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Deep learning has advanced from fully connected architectures to structured models organized into components, e.g., the transformer composed… (see more) of positional elements, modular architectures divided into slots, and graph neural nets made up of nodes. In structured models, an interesting question is how to conduct dynamic and possibly sparse communication among the separate components. Here, we explore the hypothesis that restricting the transmitted information among components to discrete representations is a beneficial bottleneck. The motivating intuition is human language in which communication occurs through discrete symbols. Even though individuals have different understandings of what a"cat"is based on their specific experiences, the shared discrete token makes it possible for communication among individuals to be unimpeded by individual differences in internal representation. To discretize the values of concepts dynamically communicated among specialist components, we extend the quantization mechanism from the Vector-Quantized Variational Autoencoder to multi-headed discretization with shared codebooks and use it for discrete-valued neural communication (DVNC). Our experiments show that DVNC substantially improves systematic generalization in a variety of architectures -- transformers, modular architectures, and graph neural networks. We also show that the DVNC is robust to the choice of hyperparameters, making the method very useful in practice. Moreover, we establish a theoretical justification of our discretization process, proving that it has the ability to increase noise robustness and reduce the underlying dimensionality of the model.
We identify and formalize a fundamental gradient descent phenomenon resulting in a learning proclivity in over-parameterized neural networks… (see more). Gradient Starvation arises when cross-entropy loss is minimized by capturing only a subset of features relevant for the task, despite the presence of other predictive features that fail to be discovered. This work provides a theoretical explanation for the emergence of such feature imbalance in neural networks. Using tools from Dynamical Systems theory, we identify simple properties of learning dynamics during gradient descent that lead to this imbalance, and prove that such a situation can be expected given certain statistical structure in training data. Based on our proposed formalism, we develop guarantees for a novel regularization method aimed at decoupling feature learning dynamics, improving accuracy and robustness in cases hindered by gradient starvation. We illustrate our findings with simple and real-world out-of-distribution (OOD) generalization experiments.
Visual environments are structured, consisting of distinct objects or entities. These entities have properties---visible or latent---that d… (see more)etermine the manner in which they interact with one another. To partition images into entities, deep-learning researchers have proposed structural inductive biases such as slot-based architectures. To model interactions among entities, equivariant graph neural nets (GNNs) are used, but these are not particularly well suited to the task for two reasons. First, GNNs do not predispose interactions to be sparse, as relationships among independent entities are likely to be. Second, GNNs do not factorize knowledge about interactions in an entity-conditional manner. As an alternative, we take inspiration from cognitive science and resurrect a classic approach, production systems, which consist of a set of rule templates that are applied by binding placeholder variables in the rules to specific entities. Rules are scored on their match to entities, and the best fitting rules are applied to update entity properties. In a series of experiments, we demonstrate that this architecture achieves a flexible, dynamic flow of control and serves to factorize entity-specific and rule-based information. This disentangling of knowledge achieves robust future-state prediction in rich visual environments, outperforming state-of-the-art methods using GNNs, and allows for the extrapolation from simple (few object) environments to more complex environments.
One of the central elements of any causal inference is an object called structural causal model (SCM), which represents a collection of mech… (see more)anisms and exogenous sources of random variation of the system under investigation (Pearl, 2000). An important property of many kinds of neural networks is universal approximability: the ability to approximate any function to arbitrary precision. Given this property, one may be tempted to surmise that a collection of neural nets is capable of learning any SCM by training on data generated by that SCM. In this paper, we show this is not the case by disentangling the notions of expressivity and learnability. Specifically, we show that the causal hierarchy theorem (Thm. 1, Bareinboim et al., 2020), which describes the limits of what can be learned from data, still holds for neural models. For instance, an arbitrarily complex and expressive neural net is unable to predict the effects of interventions given observational data alone. Given this result, we introduce a special type of SCM called a neural causal model (NCM), and formalize a new type of inductive bias to encode structural constraints necessary for performing causal inferences. Building on this new class of models, we focus on solving two canonical tasks found in the literature known as causal identification and estimation. Leveraging the neural toolbox, we develop an algorithm that is both sufficient and necessary to determine whether a causal effect can be learned from data (i.e., causal identifiability); it then estimates the effect whenever identifiability holds (causal estimation). Simulations corroborate the proposed approach.
MHC-I associated peptides (MAPs) play a central role in the elimination of virus-infected and neoplastic cells by CD8 T cells. However, accu… (see more)rately predicting the MAP repertoire remains difficult, because only a fraction of the transcriptome generates MAPs. In this study, we investigated whether codon arrangement (usage and placement) regulates MAP biogenesis. We developed an artificial neural network called Codon Arrangement MAP Predictor (CAMAP), predicting MAP presentation solely from mRNA sequences flanking the MAP-coding codons (MCCs), while excluding the MCC per se. CAMAP predictions were significantly more accurate when using original codon sequences than shuffled codon sequences which reflect amino acid usage. Furthermore, predictions were independent of mRNA expression and MAP binding affinity to MHC-I molecules and applied to several cell types and species. Combining MAP ligand scores, transcript expression level and CAMAP scores was particularly useful to increaser MAP prediction accuracy. Using an in vitro assay, we showed that varying the synonymous codons in the regions flanking the MCCs (without changing the amino acid sequence) resulted in significant modulation of MAP presentation at the cell surface. Taken together, our results demonstrate the role of codon arrangement in the regulation of MAP presentation and support integration of both translational and post-translational events in predictive algorithms to ameliorate modeling of the immunopeptidome. Author summary MHC-I associated peptides (MAPs) are small fragments of intracellular proteins presented at the surface of cells and used by the immune system to detect and eliminate cancerous or virus-infected cells. While it is theoretically possible to predict which portions of the intracellular proteins will be naturally processed by the cells to ultimately reach the surface, current methodologies have prohibitively high false discovery rates. Here we introduce an artificial neural network called Codon Arrangement MAP Predictor (CAMAP) which integrates information from mRNA-to-protein translation to other factors regulating MAP biogenesis (e.g. MAP ligand score and transcript expression levels) to improve MAP prediction accuracy. While most MAP predictive approaches focus on MAP sequences per se, CAMAP’s novelty is to analyze the MAP-flanking mRNA sequences, thereby providing completely independent information for MAP prediction. We show on several datasets that the integration of CAMAP scores with other known factors involved in MAP presentation (i.e. MAP ligand score and mRNA expression) significantly improves MAP prediction accuracy, and further validate CAMAP learned features using an in-vitro assay. These findings may have major implications for the design of vaccines against cancers and viruses, and in times of pandemics could accelerate the identification of relevant MAPs of viral origins.
Inducing causal relationships from observations is a classic problem in machine learning. Most work in causality starts from the premise tha… (see more)t the causal variables themselves are observed. However, for AI agents such as robots trying to make sense of their environment, the only observables are low-level variables like pixels in images. To generalize well, an agent must induce high-level variables, particularly those which are causal or are affected by causal variables. A central goal for AI and causality is thus the joint discovery of abstract representations and causal structure. However, we note that existing environments for studying causal induction are poorly suited for this objective because they have complicated task-specific causal graphs which are impossible to manipulate parametrically (e.g., number of nodes, sparsity, causal chain length, etc.). In this work, our goal is to facilitate research in learning representations of high-level variables as well as causal structures among them. In order to systematically probe the ability of methods to identify these variables and structures, we design a suite of benchmarking RL environments. We evaluate various representation learning algorithms from the literature and find that explicitly incorporating structure and modularity in models can help causal induction in model-based reinforcement learning.
Marine debris is severely threatening the marine lives and causing sustained pollution to the whole ecosystem. To prevent the wastes from ge… (see more)tting into the ocean, it is helpful to clean up the floating wastes in inland waters using the autonomous cleaning devices like unmanned surface vehicles. The cleaning efficiency relies on a high-accurate and robust object detection system. However, the small size of the target, the strong light reflection over water surface, and the reflection of other objects on bank-side all bring challenges to the vision-based object detection system. To promote the practical application for autonomous floating wastes cleaning, we present FloW†, the first dataset for floating waste detection in inland water areas. The dataset consists of an image sub-dataset FloW-Img and a multimodal sub-dataset FloW-RI which contains synchronized millimeter wave radar data and images. Accurate annotations for images and radar data are provided, supporting floating waste detection strategies based on image, radar data, and the fusion of two sensors. We perform several baseline experiments on our dataset, including vision-based and radar-based detection methods. The results show that, the detection accuracy is relatively low and floating waste detection still remains a challenging task.
2021-10-01
IEEE International Conference on Computer Vision (published)
