We report a neural architecture search framework, BioNAS, that is tailored for biomedical researchers to easily build, evaluate, and uncover novel knowledge from interpretable deep learning models. The introduction of knowledge dissimilarity functions in BioNAS enables the joint optimization of predictive power and biological knowledge through searching architectures in a model space. By optimizing the consistency with existing knowledge, we demonstrate that BioNAS optimal models reveal novel knowledge in both simulated data and in real data of functional genomics. BioNAS provides a useful tool for domain experts to inject their prior belief into automated machine learning and therefore making deep learning easily accessible to practitioners. BioNAS is available at https://github.com/zj-zhang/BioNAS-pub.
This paper studies a curious phenomenon in learning energy-based model (EBM) using MCMC. In each learning iteration, we generate synthesized examples by running a non-convergent, non-mixing, and non-persistent short-run MCMC toward the current model, always starting from the same initial distribution such as uniform noise distribution, and always running a fixed number of MCMC steps. After generating synthesized examples, we then update the model parameters according to the maximum likelihood learning gradient, as if the synthesized examples are fair samples from the current model. We treat this non-convergent short-run MCMC as a learned generator model or a flow model. We provide arguments for treating the learned non-convergent short-run MCMC as a valid model. We show that the learned short-run MCMC is capable of generating realistic images. More interestingly, unlike traditional EBM or MCMC, the learned short-run MCMC is capable of reconstructing observed images and interpolating between images, like generator or flow models. The code can be found in the Appendix.
This study investigates the effects of Markov Chain Monte Carlo (MCMC) sampling in unsupervised Maximum Likelihood (ML) learning. Our attention is restricted to the family of unnormalized probability densities for which the negative log density (or energy function) is a ConvNet. In general, we find that many of the techniques used to stabilize training in previous studies can have the opposite effect. Stable ML learning with a ConvNet potential can be achieved with only a few hyper-parameters and no regularization. Using this minimal framework, we identify a variety of ML learning outcomes that depend on the implementation of MCMC sampling. On one hand, we show that it is easy to train an energy-based model which can sample realistic images with short-run Langevin. ML can be effective and stable even when MCMC samples have much higher energy than true steady-state samples throughout training. Based on this insight, we introduce an ML method with purely noise-initialized MCMC, high-quality short-run synthesis, and the same budget as ML with informative MCMC initialization such as CD or PCD. Unlike previous models, our model can obtain realistic high-diversity samples from a noise signal after training with no auxiliary networks. On the other hand, ConvNet potentials learned with highly non-convergent MCMC do not have a valid steady-state and cannot be considered approximate unnormalized densities of the training data because long-run MCMC samples differ greatly from observed images. We show that it is much harder to train a ConvNet potential to learn a steady-state over realistic images. To our knowledge, long-run MCMC samples of all previous models lose the realism of short-run samples. With correct tuning of Langevin noise, we train the first ConvNet potentials for which long-run and steady-state MCMC samples are realistic images.
Autonomous driving is a challenging multiagent domain which requires optimizing complex, mixed cooperative-competitive interactions. Learning to predict contingent distributions over other vehicles' trajectories simplifies the problem, allowing approximate solutions by trajectory optimization with dynamic constraints. We take a model-based approach to prediction, in order to make use of structured prior knowledge of vehicle kinematics, and the assumption that other drivers plan trajectories to minimize an unknown cost function. We introduce a novel inverse optimal control (IOC) algorithm to learn other vehicles' cost functions in an energy-based generative model. Langevin Sampling, a Monte Carlo based sampling algorithm, is used to directly sample the control sequence. Our algorithm provides greater flexibility than standard IOC methods, and can learn higher-level, non-Markovian cost functions defined over entire trajectories. We extend weighted feature-based cost functions with neural networks to obtain NN-augmented cost functions, which combine the advantages of both model-based and model-free learning. Results show that model-based IOC can achieve state-of-the-art vehicle trajectory prediction accuracy, and naturally take scene information into account.
Accurate prediction of others' trajectories is essential for autonomous driving. Trajectory prediction is challenging because it requires reasoning about agents' past movements, social interactions among varying numbers and kinds of agents, constraints from the scene context, and the stochasticity of human behavior. Our approach models these interactions and constraints jointly within a novel Multi-Agent Tensor Fusion (MATF) network. Specifically, the model encodes multiple agents' past trajectories and the scene context into a Multi-Agent Tensor, then applies convolutional fusion to capture multiagent interactions while retaining the spatial structure of agents and the scene context. The model decodes recurrently to multiple agents' future trajectories, using adversarial loss to learn stochastic predictions. Experiments on both highway driving and pedestrian crowd datasets show that the model achieves state-of-the-art prediction accuracy.
This paper studies the supervised learning of the conditional distribution of a high-dimensional output given an input, where the output and input belong to two different modalities, e.g., the output is an image and the input is a sketch. We solve this problem by learning two models that bear similarities to those in reinforcement learning and optimal control. One model is policy-like. It generates the output directly by a non-linear transformation of the input and a noise vector. This amounts to fast thinking because the conditional generation is accomplished by direct sampling. The other model is planner-like. It learns an objective function in the form of a conditional energy function, so that the output can be generated by optimizing the objective function, or more rigorously by sampling from the conditional energy-based model. This amounts to slow thinking because the sampling process is accomplished by an iterative algorithm such as Langevin dynamics. We propose to learn the two models jointly, where the fast thinking policy-like model serves to initialize the sampling of the slow thinking planner-like model, and the planner-like model refines the initial output by an iterative algorithm. The planner-like model learns from the difference between the refined output and the observed output, while the policy-like model learns from how the planner-like model refines its initial output. We demonstrate the effectiveness of the proposed method on various image generation tasks.
This paper presents an unsupervised method to learn a neural network, namely an explainer, to interpret a pre-trained convolutional neural network (CNN), i.e., the explainer uses interpretable visual concepts to explain features in middle conv-layers of a CNN. Given feature maps of a conv-layer of the CNN, the explainer performs like an auto-encoder, which decomposes the feature maps into object-part features. The object-part features are learned to reconstruct CNN features without much loss of information. We can consider the disentangled representations of object parts a paraphrase of CNN features, which help people understand the knowledge encoded by the CNN. More crucially, we learn the explainer via knowledge distillation without using any annotations of object parts or textures for supervision. In experiments, our method was widely used to interpret features of different benchmark CNNs, and explainers significantly boosted the feature interpretability without hurting the discrimination power of the CNNs.
This paper focuses on a new task, i.e., transplanting a category-and-task-specific neural network to a generic, modular network without strong supervision. We design a functionally interpretable structure for the generic network. Like building LEGO blocks, we teach the generic network a new category by directly transplanting the module corresponding to the category from a pre-trained network with a few or even without sample annotations. Our method incrementally adds new categories to the generic network but does not affect representations of existing categories. In this way, our method breaks the typical bottleneck of learning a net for massive tasks and categories, i.e., the requirement of collecting samples for all tasks and categories at the same time before the learning begins. Thus, we use a new distillation algorithm, namely back-distillation, to overcome specific challenges of network transplanting. Our method without training samples even outperformed the baseline with 100 training samples.
This paper proposes a generic method to learn interpretable convolutional filters in a deep convolutional neural network (CNN), where each interpretable filter encodes features of a specific object part. Our method does not require additional annotations of object parts or textures for supervision. Instead, we use the same training data as traditional CNNs. Our method automatically assigns each interpretable filter in a high conv-layer with an object part of a certain category during the learning process. Such explicit knowledge representations in conv-layers of CNN help people clarify the logic encoded in the CNN, i.e., answering what patterns the CNN extracts from an input image and uses for prediction. We have tested our method using different benchmark CNNs with various structures to demonstrate the broad applicability of our method. Experiments have shown that our interpretable filters are much more semantically meaningful than traditional filters.