarial attacks. The code is available at //github.com/danawr/adversarial_attacks_and_sparse_representations.

With the increasing amount of data available to scientists in disciplines as diverse as bioinformatics, physics, and remote sensing, scientific workflow systems are becoming increasingly important for composing and executing scalable data analysis pipelines. When writing such workflows, users need to specify the resources to be reserved for tasks so that sufficient resources are allocated on the target cluster infrastructure. Crucially, underestimating a task's memory requirements can result in task failures. Therefore, users often resort to overprovisioning, resulting in significant resource wastage and decreased throughput. In this paper, we propose a novel online method that uses monitoring time series data to predict task memory usage in order to reduce the memory wastage of scientific workflow tasks. Our method predicts a task's runtime, divides it into k equally-sized segments, and learns the peak memory value for each segment depending on the total file input size. We evaluate the prototype implementation of our method using workflows from the publicly available nf-core repository, showing an average memory wastage reduction of 29.48% compared to the best state-of-the-art approach

Causal discovery is becoming a key part in medical AI research. These methods can enhance healthcare by identifying causal links between biomarkers, demographics, treatments and outcomes. They can aid medical professionals in choosing more impactful treatments and strategies. In parallel, Large Language Models (LLMs) have shown great potential in identifying patterns and generating insights from text data. In this paper we investigate applying LLMs to the problem of determining the directionality of edges in causal discovery. Specifically, we test our approach on a deidentified set of Non Small Cell Lung Cancer(NSCLC) patients that have both electronic health record and genomic panel data. Graphs are validated using Bayesian Dirichlet estimators using tabular data. Our result shows that LLMs can accurately predict the directionality of edges in causal graphs, outperforming existing state-of-the-art methods. These findings suggests that LLMs can play a significant role in advancing causal discovery and help us better understand complex systems.

Infertility is a global health problem, and an increasing number of couples are seeking medical assistance to achieve reproduction, at least half of which are caused by men. The success rate of assisted reproductive technologies depends on sperm assessment, in which experts determine whether sperm can be used for reproduction based on morphology and motility of sperm. Previous sperm assessment studies with deep learning have used datasets comprising images that include only sperm heads, which cannot consider motility and other morphologies of sperm. Furthermore, the labels of the dataset are one-hot, which provides insufficient support for experts, because assessment results are inconsistent between experts, and they have no absolute answer. Therefore, we constructed the video dataset for sperm assessment whose videos include sperm head as well as neck and tail, and its labels were annotated with soft-label. Furthermore, we proposed the sperm assessment framework and the neural network, RoSTFine, for sperm video recognition. Experimental results showed that RoSTFine could improve the sperm assessment performances compared to existing video recognition models and focus strongly on important sperm parts (i.e., head and neck).

Path reasoning methods over knowledge graphs have gained popularity for their potential to improve transparency in recommender systems. However, the resulting models still rely on pre-trained knowledge graph embeddings, fail to fully exploit the interdependence between entities and relations in the KG for recommendation, and may generate inaccurate explanations. In this paper, we introduce PEARLM, a novel approach that efficiently captures user behaviour and product-side knowledge through language modelling. With our approach, knowledge graph embeddings are directly learned from paths over the KG by the language model, which also unifies entities and relations in the same optimisation space. Constraints on the sequence decoding additionally guarantee path faithfulness with respect to the KG. Experiments on two datasets show the effectiveness of our approach compared to state-of-the-art baselines. Source code and datasets: AVAILABLE AFTER GETTING ACCEPTED.

Synthetic electronic health records (EHRs) that are both realistic and preserve privacy can serve as an alternative to real EHRs for machine learning (ML) modeling and statistical analysis. However, generating high-fidelity and granular electronic health record (EHR) data in its original, highly-dimensional form poses challenges for existing methods due to the complexities inherent in high-dimensional data. In this paper, we propose Hierarchical Autoregressive Language mOdel (HALO) for generating longitudinal high-dimensional EHR, which preserve the statistical properties of real EHR and can be used to train accurate ML models without privacy concerns. Our HALO method, designed as a hierarchical autoregressive model, generates a probability density function of medical codes, clinical visits, and patient records, allowing for the generation of realistic EHR data in its original, unaggregated form without the need for variable selection or aggregation. Additionally, our model also produces high-quality continuous variables in a longitudinal and probabilistic manner. We conducted extensive experiments and demonstrate that HALO can generate high-fidelity EHR data with high-dimensional disease code probabilities (d > 10,000), disease co-occurrence probabilities within visits (d > 1,000,000), and conditional probabilities across consecutive visits (d > 5,000,000) and achieve above 0.9 R2 correlation in comparison to real EHR data. This performance then enables downstream ML models trained on its synthetic data to achieve comparable accuracy to models trained on real data (0.938 AUROC with HALO data vs. 0.943 with real data). Finally, using a combination of real and synthetic data enhances the accuracy of ML models beyond that achieved by using only real EHR data.

Recent contrastive representation learning methods rely on estimating mutual information (MI) between multiple views of an underlying context. E.g., we can derive multiple views of a given image by applying data augmentation, or we can split a sequence into views comprising the past and future of some step in the sequence. Contrastive lower bounds on MI are easy to optimize, but have a strong underestimation bias when estimating large amounts of MI. We propose decomposing the full MI estimation problem into a sum of smaller estimation problems by splitting one of the views into progressively more informed subviews and by applying the chain rule on MI between the decomposed views. This expression contains a sum of unconditional and conditional MI terms, each measuring modest chunks of the total MI, which facilitates approximation via contrastive bounds. To maximize the sum, we formulate a contrastive lower bound on the conditional MI which can be approximated efficiently. We refer to our general approach as Decomposed Estimation of Mutual Information (DEMI). We show that DEMI can capture a larger amount of MI than standard non-decomposed contrastive bounds in a synthetic setting, and learns better representations in a vision domain and for dialogue generation.

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.

Deep neural networks (DNNs) have been found to be vulnerable to adversarial examples resulting from adding small-magnitude perturbations to inputs. Such adversarial examples can mislead DNNs to produce adversary-selected results. Different attack strategies have been proposed to generate adversarial examples, but how to produce them with high perceptual quality and more efficiently requires more research efforts. In this paper, we propose AdvGAN to generate adversarial examples with generative adversarial networks (GANs), which can learn and approximate the distribution of original instances. For AdvGAN, once the generator is trained, it can generate adversarial perturbations efficiently for any instance, so as to potentially accelerate adversarial training as defenses. We apply AdvGAN in both semi-whitebox and black-box attack settings. In semi-whitebox attacks, there is no need to access the original target model after the generator is trained, in contrast to traditional white-box attacks. In black-box attacks, we dynamically train a distilled model for the black-box model and optimize the generator accordingly. Adversarial examples generated by AdvGAN on different target models have high attack success rate under state-of-the-art defenses compared to other attacks. Our attack has placed the first with 92.76% accuracy on a public MNIST black-box attack challenge.