Fenglin Liu

NeurIPS Conference 2023 Conference Paper

Rethinking Semi-Supervised Medical Image Segmentation: A Variance-Reduction Perspective

• Chenyu You
• Weicheng Dai
• Yifei Min
• Fenglin Liu
• David Clifton
• S. Kevin Zhou
• Lawrence Staib
• James Duncan

For medical image segmentation, contrastive learning is the dominant practice to improve the quality of visual representations by contrasting semantically similar and dissimilar pairs of samples. This is enabled by the observation that without accessing ground truth labels, negative examples with truly dissimilar anatomical features, if sampled, can significantly improve the performance. In reality, however, these samples may come from similar anatomical features and the models may struggle to distinguish the minority tail-class samples, making the tail classes more prone to misclassification, both of which typically lead to model collapse. In this paper, we propose $\texttt{ARCO}$, a semi-supervised contrastive learning (CL) framework with stratified group theory for medical image segmentation. In particular, we first propose building $\texttt{ARCO}$ through the concept of variance-reduced estimation, and show that certain variance-reduction techniques are particularly beneficial in pixel/voxel-level segmentation tasks with extremely limited labels. Furthermore, we theoretically prove these sampling techniques are universal in variance reduction. Finally, we experimentally validate our approaches on eight benchmarks, i. e. , five 2D/3D medical and three semantic segmentation datasets, with different label settings, and our methods consistently outperform state-of-the-art semi-supervised methods. Additionally, we augment the CL frameworks with these sampling techniques and demonstrate significant gains over previous methods. We believe our work is an important step towards semi-supervised medical image segmentation by quantifying the limitation of current self-supervision objectives for accomplishing such challenging safety-critical tasks.

NeurIPS Conference 2022 Conference Paper

Class-Aware Adversarial Transformers for Medical Image Segmentation

• Chenyu You
• Ruihan Zhao
• Fenglin Liu
• Siyuan Dong
• Sandeep Chinchali
• Ufuk Topcu
• Lawrence Staib
• James Duncan

Transformers have made remarkable progress towards modeling long-range dependencies within the medical image analysis domain. However, current transformer-based models suffer from several disadvantages: (1) existing methods fail to capture the important features of the images due to the naive tokenization scheme; (2) the models suffer from information loss because they only consider single-scale feature representations; and (3) the segmentation label maps generated by the models are not accurate enough without considering rich semantic contexts and anatomical textures. In this work, we present CASTformer, a novel type of adversarial transformers, for 2D medical image segmentation. First, we take advantage of the pyramid structure to construct multi-scale representations and handle multi-scale variations. We then design a novel class-aware transformer module to better learn the discriminative regions of objects with semantic structures. Lastly, we utilize an adversarial training strategy that boosts segmentation accuracy and correspondingly allows a transformer-based discriminator to capture high-level semantically correlated contents and low-level anatomical features. Our experiments demonstrate that CASTformer dramatically outperforms previous state-of-the-art transformer-based approaches on three benchmarks, obtaining 2. 54%-5. 88% absolute improvements in Dice over previous models. Further qualitative experiments provide a more detailed picture of the model’s inner workings, shed light on the challenges in improved transparency, and demonstrate that transfer learning can greatly improve performance and reduce the size of medical image datasets in training, making CASTformer a strong starting point for downstream medical image analysis tasks.

NeurIPS Conference 2022 Conference Paper

Expectation-Maximization Contrastive Learning for Compact Video-and-Language Representations

• Peng Jin
• Jinfa Huang
• Fenglin Liu
• Xian Wu
• Shen Ge
• Guoli Song
• David Clifton
• Jie Chen

Most video-and-language representation learning approaches employ contrastive learning, e. g. , CLIP, to project the video and text features into a common latent space according to the semantic similarities of text-video pairs. However, such learned shared latent spaces are not often optimal, and the modality gap between visual and textual representation can not be fully eliminated. In this paper, we propose Expectation-Maximization Contrastive Learning (EMCL) to learn compact video-and-language representations. Specifically, we use the Expectation-Maximization algorithm to find a compact set of bases for the latent space, where the features could be concisely represented as the linear combinations of these bases. Such feature decomposition of video-and-language representations reduces the rank of the latent space, resulting in increased representing power for the semantics. Extensive experiments on three benchmark text-video retrieval datasets prove that our EMCL can learn more discriminative video-and-language representations than previous methods, and significantly outperform previous state-of-the-art methods across all metrics. More encouragingly, the proposed method can be applied to boost the performance of existing approaches either as a jointly training layer or an out-of-the-box inference module with no extra training, making it easy to be incorporated into any existing methods.

NeurIPS Conference 2022 Conference Paper

Retrieve, Reason, and Refine: Generating Accurate and Faithful Patient Instructions

• Fenglin Liu
• Bang Yang
• Chenyu You
• Xian Wu
• Shen Ge
• Zhangdaihong Liu
• Xu Sun
• Yang Yang

The "Patient Instruction" (PI), which contains critical instructional information provided both to carers and to the patient at the time of discharge, is essential for the patient to manage their condition outside hospital. An accurate and easy-to-follow PI can improve the self-management of patients which can in turn reduce hospital readmission rates. However, writing an appropriate PI can be extremely time consuming for physicians, and is subject to being incomplete or error-prone for (potentially overworked) physicians. Therefore, we propose a new task that can provide an objective means of avoiding incompleteness, while reducing clinical workload: the automatic generation of the PI, which is imagined as being a document that the clinician can review, modify, and approve as necessary (rather than taking the human "out of the loop"). We build a benchmark clinical dataset and propose the Re$^3$Writer, which imitates the working patterns of physicians to first retrieve related working experience from historical PIs written by physicians, then reason related medical knowledge. Finally, it refines the retrieved working experience and reasoned medical knowledge to extract useful information, which is used to generate the PI for previously-unseen patient according to their health records during hospitalization. Our experiments show that, using our method, the performance of 6 different models can be substantially boosted across all metrics, with up to 20%, 11%, and 19% relative improvements in BLEU-4, ROUGE-L, and METEOR, respectively. Meanwhile, we show results from human evaluations to measure the effectiveness in terms of its usefulness for clinical practice. The code is available at https: //github. com/AI-in-Health/Patient-Instructions.

AAAI Conference 2021 Conference Paper

Audio-Oriented Multimodal Machine Comprehension via Dynamic Inter- and Intra-modality Attention

• Zhiqi Huang
• Fenglin Liu
• Xian Wu
• Shen Ge
• Helin Wang
• Wei Fan
• Yuexian Zou

While Machine Comprehension (MC) has attracted extensive research interests in recent years, existing approaches mainly belong to the category of Machine Reading Comprehension task which mines textual inputs (paragraphs and questions) to predict the answers (choices or text spans). However, there are a lot of MC tasks that accept audio input in addition to the textual input, e. g. English listening comprehension test. In this paper, we target the problem of Audio- Oriented Multimodal Machine Comprehension, and its goal is to answer questions based on the given audio and textual information. To solve this problem, we propose a Dynamic Inter- and Intra-modality Attention (DIIA) model to effectively fuse the two modalities (audio and textual). DIIA can work as an independent component and thus be easily integrated into existing MC models. Moreover, we further develop a Multimodal Knowledge Distillation (MKD) module to enable our multimodal MC model to accurately predict the answers based only on either the text or the audio. As a result, the proposed approach can handle various tasks including: Audio-Oriented Multimodal Machine Comprehension, Machine Reading Comprehension and Machine Listening Comprehension, in a single model, making fair comparisons possible between our model and the existing unimodal MC models. Experimental results and analysis prove the effectiveness of the proposed approaches. First, the proposed DIIA boosts the baseline models by up to 21. 08% in terms of accuracy; Second, under the unimodal scenarios, the MKD module allows our multimodal MC model to significantly outperform the unimodal models by up to 18. 87%, which are trained and tested with only audio or textual data.

NeurIPS Conference 2021 Conference Paper

Auto-Encoding Knowledge Graph for Unsupervised Medical Report Generation

• Fenglin Liu
• Chenyu You
• Xian Wu
• Shen Ge
• Sheng Wang
• Xu Sun

Medical report generation, which aims to automatically generate a long and coherent report of a given medical image, has been receiving growing research interests. Existing approaches mainly adopt a supervised manner and heavily rely on coupled image-report pairs. However, in the medical domain, building a large-scale image-report paired dataset is both time-consuming and expensive. To relax the dependency on paired data, we propose an unsupervised model Knowledge Graph Auto-Encoder (KGAE) which accepts independent sets of images and reports in training. KGAE consists of a pre-constructed knowledge graph, a knowledge-driven encoder and a knowledge-driven decoder. The knowledge graph works as the shared latent space to bridge the visual and textual domains; The knowledge-driven encoder projects medical images and reports to the corresponding coordinates in this latent space and the knowledge-driven decoder generates a medical report given a coordinate in this space. Since the knowledge-driven encoder and decoder can be trained with independent sets of images and reports, KGAE is unsupervised. The experiments show that the unsupervised KGAE generates desirable medical reports without using any image-report training pairs. Moreover, KGAE can also work in both semi-supervised and supervised settings, and accept paired images and reports in training. By further fine-tuning with image-report pairs, KGAE consistently outperforms the current state-of-the-art models on two datasets.

AAAI Conference 2021 Conference Paper

Non-Autoregressive Coarse-to-Fine Video Captioning

• Bang Yang
• Yuexian Zou
• Fenglin Liu
• Can Zhang

It is encouraged to see that progress has been made to bridge videos and natural language. However, mainstream video captioning methods suffer from slow inference speed due to the sequential manner of autoregressive decoding, and prefer generating generic descriptions due to the insufficient training of visual words (e. g. , nouns and verbs) and inadequate decoding paradigm. In this paper, we propose a nonautoregressive decoding based model with a coarse-to-fine captioning procedure to alleviate these defects. In implementations, we employ a bi-directional self-attention based network as our language model for achieving inference speedup, based on which we decompose the captioning procedure into two stages, where the model has different focuses. Specifically, given that visual words determine the semantic correctness of captions, we design a mechanism of generating visual words to not only promote the training of scene-related words but also capture relevant details from videos to construct a coarse-grained sentence “template”. Thereafter, we devise dedicated decoding algorithms that fill in the “template” with suitable words and modify inappropriate phrasing via iterative refinement to obtain a fine-grained description. Extensive experiments on two mainstream video captioning benchmarks, i. e. , MSVD and MSR-VTT, demonstrate that our approach achieves state-of-the-art performance, generates diverse descriptions, and obtains high inference efficiency.

AIIM Journal 2020 Journal Article

Classification of myocardial infarction based on hybrid feature extraction and artificial intelligence tools by adopting tunable-Q wavelet transform (TQWT), variational mode decomposition (VMD) and neural networks

• Wei Zeng
• Jian Yuan
• Chengzhi Yuan
• Qinghui Wang
• Fenglin Liu
• Ying Wang

AAAI Conference 2020 Conference Paper

Federated Learning for Vision-and-Language Grounding Problems

• Fenglin Liu
• Xian Wu
• Shen Ge
• Wei Fan
• Yuexian Zou

Recently, vision-and-language grounding problems, e. g. , image captioning and visual question answering (VQA), has attracted extensive interests from both academic and industrial worlds. However, given the similarity of these tasks, the efforts to obtain better results by combining the merits of their algorithms are not well studied. Inspired by the recent success of federated learning, we propose a federated learning framework to obtain various types of image representations from different tasks, which are then fused together to form finegrained image representations. The representations merge useful features from different vision-and-language grounding problems, and are thus much more powerful than the original representations alone in individual tasks. To learn such image representations, we propose the Aligning, Integrating and Mapping Network (aimNet). The aimNet is validated on three federated learning settings, which include horizontal federated learning, vertical federated learning, and federated transfer learning. Experiments of aimNet-based federated learning framework on two representative tasks, i. e. , image captioning and VQA, demonstrate the effective and universal improvements of all metrics over the baselines. In image captioning, we are able to get 14% and 13% relative gain on the taskspecific metrics CIDEr and SPICE, respectively. In VQA, we could also boost the performance of strong baselines by up to 3%.

NeurIPS Conference 2020 Conference Paper

Prophet Attention: Predicting Attention with Future Attention

• Fenglin Liu
• Xuancheng Ren
• Xian Wu
• Shen Ge
• Wei Fan
• Yuexian Zou
• Xu Sun

Recently, attention based models have been used extensively in many sequence-to-sequence learning systems. Especially for image captioning, the attention based models are expected to ground correct image regions with proper generated words. However, for each time step in the decoding process, the attention based models usually use the hidden state of the current input to attend to the image regions. Under this setting, these attention models have a deviated focus'' problem that they calculate the attention weights based on previous words instead of the one to be generated, impairing the performance of both grounding and captioning. In this paper, we propose the Prophet Attention, similar to the form of self-supervision. In the training stage, this module utilizes the future information to calculate the ideal'' attention weights towards image regions. These calculated ideal'' weights are further used to regularize the deviated'' attention. In this manner, image regions are grounded with the correct words. The proposed Prophet Attention can be easily incorporated into existing image captioning models to improve their performance of both grounding and captioning. The experiments on the Flickr30k Entities and the MSCOCO datasets show that the proposed Prophet Attention consistently outperforms baselines in both automatic metrics and human evaluations. It is worth noticing that we set new state-of-the-arts on the two benchmark datasets and achieve the 1st place on the leaderboard of the online MSCOCO benchmark in terms of the default ranking score, i. e. , CIDEr-c40.

NeurIPS Conference 2019 Conference Paper

Aligning Visual Regions and Textual Concepts for Semantic-Grounded Image Representations

• Fenglin Liu
• Yuanxin Liu
• Xuancheng Ren
• Xiaodong He
• Xu Sun

In vision-and-language grounding problems, fine-grained representations of the image are considered to be of paramount importance. Most of the current systems incorporate visual features and textual concepts as a sketch of an image. However, plainly inferred representations are usually undesirable in that they are composed of separate components, the relations of which are elusive. In this work, we aim at representing an image with a set of integrated visual regions and corresponding textual concepts, reflecting certain semantics. To this end, we build the Mutual Iterative Attention (MIA) module, which integrates correlated visual features and textual concepts, respectively, by aligning the two modalities. We evaluate the proposed approach on two representative vision-and-language grounding tasks, i. e. , image captioning and visual question answering. In both tasks, the semantic-grounded image representations consistently boost the performance of the baseline models under all metrics across the board. The results demonstrate that our approach is effective and generalizes well to a wide range of models for image-related applications. (The code is available at \url{https: //github. com/fenglinliu98/MIA)

IJCAI Conference 2019 Conference Paper

Exploring and Distilling Cross-Modal Information for Image Captioning

• Fenglin Liu
• Xuancheng Ren
• Yuanxin Liu
• Kai Lei
• Xu Sun

Recently, attention-based encoder-decoder models have been used extensively in image captioning. Yet there is still great difficulty for the current methods to achieve deep image understanding. In this work, we argue that such understanding requires visual attention to correlated image regions and semantic attention to coherent attributes of interest. To perform effective attention, we explore image captioning from a cross-modal perspective and propose the Global-and-Local Information Exploring-and-Distilling approach that explores and distills the source information in vision and language. It globally provides the aspect vector, a spatial and relational representation of images based on caption contexts, through the extraction of salient region groupings and attribute collocations, and locally extracts the fine-grained regions and attributes in reference to the aspect vector for word selection. Our fully-attentive model achieves a CIDEr score of 129. 3 in offline COCO evaluation with remarkable efficiency in terms of accuracy, speed, and parameter budget.