arXiv subjects

Yizhe Zhang

Publications and source records attributed to Yizhe Zhang.

At least 109 records · Page 6Linked to original sources

arXiv2023

Interactive Text Generation

Users interact with text, image, code, or other editors on a daily basis. However, machine learning models are rarely trained in the settings that reflect the interactivity between users and their editor. This is understandable as training AI models with real users is not only slow and costly, but what these models learn may be specific to user interface design choices. Unfortunately, this means most of the research on text, code, and image generation has focused on non-interactive settings, whereby the model is expected to get everything right without accounting for any input from a user who may be willing to help. We introduce a new Interactive Text Generation task that allows training generation models interactively without the costs of involving real users, by using user simulators that provide edits that guide the model towards a given target text. We train our interactive models using Imitation Learning, and our experiments against competitive non-interactive generation models show that models trained interactively are superior to their non-interactive counterparts, even when all models are given the same budget of user inputs or edits.

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arXiv2023

Knowledge Extraction and Distillation from Large-Scale Image-Text Colonoscopy Records Leveraging Large Language and Vision Models

The development of artificial intelligence systems for colonoscopy analysis often necessitates expert-annotated image datasets. However, limitations in dataset size and diversity impede model performance and generalisation. Image-text colonoscopy records from routine clinical practice, comprising millions of images and text reports, serve as a valuable data source, though annotating them is labour-intensive. Here we leverage recent advancements in large language and vision models and propose EndoKED, a data mining paradigm for deep knowledge extraction and distillation. EndoKED automates the transformation of raw colonoscopy records into image datasets with pixel-level annotation. We validate EndoKED using multi-centre datasets of raw colonoscopy records (~1 million images), demonstrating its superior performance in training polyp detection and segmentation models. Furthermore, the EndoKED pre-trained vision backbone enables data-efficient and generalisable learning for optical biopsy, achieving expert-level performance in both retrospective and prospective validation.

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arXiv2023

RR-CP: Reliable-Region-Based Conformal Prediction for Trustworthy Medical Image Classification

Conformal prediction (CP) generates a set of predictions for a given test sample such that the prediction set almost always contains the true label (e.g., 99.5\% of the time). CP provides comprehensive predictions on possible labels of a given test sample, and the size of the set indicates how certain the predictions are (e.g., a set larger than one is `uncertain'). Such distinct properties of CP enable effective collaborations between human experts and medical AI models, allowing efficient intervention and quality check in clinical decision-making. In this paper, we propose a new method called Reliable-Region-Based Conformal Prediction (RR-CP), which aims to impose a stronger statistical guarantee so that the user-specified error rate (e.g., 0.5\%) can be achieved in the test time, and under this constraint, the size of the prediction set is optimized (to be small). We consider a small prediction set size an important measure only when the user-specified error rate is achieved. Experiments on five public datasets show that our RR-CP performs well: with a reasonably small-sized prediction set, it achieves the user-specified error rate (e.g., 0.5\%) significantly more frequently than exiting CP methods.

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arXiv2023

SamDSK: Combining Segment Anything Model with Domain-Specific Knowledge for Semi-Supervised Learning in Medical Image Segmentation

The Segment Anything Model (SAM) exhibits a capability to segment a wide array of objects in natural images, serving as a versatile perceptual tool for various downstream image segmentation tasks. In contrast, medical image segmentation tasks often rely on domain-specific knowledge (DSK). In this paper, we propose a novel method that combines the segmentation foundation model (i.e., SAM) with domain-specific knowledge for reliable utilization of unlabeled images in building a medical image segmentation model. Our new method is iterative and consists of two main stages: (1) segmentation model training; (2) expanding the labeled set by using the trained segmentation model, an unlabeled set, SAM, and domain-specific knowledge. These two stages are repeated until no more samples are added to the labeled set. A novel optimal-matching-based method is developed for combining the SAM-generated segmentation proposals and pixel-level and image-level DSK for constructing annotations of unlabeled images in the iterative stage (2). In experiments, we demonstrate the effectiveness of our proposed method for breast cancer segmentation in ultrasound images, polyp segmentation in endoscopic images, and skin lesion segmentation in dermoscopic images. Our work initiates a new direction of semi-supervised learning for medical image segmentation: the segmentation foundation model can be harnessed as a valuable tool for label-efficient segmentation learning in medical image segmentation.

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arXiv2023

Stabilizing Transformer Training by Preventing Attention Entropy Collapse

Training stability is of great importance to Transformers. In this work, we investigate the training dynamics of Transformers by examining the evolution of the attention layers. In particular, we track the attention entropy for each attention head during the course of training, which is a proxy for model sharpness. We identify a common pattern across different architectures and tasks, where low attention entropy is accompanied by high training instability, which can take the form of oscillating loss or divergence. We denote the pathologically low attention entropy, corresponding to highly concentrated attention scores, as $\textit{entropy collapse}$. As a remedy, we propose $σ$Reparam, a simple and efficient solution where we reparametrize all linear layers with spectral normalization and an additional learned scalar. We demonstrate that $σ$Reparam successfully prevents entropy collapse in the attention layers, promoting more stable training. Additionally, we prove a tight lower bound of the attention entropy, which decreases exponentially fast with the spectral norm of the attention logits, providing additional motivation for our approach. We conduct experiments with $σ$Reparam on image classification, image self-supervised learning, machine translation, speech recognition, and language modeling tasks. We show that $σ$Reparam provides stability and robustness with respect to the choice of hyperparameters, going so far as enabling training (a) a Vision Transformer {to competitive performance} without warmup, weight decay, layer normalization or adaptive optimizers; (b) deep architectures in machine translation and (c) speech recognition to competitive performance without warmup and adaptive optimizers. Code is available at \url{https://github.com/apple/ml-sigma-reparam}.

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arXiv2023

Input Augmentation with SAM: Boosting Medical Image Segmentation with Segmentation Foundation Model

The Segment Anything Model (SAM) is a recently developed large model for general-purpose segmentation for computer vision tasks. SAM was trained using 11 million images with over 1 billion masks and can produce segmentation results for a wide range of objects in natural scene images. SAM can be viewed as a general perception model for segmentation (partitioning images into semantically meaningful regions). Thus, how to utilize such a large foundation model for medical image segmentation is an emerging research target. This paper shows that although SAM does not immediately give high-quality segmentation for medical image data, its generated masks, features, and stability scores are useful for building and training better medical image segmentation models. In particular, we demonstrate how to use SAM to augment image input for commonly-used medical image segmentation models (e.g., U-Net). Experiments on three segmentation tasks show the effectiveness of our proposed SAMAug method. The code is available at \url{https://github.com/yizhezhang2000/SAMAug}.

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arXiv2023

BOOT: Data-free Distillation of Denoising Diffusion Models with Bootstrapping

Diffusion models have demonstrated excellent potential for generating diverse images. However, their performance often suffers from slow generation due to iterative denoising. Knowledge distillation has been recently proposed as a remedy that can reduce the number of inference steps to one or a few without significant quality degradation. However, existing distillation methods either require significant amounts of offline computation for generating synthetic training data from the teacher model or need to perform expensive online learning with the help of real data. In this work, we present a novel technique called BOOT, that overcomes these limitations with an efficient data-free distillation algorithm. The core idea is to learn a time-conditioned model that predicts the output of a pre-trained diffusion model teacher given any time step. Such a model can be efficiently trained based on bootstrapping from two consecutive sampled steps. Furthermore, our method can be easily adapted to large-scale text-to-image diffusion models, which are challenging for conventional methods given the fact that the training sets are often large and difficult to access. We demonstrate the effectiveness of our approach on several benchmark datasets in the DDIM setting, achieving comparable generation quality while being orders of magnitude faster than the diffusion teacher. The text-to-image results show that the proposed approach is able to handle highly complex distributions, shedding light on more efficient generative modeling.

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arXiv2023

Can SAM Segment Polyps?

Recently, Meta AI Research releases a general Segment Anything Model (SAM), which has demonstrated promising performance in several segmentation tasks. As we know, polyp segmentation is a fundamental task in the medical imaging field, which plays a critical role in the diagnosis and cure of colorectal cancer. In particular, applying SAM to the polyp segmentation task is interesting. In this report, we evaluate the performance of SAM in segmenting polyps, in which SAM is under unprompted settings. We hope this report will provide insights to advance this polyp segmentation field and promote more interesting works in the future. This project is publicly at https://github.com/taozh2017/SAMPolyp.

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arXiv2023

GPT4MIA: Utilizing Generative Pre-trained Transformer (GPT-3) as A Plug-and-Play Transductive Model for Medical Image Analysis

In this paper, we propose a novel approach (called GPT4MIA) that utilizes Generative Pre-trained Transformer (GPT) as a plug-and-play transductive inference tool for medical image analysis (MIA). We provide theoretical analysis on why a large pre-trained language model such as GPT-3 can be used as a plug-and-play transductive inference model for MIA. At the methodological level, we develop several technical treatments to improve the efficiency and effectiveness of GPT4MIA, including better prompt structure design, sample selection, and prompt ordering of representative samples/features. We present two concrete use cases (with workflow) of GPT4MIA: (1) detecting prediction errors and (2) improving prediction accuracy, working in conjecture with well-established vision-based models for image classification (e.g., ResNet). Experiments validate that our proposed method is effective for these two tasks. We further discuss the opportunities and challenges in utilizing Transformer-based large language models for broader MIA applications.

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arXiv2023

Towards More Efficient Insertion Transformer with Fractional Positional Encoding

Auto-regressive neural sequence models have been shown to be effective across text generation tasks. However, their left-to-right decoding order prevents generation from being parallelized. Insertion Transformer (Stern et al., 2019) is an attractive alternative that allows outputting multiple tokens in a single generation step. Nevertheless, due to the incompatibility between absolute positional encoding and insertion-based generation schemes, it needs to refresh the encoding of every token in the generated partial hypothesis at each step, which could be costly. We design a novel reusable positional encoding scheme for Insertion Transformers called Fractional Positional Encoding (FPE), which allows reusing representations calculated in previous steps. Empirical studies on various text generation tasks demonstrate the effectiveness of FPE, which leads to floating-point operation reduction and latency improvements on batched decoding.

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arXiv2022

EndoBoost: a plug-and-play module for false positive suppression during computer-aided polyp detection in real-world colonoscopy (with dataset)

The advance of computer-aided detection systems using deep learning opened a new scope in endoscopic image analysis. However, the learning-based models developed on closed datasets are susceptible to unknown anomalies in complex clinical environments. In particular, the high false positive rate of polyp detection remains a major challenge in clinical practice. In this work, we release the FPPD-13 dataset, which provides a taxonomy and real-world cases of typical false positives during computer-aided polyp detection in real-world colonoscopy. We further propose a post-hoc module EndoBoost, which can be plugged into generic polyp detection models to filter out false positive predictions. This is realized by generative learning of the polyp manifold with normalizing flows and rejecting false positives through density estimation. Compared to supervised classification, this anomaly detection paradigm achieves better data efficiency and robustness in open-world settings. Extensive experiments demonstrate a promising false positive suppression in both retrospective and prospective validation. In addition, the released dataset can be used to perform 'stress' tests on established detection systems and encourages further research toward robust and reliable computer-aided endoscopic image analysis. The dataset and code will be publicly available at http://endoboost.miccai.cloud.

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arXiv2022

Bridging the Training-Inference Gap for Dense Phrase Retrieval

Building dense retrievers requires a series of standard procedures, including training and validating neural models and creating indexes for efficient search. However, these procedures are often misaligned in that training objectives do not exactly reflect the retrieval scenario at inference time. In this paper, we explore how the gap between training and inference in dense retrieval can be reduced, focusing on dense phrase retrieval (Lee et al., 2021) where billions of representations are indexed at inference. Since validating every dense retriever with a large-scale index is practically infeasible, we propose an efficient way of validating dense retrievers using a small subset of the entire corpus. This allows us to validate various training strategies including unifying contrastive loss terms and using hard negatives for phrase retrieval, which largely reduces the training-inference discrepancy. As a result, we improve top-1 phrase retrieval accuracy by 2~3 points and top-20 passage retrieval accuracy by 2~4 points for open-domain question answering. Our work urges modeling dense retrievers with careful consideration of training and inference via efficient validation while advancing phrase retrieval as a general solution for dense retrieval.

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arXiv2022

Linearizing Transformer with Key-Value Memory

Efficient transformer variants with linear time complexity have been developed to mitigate the quadratic computational overhead of the vanilla transformer. Among them are low-rank projection methods such as Linformer and kernel-based Transformers. Despite their unique merits, they usually suffer from a performance drop comparing with the vanilla transformer on many sequence generation tasks, and often fail to obtain computation gain when the generation is short. We propose MemSizer, an approach towards closing the performance gap while improving the efficiency even with short generation. It projects the source sequences into lower dimension representations like Linformer, while enjoying efficient recurrent-style incremental computation similar to kernel-based transformers. This yields linear computation time and constant memory complexity at inference time. MemSizer also employs a lightweight multi-head mechanism which renders the computation as light as a single-head model. We demonstrate that MemSizer provides an improved balance between efficiency and accuracy over the vanilla transformer and other efficient transformer variants in three typical sequence generation tasks, including machine translation, abstractive text summarization, and language modeling.

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arXiv2022

f-DM: A Multi-stage Diffusion Model via Progressive Signal Transformation

Diffusion models (DMs) have recently emerged as SoTA tools for generative modeling in various domains. Standard DMs can be viewed as an instantiation of hierarchical variational autoencoders (VAEs) where the latent variables are inferred from input-centered Gaussian distributions with fixed scales and variances. Unlike VAEs, this formulation limits DMs from changing the latent spaces and learning abstract representations. In this work, we propose f-DM, a generalized family of DMs which allows progressive signal transformation. More precisely, we extend DMs to incorporate a set of (hand-designed or learned) transformations, where the transformed input is the mean of each diffusion step. We propose a generalized formulation and derive the corresponding de-noising objective with a modified sampling algorithm. As a demonstration, we apply f-DM in image generation tasks with a range of functions, including down-sampling, blurring, and learned transformations based on the encoder of pretrained VAEs. In addition, we identify the importance of adjusting the noise levels whenever the signal is sub-sampled and propose a simple rescaling recipe. f-DM can produce high-quality samples on standard image generation benchmarks like FFHQ, AFHQ, LSUN, and ImageNet with better efficiency and semantic interpretation.

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arXiv2022

Data-Driven Deep Supervision for Skin Lesion Classification

Automatic classification of pigmented, non-pigmented, and depigmented non-melanocytic skin lesions have garnered lots of attention in recent years. However, imaging variations in skin texture, lesion shape, depigmentation contrast, lighting condition, etc. hinder robust feature extraction, affecting classification accuracy. In this paper, we propose a new deep neural network that exploits input data for robust feature extraction. Specifically, we analyze the convolutional network's behavior (field-of-view) to find the location of deep supervision for improved feature extraction. To achieve this, first, we perform activation mapping to generate an object mask, highlighting the input regions most critical for classification output generation. Then the network layer whose layer-wise effective receptive field matches the approximated object shape in the object mask is selected as our focus for deep supervision. Utilizing different types of convolutional feature extractors and classifiers on three melanoma detection datasets and two vitiligo detection datasets, we verify the effectiveness of our new method.

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arXiv2022

Usable Region Estimate for Assessing Practical Usability of Medical Image Segmentation Models

We aim to quantitatively measure the practical usability of medical image segmentation models: to what extent, how often, and on which samples a model's predictions can be used/trusted. We first propose a measure, Correctness-Confidence Rank Correlation (CCRC), to capture how predictions' confidence estimates correlate with their correctness scores in rank. A model with a high value of CCRC means its prediction confidences reliably suggest which samples' predictions are more likely to be correct. Since CCRC does not capture the actual prediction correctness, it alone is insufficient to indicate whether a prediction model is both accurate and reliable to use in practice. Therefore, we further propose another method, Usable Region Estimate (URE), which simultaneously quantifies predictions' correctness and reliability of confidence assessments in one estimate. URE provides concrete information on to what extent a model's predictions are usable. In addition, the sizes of usable regions (UR) can be utilized to compare models: A model with a larger UR can be taken as a more usable and hence better model. Experiments on six datasets validate that the proposed evaluation methods perform well, providing a concrete and concise measure for the practical usability of medical image segmentation models. Code is made available at https://github.com/yizhezhang2000/ure.

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arXiv2022

H-EMD: A Hierarchical Earth Mover's Distance Method for Instance Segmentation

Deep learning (DL) based semantic segmentation methods have achieved excellent performance in biomedical image segmentation, producing high quality probability maps to allow extraction of rich instance information to facilitate good instance segmentation. While numerous efforts were put into developing new DL semantic segmentation models, less attention was paid to a key issue of how to effectively explore their probability maps to attain the best possible instance segmentation. We observe that probability maps by DL semantic segmentation models can be used to generate many possible instance candidates, and accurate instance segmentation can be achieved by selecting from them a set of "optimized" candidates as output instances. Further, the generated instance candidates form a well-behaved hierarchical structure (a forest), which allows selecting instances in an optimized manner. Hence, we propose a novel framework, called hierarchical earth mover's distance (H-EMD), for instance segmentation in biomedical 2D+time videos and 3D images, which judiciously incorporates consistent instance selection with semantic-segmentation-generated probability maps. H-EMD contains two main stages. (1) Instance candidate generation: capturing instance-structured information in probability maps by generating many instance candidates in a forest structure. (2) Instance candidate selection: selecting instances from the candidate set for final instance segmentation. We formulate a key instance selection problem on the instance candidate forest as an optimization problem based on the earth mover's distance (EMD), and solve it by integer linear programming. Extensive experiments on eight biomedical video or 3D datasets demonstrate that H-EMD consistently boosts DL semantic segmentation models and is highly competitive with state-of-the-art methods.

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arXiv2022

A Token-level Reference-free Hallucination Detection Benchmark for Free-form Text Generation

Large pretrained generative models like GPT-3 often suffer from hallucinating non-existent or incorrect content, which undermines their potential merits in real applications. Existing work usually attempts to detect these hallucinations based on a corresponding oracle reference at a sentence or document level. However ground-truth references may not be readily available for many free-form text generation applications, and sentence- or document-level detection may fail to provide the fine-grained signals that would prevent fallacious content in real time. As a first step to addressing these issues, we propose a novel token-level, reference-free hallucination detection task and an associated annotated dataset named HaDes (HAllucination DEtection dataSet). To create this dataset, we first perturb a large number of text segments extracted from English language Wikipedia, and then verify these with crowd-sourced annotations. To mitigate label imbalance during annotation, we utilize an iterative model-in-loop strategy. We conduct comprehensive data analyses and create multiple baseline models.

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