Chromosome analysis is essential for diagnosing genetic disorders. For hematologic malignancies, identification of somatic clonal aberrations by karyotype analysis remains the standard of care. However, karyotyping is costly and time-consuming because of the largely manual process and the expertise required in identifying and annotating aberrations. Efforts to automate karyotype analysis to date fell short in aberration detection. Using a training set of ~10k patient specimens and ~50k karyograms from over 5 years from the Fred Hutchinson Cancer Center, we created a labeled set of images representing individual chromosomes. These individual chromosomes were used to train and assess deep learning models for classifying the 24 human chromosomes and identifying chromosomal aberrations. The top-accuracy models utilized the recently introduced Topological Vision Transformers (TopViTs) with 2-level-block-Toeplitz masking, to incorporate structural inductive bias. TopViT outperformed CNN (Inception) models with >99.3% accuracy for chromosome identification, and exhibited accuracies >99% for aberration detection in most aberrations. Notably, we were able to show high-quality performance even in "few shot" learning scenarios. Incorporating the definition of clonality substantially improved both precision and recall (sensitivity). When applied to "zero shot" scenarios, the model captured aberrations without training, with perfect precision at >50% recall. Together these results show that modern deep learning models can approach expert-level performance for chromosome aberration detection. To our knowledge, this is the first study demonstrating the downstream effectiveness of TopViTs. These results open up exciting opportunities for not only expediting patient results but providing a scalable technology for early screening of low-abundance chromosomal lesions.
Uniformly valid inference for cointegrated vector autoregressive processes has so far proven difficult due to certain discontinuities arising in the asymptotic distribution of the least squares estimator. We extend asymptotic results from the univariate case to multiple dimensions and show how inference can be based on these results. Furthermore, we show that lag augmentation and a recent instrumental variable procedure can also yield uniformly valid tests and confidence regions. We verify the theoretical findings and investigate finite sample properties in simulation experiments for two specific examples.
Sequence prediction on temporal data requires the ability to understand compositional structures of multi-level semantics beyond individual and contextual properties. The task of temporal action segmentation, which aims at translating an untrimmed activity video into a sequence of action segments, remains challenging for this reason. This paper addresses the problem by introducing an effective activity grammar to guide neural predictions for temporal action segmentation. We propose a novel grammar induction algorithm that extracts a powerful context-free grammar from action sequence data. We also develop an efficient generalized parser that transforms frame-level probability distributions into a reliable sequence of actions according to the induced grammar with recursive rules. Our approach can be combined with any neural network for temporal action segmentation to enhance the sequence prediction and discover its compositional structure. Experimental results demonstrate that our method significantly improves temporal action segmentation in terms of both performance and interpretability on two standard benchmarks, Breakfast and 50 Salads.
We propose a novel machine learning algorithm for simulating radiative transfer. Our algorithm is based on physics informed neural networks (PINNs), which are trained by minimizing the residual of the underlying radiative tranfer equations. We present extensive experiments and theoretical error estimates to demonstrate that PINNs provide a very easy to implement, fast, robust and accurate method for simulating radiative transfer. We also present a PINN based algorithm for simulating inverse problems for radiative transfer efficiently.
We introduce three notions of multivariate median bias, namely, rectilinear, Tukey, and orthant median bias. Each of these median biases is zero under a suitable notion of multivariate symmetry. We study the coverage probabilities of rectangular hull of $B$ independent multivariate estimators, with special attention to the number of estimators $B$ needed to ensure a miscoverage of at most $\alpha$. It is proved that for estimators with zero orthant median bias, we need $B\geq c\log_2(d/\alpha)$ for some constant $c > 0$. Finally, we show that there exists an asymptotically valid (non-trivial) confidence region for a multivariate parameter $\theta_0$ if and only if there exists a (non-trivial) estimator with an asymptotic orthant median bias of zero.
Geometric deep learning (GDL), which is based on neural network architectures that incorporate and process symmetry information, has emerged as a recent paradigm in artificial intelligence. GDL bears particular promise in molecular modeling applications, in which various molecular representations with different symmetry properties and levels of abstraction exist. This review provides a structured and harmonized overview of molecular GDL, highlighting its applications in drug discovery, chemical synthesis prediction, and quantum chemistry. Emphasis is placed on the relevance of the learned molecular features and their complementarity to well-established molecular descriptors. This review provides an overview of current challenges and opportunities, and presents a forecast of the future of GDL for molecular sciences.
Humans perceive the world by concurrently processing and fusing high-dimensional inputs from multiple modalities such as vision and audio. Machine perception models, in stark contrast, are typically modality-specific and optimised for unimodal benchmarks, and hence late-stage fusion of final representations or predictions from each modality (`late-fusion') is still a dominant paradigm for multimodal video classification. Instead, we introduce a novel transformer based architecture that uses `fusion bottlenecks' for modality fusion at multiple layers. Compared to traditional pairwise self-attention, our model forces information between different modalities to pass through a small number of bottleneck latents, requiring the model to collate and condense the most relevant information in each modality and only share what is necessary. We find that such a strategy improves fusion performance, at the same time reducing computational cost. We conduct thorough ablation studies, and achieve state-of-the-art results on multiple audio-visual classification benchmarks including Audioset, Epic-Kitchens and VGGSound. All code and models will be released.
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.
Transformer is a type of deep neural network mainly based on self-attention mechanism which is originally applied in natural language processing field. Inspired by the strong representation ability of transformer, researchers propose to extend transformer for computer vision tasks. Transformer-based models show competitive and even better performance on various visual benchmarks compared to other network types such as convolutional networks and recurrent networks. In this paper we provide a literature review of these visual transformer models by categorizing them in different tasks and analyze the advantages and disadvantages of these methods. In particular, the main categories include the basic image classification, high-level vision, low-level vision and video processing. Self-attention in computer vision is also briefly revisited as self-attention is the base component in transformer. Efficient transformer methods are included for pushing transformer into real applications. Finally, we give a discussion about the further research directions for visual transformer.
Embedding entities and relations into a continuous multi-dimensional vector space have become the dominant method for knowledge graph embedding in representation learning. However, most existing models ignore to represent hierarchical knowledge, such as the similarities and dissimilarities of entities in one domain. We proposed to learn a Domain Representations over existing knowledge graph embedding models, such that entities that have similar attributes are organized into the same domain. Such hierarchical knowledge of domains can give further evidence in link prediction. Experimental results show that domain embeddings give a significant improvement over the most recent state-of-art baseline knowledge graph embedding models.
Graph neural networks (GNNs) are a popular class of machine learning models whose major advantage is their ability to incorporate a sparse and discrete dependency structure between data points. Unfortunately, GNNs can only be used when such a graph-structure is available. In practice, however, real-world graphs are often noisy and incomplete or might not be available at all. With this work, we propose to jointly learn the graph structure and the parameters of graph convolutional networks (GCNs) by approximately solving a bilevel program that learns a discrete probability distribution on the edges of the graph. This allows one to apply GCNs not only in scenarios where the given graph is incomplete or corrupted but also in those where a graph is not available. We conduct a series of experiments that analyze the behavior of the proposed method and demonstrate that it outperforms related methods by a significant margin.