We consider the problem of estimating fold-changes in the expected value of a multivariate outcome that is observed subject to unknown sample-specific and category-specific perturbations. We are motivated by high-throughput sequencing studies of the abundance of microbial taxa, in which microbes are systematically over- and under-detected relative to their true abundances. Our log-linear model admits a partially identifiable estimand, and we establish full identifiability by imposing interpretable parameter constraints. To reduce bias and guarantee the existence of parameter estimates in the presence of sparse observations, we apply an asymptotically negligible and constraint-invariant penalty to our estimating function. We develop a fast coordinate descent algorithm for estimation, and an augmented Lagrangian algorithm for estimation under null hypotheses. We construct a model-robust score test, and demonstrate valid inference even for small sample sizes and violated distributional assumptions. The flexibility of the approach and comparisons to related methods are illustrated via a meta-analysis of microbial associations with colorectal cancer.
Lengthy evaluation times are common in many optimization problems such as direct policy search tasks, especially when they involve conducting evaluations in the physical world, e.g. in robotics applications. Often when evaluating solution over a fixed time period it becomes clear that the objective value will not increase with additional computation time (for example when a two wheeled robot continuously spins on the spot). In such cases, it makes sense to stop the evaluation early to save computation time. However, most approaches to stop the evaluation are problem specific and need to be specifically designed for the task at hand. Therefore, we propose an early stopping method for direct policy search. The proposed method only looks at the objective value at each time step and requires no problem specific knowledge. We test the introduced stopping criterion in five direct policy search environments drawn from games, robotics and classic control domains, and show that it can save up to 75% of the computation time. We also compare it with problem specific stopping criteria and show that it performs comparably, while being more generally applicable.
Meshfree simulation methods are emerging as compelling alternatives to conventional mesh-based approaches, particularly in the fields of Computational Fluid Dynamics (CFD) and continuum mechanics. In this publication, we provide a comprehensive overview of our research combining Machine Learning (ML) and Fraunhofer's MESHFREE software (www.meshfree.eu), a powerful tool utilizing a numerical point cloud in a Generalized Finite Difference Method (GFDM). This tool enables the effective handling of complex flow domains, moving geometries, and free surfaces, while allowing users to finely tune local refinement and quality parameters for an optimal balance between computation time and results accuracy. However, manually determining the optimal parameter combination poses challenges, especially for less experienced users. We introduce a novel ML-optimized approach, using active learning, regression trees, and visualization on MESHFREE simulation data, demonstrating the impact of input combinations on results quality and computation time. This research contributes valuable insights into parameter optimization in meshfree simulations, enhancing accessibility and usability for a broader user base in scientific and engineering applications.
Cross-modal retrieval (CMR) aims to establish interaction between different modalities, among which supervised CMR is emerging due to its flexibility in learning semantic category discrimination. Despite the remarkable performance of previous supervised CMR methods, much of their success can be attributed to the well-annotated data. However, even for unimodal data, precise annotation is expensive and time-consuming, and it becomes more challenging with the multimodal scenario. In practice, massive multimodal data are collected from the Internet with coarse annotation, which inevitably introduces noisy labels. Training with such misleading labels would bring two key challenges -- enforcing the multimodal samples to \emph{align incorrect semantics} and \emph{widen the heterogeneous gap}, resulting in poor retrieval performance. To tackle these challenges, this work proposes UOT-RCL, a Unified framework based on Optimal Transport (OT) for Robust Cross-modal Retrieval. First, we propose a semantic alignment based on partial OT to progressively correct the noisy labels, where a novel cross-modal consistent cost function is designed to blend different modalities and provide precise transport cost. Second, to narrow the discrepancy in multi-modal data, an OT-based relation alignment is proposed to infer the semantic-level cross-modal matching. Both of these two components leverage the inherent correlation among multi-modal data to facilitate effective cost function. The experiments on three widely-used cross-modal retrieval datasets demonstrate that our UOT-RCL surpasses the state-of-the-art approaches and significantly improves the robustness against noisy labels.
Generative models are invaluable in many fields of science because of their ability to capture high-dimensional and complicated distributions, such as photo-realistic images, protein structures, and connectomes. How do we evaluate the samples these models generate? This work aims to provide an accessible entry point to understanding popular notions of statistical distances, requiring only foundational knowledge in mathematics and statistics. We focus on four commonly used notions of statistical distances representing different methodologies: Using low-dimensional projections (Sliced-Wasserstein; SW), obtaining a distance using classifiers (Classifier Two-Sample Tests; C2ST), using embeddings through kernels (Maximum Mean Discrepancy; MMD), or neural networks (Fr\'echet Inception Distance; FID). We highlight the intuition behind each distance and explain their merits, scalability, complexity, and pitfalls. To demonstrate how these distances are used in practice, we evaluate generative models from different scientific domains, namely a model of decision making and a model generating medical images. We showcase that distinct distances can give different results on similar data. Through this guide, we aim to help researchers to use, interpret, and evaluate statistical distances for generative models in science.
Geometric regularity, which leverages data symmetry, has been successfully incorporated into deep learning architectures such as CNNs, RNNs, GNNs, and Transformers. While this concept has been widely applied in robotics to address the curse of dimensionality when learning from high-dimensional data, the inherent reflectional and rotational symmetry of robot structures has not been adequately explored. Drawing inspiration from cooperative multi-agent reinforcement learning, we introduce novel network structures for single-agent control learning that explicitly capture these symmetries. Moreover, we investigate the relationship between the geometric prior and the concept of Parameter Sharing in multi-agent reinforcement learning. Last but not the least, we implement the proposed framework in online and offline learning methods to demonstrate its ease of use. Through experiments conducted on various challenging continuous control tasks on simulators and real robots, we highlight the significant potential of the proposed geometric regularity in enhancing robot learning capabilities.
Solving inverse problems requires the knowledge of the forward operator, but accurate models can be computationally expensive and hence cheaper variants that do not compromise the reconstruction quality are desired. This chapter reviews reconstruction methods in inverse problems with learned forward operators that follow two different paradigms. The first one is completely agnostic to the forward operator and learns its restriction to the subspace spanned by the training data. The framework of regularisation by projection is then used to find a reconstruction. The second one uses a simplified model of the physics of the measurement process and only relies on the training data to learn a model correction. We present the theory of these two approaches and compare them numerically. A common theme emerges: both methods require, or at least benefit from, training data not only for the forward operator, but also for its adjoint.
In pace with developments in the research field of artificial intelligence, knowledge graphs (KGs) have attracted a surge of interest from both academia and industry. As a representation of semantic relations between entities, KGs have proven to be particularly relevant for natural language processing (NLP), experiencing a rapid spread and wide adoption within recent years. Given the increasing amount of research work in this area, several KG-related approaches have been surveyed in the NLP research community. However, a comprehensive study that categorizes established topics and reviews the maturity of individual research streams remains absent to this day. Contributing to closing this gap, we systematically analyzed 507 papers from the literature on KGs in NLP. Our survey encompasses a multifaceted review of tasks, research types, and contributions. As a result, we present a structured overview of the research landscape, provide a taxonomy of tasks, summarize our findings, and highlight directions for future work.
Incompleteness is a common problem for existing knowledge graphs (KGs), and the completion of KG which aims to predict links between entities is challenging. Most existing KG completion methods only consider the direct relation between nodes and ignore the relation paths which contain useful information for link prediction. Recently, a few methods take relation paths into consideration but pay less attention to the order of relations in paths which is important for reasoning. In addition, these path-based models always ignore nonlinear contributions of path features for link prediction. To solve these problems, we propose a novel KG completion method named OPTransE. Instead of embedding both entities of a relation into the same latent space as in previous methods, we project the head entity and the tail entity of each relation into different spaces to guarantee the order of relations in the path. Meanwhile, we adopt a pooling strategy to extract nonlinear and complex features of different paths to further improve the performance of link prediction. Experimental results on two benchmark datasets show that the proposed model OPTransE performs better than state-of-the-art methods.
We examine the problem of question answering over knowledge graphs, focusing on simple questions that can be answered by the lookup of a single fact. Adopting a straightforward decomposition of the problem into entity detection, entity linking, relation prediction, and evidence combination, we explore simple yet strong baselines. On the popular SimpleQuestions dataset, we find that basic LSTMs and GRUs plus a few heuristics yield accuracies that approach the state of the art, and techniques that do not use neural networks also perform reasonably well. These results show that gains from sophisticated deep learning techniques proposed in the literature are quite modest and that some previous models exhibit unnecessary complexity.
Image segmentation is still an open problem especially when intensities of the interested objects are overlapped due to the presence of intensity inhomogeneity (also known as bias field). To segment images with intensity inhomogeneities, a bias correction embedded level set model is proposed where Inhomogeneities are Estimated by Orthogonal Primary Functions (IEOPF). In the proposed model, the smoothly varying bias is estimated by a linear combination of a given set of orthogonal primary functions. An inhomogeneous intensity clustering energy is then defined and membership functions of the clusters described by the level set function are introduced to rewrite the energy as a data term of the proposed model. Similar to popular level set methods, a regularization term and an arc length term are also included to regularize and smooth the level set function, respectively. The proposed model is then extended to multichannel and multiphase patterns to segment colourful images and images with multiple objects, respectively. It has been extensively tested on both synthetic and real images that are widely used in the literature and public BrainWeb and IBSR datasets. Experimental results and comparison with state-of-the-art methods demonstrate that advantages of the proposed model in terms of bias correction and segmentation accuracy.