Hierarchical discriminative learning improves visual representations of biomedical microscopy

Learning high-quality, self-supervised, visual representations is essential to advance the role of computer vision in biomedical microscopy and clinical medicine. Previous work has focused on self-supervised representation learning (SSL) methods developed for instance discrimination and applied them directly to image patches, or fields-of-view, sampled from gigapixel whole-slide images (WSIs) used for cancer diagnosis. However, this strategy is limited because it (1) assumes patches from the same patient are independent, (2) neglects the patient-slide-patch hierarchy of clinical biomedical microscopy, and (3) requires strong data augmentations that can degrade downstream performance. Importantly, sampled patches from WSIs of a patient's tumor are a diverse set of image examples that capture the same underlying cancer diagnosis. This motivated HiDisc, a data-driven method that leverages the inherent patient-slide-patch hierarchy of clinical biomedical microscopy to define a hierarchical discriminative learning task that implicitly learns features of the underlying diagnosis. HiDisc uses a self-supervised contrastive learning framework in which positive patch pairs are defined based on a common ancestry in the data hierarchy, and a unified patch, slide, and patient discriminative learning objective is used for visual SSL. We benchmark HiDisc visual representations on two vision tasks using two biomedical microscopy datasets, and demonstrate that (1) HiDisc pretraining outperforms current state-of-the-art self-supervised pretraining methods for cancer diagnosis and genetic mutation prediction, and (2) HiDisc learns high-quality visual representations using natural patch diversity without strong data augmentations.

Preference Transformer: Modeling Human Preferences using Transformers for RL

Preference-based reinforcement learning (RL) provides a framework to train agents using human preferences between two behaviors. However, preference-based RL has been challenging to scale since it requires a large amount of human feedback to learn a reward function aligned with human intent. In this paper, we present Preference Transformer, a neural architecture that models human preferences using transformers. Unlike prior approaches assuming human judgment is based on the Markovian rewards which contribute to the decision equally, we introduce a new preference model based on the weighted sum of non-Markovian rewards. We then design the proposed preference model using a transformer architecture that stacks causal and bidirectional self-attention layers. We demonstrate that Preference Transformer can solve a variety of control tasks using real human preferences, while prior approaches fail to work. We also show that Preference Transformer can induce a well-specified reward and attend to critical events in the trajectory by automatically capturing the temporal dependencies in human decision-making. Code is available on the project website: https://sites.google.com/view/preference-transformer.

Unsupervised Task Graph Generation from Instructional Video Transcripts

This work explores the problem of generating task graphs of real-world activities. Different from prior formulations, we consider a setting where text transcripts of instructional videos performing a real-world activity (e.g., making coffee) are provided and the goal is to identify the key steps relevant to the task as well as the dependency relationship between these key steps. We propose a novel task graph generation approach that combines the reasoning capabilities of instruction-tuned language models along with clustering and ranking components to generate accurate task graphs in a completely unsupervised manner. We show that the proposed approach generates more accurate task graphs compared to a supervised learning approach on tasks from the ProceL and CrossTask datasets.

Multimodal Subtask Graph Generation from Instructional Videos

Real-world tasks consist of multiple inter-dependent subtasks (e.g., a dirty pan needs to be washed before it can be used for cooking). In this work, we aim to model the causal dependencies between such subtasks from instructional videos describing the task. This is a challenging problem since complete information about the world is often inaccessible from videos, which demands robust learning mechanisms to understand the causal structure of events. We present Multimodal Subtask Graph Generation (MSG2), an approach that constructs a Subtask Graph defining the dependency between a task's subtasks relevant to a task from noisy web videos. Graphs generated by our multimodal approach are closer to human-annotated graphs compared to prior approaches. MSG2 further performs the downstream task of next subtask prediction 85% and 30% more accurately than recent video transformer models in the ProceL and CrossTask datasets, respectively.

Learning to Unlearn: Instance-wise Unlearning for Pre-trained Classifiers

Since the recent advent of regulations for data protection (e.g., the General Data Protection Regulation), there has been increasing demand in deleting information learned from sensitive data in pre-trained models without retraining from scratch. The inherent vulnerability of neural networks towards adversarial attacks and unfairness also calls for a robust method to remove or correct information in an instance-wise fashion, while retaining the predictive performance across remaining data. To this end, we define instance-wise unlearning, of which the goal is to delete information on a set of instances from a pre-trained model, by either misclassifying each instance away from its original prediction or relabeling the instance to a different label. We also propose two methods that reduce forgetting on the remaining data: 1) utilizing adversarial examples to overcome forgetting at the representation-level and 2) leveraging weight importance metrics to pinpoint network parameters guilty of propagating unwanted information. Both methods only require the pre-trained model and data instances to forget, allowing painless application to real-life settings where the entire training set is unavailable. Through extensive experimentation on various image classification benchmarks, we show that our approach effectively preserves knowledge of remaining data while unlearning given instances in both single-task and continual unlearning scenarios.

Transferring Pre-trained Multimodal Representations with Cross-modal Similarity Matching

Despite surprising performance on zero-shot transfer, pre-training a large-scale multimodal model is often prohibitive as it requires a huge amount of data and computing resources. In this paper, we propose a method (BeamCLIP) that can effectively transfer the representations of a large pre-trained multimodal model (CLIP-ViT) into a small target model (e.g., ResNet-18). For unsupervised transfer, we introduce cross-modal similarity matching (CSM) that enables a student model to learn the representations of a teacher model by matching the relative similarity distribution across text prompt embeddings. To better encode the text prompts, we design context-based prompt augmentation (CPA) that can alleviate the lexical ambiguity of input text prompts. Our experiments show that unsupervised representation transfer of a pre-trained vision-language model enables a small ResNet-18 to achieve a better ImageNet-1K top-1 linear probe accuracy (66.2%) than vision-only self-supervised learning (SSL) methods (e.g., SimCLR: 51.8%, SwAV: 63.7%), while closing the gap with supervised learning (69.8%).

Neural Shape Compiler: A Unified Framework for Transforming between Text, Point Cloud, and Program

3D shapes have complementary abstractions from low-level geometry to part-based hierarchies to languages, which convey different levels of information. This paper presents a unified framework to translate between pairs of shape abstractions: $\textit{Text}$ $\Longleftrightarrow$ $\textit{Point Cloud}$ $\Longleftrightarrow$ $\textit{Program}$. We propose $\textbf{Neural Shape Compiler}$ to model the abstraction transformation as a conditional generation process. It converts 3D shapes of three abstract types into unified discrete shape code, transforms each shape code into code of other abstract types through the proposed $\textit{ShapeCode Transformer}$, and decodes them to output the target shape abstraction. Point Cloud code is obtained in a class-agnostic way by the proposed $\textit{Point}$VQVAE. On Text2Shape, ShapeGlot, ABO, Genre, and Program Synthetic datasets, Neural Shape Compiler shows strengths in $\textit{Text}$ $\Longrightarrow$ $\textit{Point Cloud}$, $\textit{Point Cloud}$ $\Longrightarrow$ $\textit{Text}$, $\textit{Point Cloud}$ $\Longrightarrow$ $\textit{Program}$, and Point Cloud Completion tasks. Additionally, Neural Shape Compiler benefits from jointly training on all heterogeneous data and tasks.

Significantly improving zero-shot X-ray pathology classification via fine-tuning pre-trained image-text encoders

Deep neural networks have been successfully adopted to diverse domains including pathology classification based on medical images. However, large-scale and high-quality data to train powerful neural networks are rare in the medical domain as the labeling must be done by qualified experts. Researchers recently tackled this problem with some success by taking advantage of models pre-trained on large-scale general domain data. Specifically, researchers took contrastive image-text encoders (e.g., CLIP) and fine-tuned it with chest X-ray images and paired reports to perform zero-shot pathology classification, thus completely removing the need for pathology-annotated images to train a classification model. Existing studies, however, fine-tuned the pre-trained model with the same contrastive learning objective, and failed to exploit the multi-labeled nature of medical image-report pairs. In this paper, we propose a new fine-tuning strategy based on sentence sampling and positive-pair loss relaxation for improving the downstream zero-shot pathology classification performance, which can be applied to any pre-trained contrastive image-text encoders. Our method consistently showed dramatically improved zero-shot pathology classification performance on four different chest X-ray datasets and 3 different pre-trained models (5.77% average AUROC increase). In particular, fine-tuning CLIP with our method showed much comparable or marginally outperformed to board-certified radiologists (0.619 vs 0.625 in F1 score and 0.530 vs 0.544 in MCC) in zero-shot classification of five prominent diseases from the CheXpert dataset.

Transformers meet Stochastic Block Models: Attention with Data-Adaptive Sparsity and Cost

To overcome the quadratic cost of self-attention, recent works have proposed various sparse attention modules, most of which fall under one of two groups: 1) sparse attention under a hand-crafted patterns and 2) full attention followed by a sparse variant of softmax such as $\alpha$-entmax. Unfortunately, the first group lacks adaptability to data while the second still requires quadratic cost in training. In this work, we propose SBM-Transformer, a model that resolves both problems by endowing each attention head with a mixed-membership Stochastic Block Model (SBM). Then, each attention head data-adaptively samples a bipartite graph, the adjacency of which is used as an attention mask for each input. During backpropagation, a straight-through estimator is used to flow gradients beyond the discrete sampling step and adjust the probabilities of sampled edges based on the predictive loss. The forward and backward cost are thus linear to the number of edges, which each attention head can also choose flexibly based on the input. By assessing the distribution of graphs, we theoretically show that SBM-Transformer is a universal approximator for arbitrary sequence-to-sequence functions in expectation. Empirical evaluations under the LRA and GLUE benchmarks demonstrate that our model outperforms previous efficient variants as well as the original Transformer with full attention. Our implementation can be found in https://github.com/sc782/SBM-Transformer .

UniCLIP: Unified Framework for Contrastive Language-Image Pre-training

Pre-training vision-language models with contrastive objectives has shown promising results that are both scalable to large uncurated datasets and transferable to many downstream applications. Some following works have targeted to improve data efficiency by adding self-supervision terms, but inter-domain (image-text) contrastive loss and intra-domain (image-image) contrastive loss are defined on individual spaces in those works, so many feasible combinations of supervision are overlooked. To overcome this issue, we propose UniCLIP, a Unified framework for Contrastive Language-Image Pre-training. UniCLIP integrates the contrastive loss of both inter-domain pairs and intra-domain pairs into a single universal space. The discrepancies that occur when integrating contrastive loss between different domains are resolved by the three key components of UniCLIP: (1) augmentation-aware feature embedding, (2) MP-NCE loss, and (3) domain dependent similarity measure. UniCLIP outperforms previous vision-language pre-training methods on various single- and multi-modality downstream tasks. In our experiments, we show that each component that comprises UniCLIP contributes well to the final performance.