Pre-training has shown success in different areas of machine learning, such as Computer Vision, Natural Language Processing (NLP), and medical imaging. However, it has not been fully explored for clinical data analysis. An immense amount of clinical records are recorded, but still, data and labels can be scarce for data collected in small hospitals or dealing with rare diseases. In such scenarios, pre-training on a larger set of unlabelled clinical data could improve performance. In this paper, we propose novel unsupervised pre-training techniques designed for heterogeneous, multi-modal clinical data for patient outcome prediction inspired by masked language modeling (MLM), by leveraging graph deep learning over population graphs. To this end, we further propose a graph-transformer-based network, designed to handle heterogeneous clinical data. By combining masking-based pre-training with a transformer-based network, we translate the success of masking-based pre-training in other domains to heterogeneous clinical data. We show the benefit of our pre-training method in a self-supervised and a transfer learning setting, utilizing three medical datasets TADPOLE, MIMIC-III, and a Sepsis Prediction Dataset. We find that our proposed pre-training methods help in modeling the data at a patient and population level and improve performance in different fine-tuning tasks on all datasets.
We leverage pre-trained language models to solve the task of complex NER for two low-resource languages: Chinese and Spanish. We use the technique of Whole Word Masking(WWM) to boost the performance of masked language modeling objective on large and unsupervised corpora. We experiment with multiple neural network architectures, incorporating CRF, BiLSTMs, and Linear Classifiers on top of a fine-tuned BERT layer. All our models outperform the baseline by a significant margin and our best performing model obtains a competitive position on the evaluation leaderboard for the blind test set.
Recently, significant progress has been made in masked image modeling to catch up to masked language modeling. However, unlike words in NLP, the lack of semantic decomposition of images still makes masked autoencoding (MAE) different between vision and language. In this paper, we explore a potential visual analogue of words, i.e., semantic parts, and we integrate semantic information into the training process of MAE by proposing a Semantic-Guided Masking strategy. Compared to widely adopted random masking, our masking strategy can gradually guide the network to learn various information, i.e., from intra-part patterns to inter-part relations. In particular, we achieve this in two steps. 1) Semantic part learning: we design a self-supervised part learning method to obtain semantic parts by leveraging and refining the multi-head attention of a ViT-based encoder. 2) Semantic-guided MAE (SemMAE) training: we design a masking strategy that varies from masking a portion of patches in each part to masking a portion of (whole) parts in an image. Extensive experiments on various vision tasks show that SemMAE can learn better image representation by integrating semantic information. In particular, SemMAE achieves 84.5% fine-tuning accuracy on ImageNet-1k, which outperforms the vanilla MAE by 1.4%. In the semantic segmentation and fine-grained recognition tasks, SemMAE also brings significant improvements and yields the state-of-the-art performance.
Accurate prediction of Drug-Target Affinity (DTA) is of vital importance in early-stage drug discovery, facilitating the identification of drugs that can effectively interact with specific targets and regulate their activities. While wet experiments remain the most reliable method, they are time-consuming and resource-intensive, resulting in limited data availability that poses challenges for deep learning approaches. Existing methods have primarily focused on developing techniques based on the available DTA data, without adequately addressing the data scarcity issue. To overcome this challenge, we present the SSM-DTA framework, which incorporates three simple yet highly effective strategies: (1) A multi-task training approach that combines DTA prediction with masked language modeling (MLM) using paired drug-target data. (2) A semi-supervised training method that leverages large-scale unpaired molecules and proteins to enhance drug and target representations. This approach differs from previous methods that only employed molecules or proteins in pre-training. (3) The integration of a lightweight cross-attention module to improve the interaction between drugs and targets, further enhancing prediction accuracy. Through extensive experiments on benchmark datasets such as BindingDB, DAVIS, and KIBA, we demonstrate the superior performance of our framework. Additionally, we conduct case studies on specific drug-target binding activities, virtual screening experiments, drug feature visualizations, and real-world applications, all of which showcase the significant potential of our work. In conclusion, our proposed SSM-DTA framework addresses the data limitation challenge in DTA prediction and yields promising results, paving the way for more efficient and accurate drug discovery processes. Our code is available at $\href{https://github.com/QizhiPei/SSM-DTA}{Github}$.
Video question answering (VideoQA) is a complex task that requires diverse multi-modal data for training. Manual annotation of question and answers for videos, however, is tedious and prohibits scalability. To tackle this problem, recent methods consider zero-shot settings with no manual annotation of visual question-answer. In particular, a promising approach adapts frozen autoregressive language models pretrained on Web-scale text-only data to multi-modal inputs. In contrast, we here build on frozen bidirectional language models (BiLM) and show that such an approach provides a stronger and cheaper alternative for zero-shot VideoQA. In particular, (i) we combine visual inputs with the frozen BiLM using light trainable modules, (ii) we train such modules using Web-scraped multi-modal data, and finally (iii) we perform zero-shot VideoQA inference through masked language modeling, where the masked text is the answer to a given question. Our proposed approach, FrozenBiLM, outperforms the state of the art in zero-shot VideoQA by a significant margin on a variety of datasets, including LSMDC-FiB, iVQA, MSRVTT-QA, MSVD-QA, ActivityNet-QA, TGIF-FrameQA, How2QA and TVQA. It also demonstrates competitive performance in the few-shot and fully-supervised setting. Our code and models are publicly available at https://github.com/antoyang/FrozenBiLM.
Unified vision-language frameworks have greatly advanced in recent years, most of which adopt an encoder-decoder architecture to unify image-text tasks as sequence-to-sequence generation. However, existing video-language (VidL) models still require task-specific designs in model architecture and training objectives for each task. In this work, we explore a unified VidL framework LAVENDER, where Masked Language Modeling (MLM) is used as the common interface for all pre-training and downstream tasks. Such unification leads to a simplified model architecture, where only a lightweight MLM head, instead of a decoder with much more parameters, is needed on top of the multimodal encoder. Surprisingly, experimental results show that this unified framework achieves competitive performance on 14 VidL benchmarks, covering video question answering, text-to-video retrieval and video captioning. Extensive analyses further demonstrate the advantage of LAVENDER over existing VidL methods in: (i) supporting all downstream tasks with just a single set of parameter values when multi-task finetuned; (ii) few-shot generalization on various downstream tasks; and (iii) enabling zero-shot evaluation on video question answering tasks. Code is available at https://github.com/microsoft/LAVENDER.
We present GLIPv2, a grounded VL understanding model, that serves both localization tasks (e.g., object detection, instance segmentation) and Vision-Language (VL) understanding tasks (e.g., VQA, image captioning). GLIPv2 elegantly unifies localization pre-training and Vision-Language Pre-training (VLP) with three pre-training tasks: phrase grounding as a VL reformulation of the detection task, region-word contrastive learning as a novel region-word level contrastive learning task, and the masked language modeling. This unification not only simplifies the previous multi-stage VLP procedure but also achieves mutual benefits between localization and understanding tasks. Experimental results show that a single GLIPv2 model (all model weights are shared) achieves near SoTA performance on various localization and understanding tasks. The model also shows (1) strong zero-shot and few-shot adaption performance on open-vocabulary object detection tasks and (2) superior grounding capability on VL understanding tasks. Code will be released at https://github.com/microsoft/GLIP.
In this paper, we introduce Cross-View Language Modeling, a simple and effective pre-training framework that unifies cross-lingual and cross-modal pre-training with shared architectures and objectives. Our approach is motivated by a key observation that cross-lingual and cross-modal pre-training share the same goal of aligning two different views of the same object into a common semantic space. To this end, the cross-view language modeling framework considers both multi-modal data (i.e., image-caption pairs) and multi-lingual data (i.e., parallel sentence pairs) as two different views of the same object, and trains the model to align the two views by maximizing the mutual information between them with conditional masked language modeling and contrastive learning. We pre-train CCLM, a Cross-lingual Cross-modal Language Model, with the cross-view language modeling framework. Empirical results on IGLUE, a multi-lingual multi-modal benchmark, and two multi-lingual image-text retrieval datasets show that while conceptually simpler, CCLM significantly outperforms the prior state-of-the-art with an average absolute improvement of over 10%. Moreover, CCLM is the first multi-lingual multi-modal pre-trained model that surpasses the translate-test performance of representative English vision-language models by zero-shot cross-lingual transfer.
Conditional inference on arbitrary subsets of variables is a core problem in probabilistic inference with important applications such as masked language modeling and image inpainting. In recent years, the family of Any-Order Autoregressive Models (AO-ARMs) -- closely related to popular models such as BERT and XLNet -- has shown breakthrough performance in arbitrary conditional tasks across a sweeping range of domains. But, in spite of their success, in this paper we identify significant improvements to be made to previous formulations of AO-ARMs. First, we show that AO-ARMs suffer from redundancy in their probabilistic model, i.e., they define the same distribution in multiple different ways. We alleviate this redundancy by training on a smaller set of univariate conditionals that still maintains support for efficient arbitrary conditional inference. Second, we upweight the training loss for univariate conditionals that are evaluated more frequently during inference. Our method leads to improved performance with no compromises on tractability, giving state-of-the-art likelihoods in arbitrary conditional modeling on text (Text8), image (CIFAR10, ImageNet32), and continuous tabular data domains.
Despite pre-training's progress in many important NLP tasks, it remains to explore effective pre-training strategies for dense retrieval. In this paper, we propose RetroMAE, a new retrieval oriented pre-training paradigm based on Masked Auto-Encoder (MAE). RetroMAE is highlighted by three critical designs. 1) A novel MAE workflow, where the input sentence is polluted for encoder and decoder with different masks. The sentence embedding is generated from the encoder's masked input; then, the original sentence is recovered based on the sentence embedding and the decoder's masked input via masked language modeling. 2) Asymmetric model structure, with a full-scale BERT like transformer as encoder, and a one-layer transformer as decoder. 3) Asymmetric masking ratios, with a moderate ratio for encoder: 15~30%, and an aggressive ratio for decoder: 50~70%. Our framework is simple to realize and empirically competitive: the pre-trained models dramatically improve the SOTA performances on a wide range of dense retrieval benchmarks, like BEIR and MS MARCO. The source code and pre-trained models are made publicly available at https://github.com/staoxiao/RetroMAE so as to inspire more interesting research.
The detection and normalization of temporal expressions is an important task and preprocessing step for many applications. However, prior work on normalization is rule-based, which severely limits the applicability in real-world multilingual settings, due to the costly creation of new rules. We propose a novel neural method for normalizing temporal expressions based on masked language modeling. Our multilingual method outperforms prior rule-based systems in many languages, and in particular, for low-resource languages with performance improvements of up to 33 F1 on average compared to the state of the art.
Self-supervised learning (SSL) methods such as masked language modeling have shown massive performance gains by pretraining transformer models for a variety of natural language processing tasks. The follow-up research adapted similar methods like masked image modeling in vision transformer and demonstrated improvements in the image classification task. Such simple self-supervised methods are not exhaustively studied for object detection transformers (DETR, Deformable DETR) as their transformer encoder modules take input in the convolutional neural network (CNN) extracted feature space rather than the image space as in general vision transformers. However, the CNN feature maps still maintain the spatial relationship and we utilize this property to design self-supervised learning approaches to train the encoder of object detection transformers in pretraining and multi-task learning settings. We explore common self-supervised methods based on image reconstruction, masked image modeling and jigsaw. Preliminary experiments in the iSAID dataset demonstrate faster convergence of DETR in the initial epochs in both pretraining and multi-task learning settings; nonetheless, similar improvement is not observed in the case of multi-task learning with Deformable DETR. The code for our experiments with DETR and Deformable DETR are available at https://github.com/gokulkarthik/detr and https://github.com/gokulkarthik/Deformable-DETR respectively.
Prompt-based fine-tuning has boosted the performance of Pre-trained Language Models (PLMs) on few-shot text classification by employing task-specific prompts. Yet, PLMs are unfamiliar with prompt-style expressions during pre-training, which limits the few-shot learning performance on downstream tasks. It would be desirable if the models can acquire some prompting knowledge before adaptation to specific NLP tasks. We present the Unified Prompt Tuning (UPT) framework, leading to better few-shot text classification for BERT-style models by explicitly capturing prompting semantics from non-target NLP datasets. In UPT, a novel paradigm Prompt-Options-Verbalizer is proposed for joint prompt learning across different NLP tasks, forcing PLMs to capture task-invariant prompting knowledge. We further design a self-supervised task named Knowledge-enhanced Selective Masked Language Modeling to improve the PLM's generalization abilities for accurate adaptation to previously unseen tasks. After multi-task learning across multiple tasks, the PLM can be better prompt-tuned towards any dissimilar target tasks in low-resourced settings. Experiments over a variety of NLP tasks show that UPT consistently outperforms state-of-the-arts for prompt-based fine-tuning.
Extractive Question Answering (EQA) is one of the most important tasks in Machine Reading Comprehension (MRC), which can be solved by fine-tuning the span selecting heads of Pre-trained Language Models (PLMs). However, most existing approaches for MRC may perform poorly in the few-shot learning scenario. To solve this issue, we propose a novel framework named Knowledge Enhanced Contrastive Prompt-tuning (KECP). Instead of adding pointer heads to PLMs, we introduce a seminal paradigm for EQA that transform the task into a non-autoregressive Masked Language Modeling (MLM) generation problem. Simultaneously, rich semantics from the external knowledge base (KB) and the passage context are support for enhancing the representations of the query. In addition, to boost the performance of PLMs, we jointly train the model by the MLM and contrastive learning objectives. Experiments on multiple benchmarks demonstrate that our method consistently outperforms state-of-the-art approaches in few-shot settings by a large margin.
In recent years, the pre-training-then-fine-tuning paradigm has yielded immense success on a wide spectrum of cross-modal tasks, such as visual question answering (VQA), in which a visual-language (VL) model is first optimized via self-supervised task objectives, e.g., masked language modeling (MLM) and image-text matching (ITM), and then fine-tuned to adapt to downstream task (e.g., VQA) via a brand-new objective function, e.g., answer prediction. The inconsistency of the objective forms not only severely limits the generalization of pre-trained VL models to downstream tasks, but also requires a large amount of labeled data for fine-tuning. To alleviate the problem, we propose an innovative VL fine-tuning paradigm (named Declaration-based Prompt Tuning, abbreviated as DPT), which jointly optimizes the objectives of pre-training and fine-tuning of VQA model, boosting the effective adaptation of pre-trained VL models to the downstream task. Specifically, DPT reformulates the objective form of VQA task via (1) textual adaptation, which converts the given questions into declarative sentence-form for prompt-tuning, and (2) task adaptation, which optimizes the objective function of VQA problem in the manner of pre-training phase. Experimental results on GQA dataset show that DPT outperforms the fine-tuned counterpart by a large margin regarding accuracy in both fully-supervised (2.68%) and zero-shot/few-shot (over 31%) settings. All the data and codes will be available to facilitate future research.
The impressive performance of GPT-3 using natural language prompts and in-context learning has inspired work on better fine-tuning of moderately-sized models under this paradigm. Following this line of work, we present a contrastive learning framework that clusters inputs from the same class for better generality of models trained with only limited examples. Specifically, we propose a supervised contrastive framework that clusters inputs from the same class under different augmented "views" and repel the ones from different classes. We create different "views" of an example by appending it with different language prompts and contextual demonstrations. Combining a contrastive loss with the standard masked language modeling (MLM) loss in prompt-based few-shot learners, the experimental results show that our method can improve over the state-of-the-art methods in a diverse set of 15 language tasks. Our framework makes minimal assumptions on the task or the base model, and can be applied to many recent methods with little modification. The code will be made available at: https://github.com/yiren-jian/LM-SupCon.
Recently, vision-language joint representation learning has proven to be highly effective in various scenarios. In this paper, we specifically adapt vision-language joint learning for scene text detection, a task that intrinsically involves cross-modal interaction between the two modalities: vision and language, since text is the written form of language. Concretely, we propose to learn contextualized, joint representations through vision-language pre-training, for the sake of enhancing the performance of scene text detectors. Towards this end, we devise a pre-training architecture with an image encoder, a text encoder and a cross-modal encoder, as well as three pretext tasks: image-text contrastive learning (ITC), masked language modeling (MLM) and word-in-image prediction (WIP). The pre-trained model is able to produce more informative representations with richer semantics, which could readily benefit existing scene text detectors (such as EAST and PSENet) in the down-stream text detection task. Extensive experiments on standard benchmarks demonstrate that the proposed paradigm can significantly improve the performance of various representative text detectors, outperforming previous pre-training approaches. The code and pre-trained models will be publicly released.
Being a popular mode of text-based communication in multilingual communities, code-mixing in online social media has became an important subject to study. Learning the semantics and morphology of code-mixed language remains a key challenge, due to scarcity of data and unavailability of robust and language-invariant representation learning technique. Any morphologically-rich language can benefit from character, subword, and word-level embeddings, aiding in learning meaningful correlations. In this paper, we explore a hierarchical transformer-based architecture (HIT) to learn the semantics of code-mixed languages. HIT consists of multi-headed self-attention and outer product attention components to simultaneously comprehend the semantic and syntactic structures of code-mixed texts. We evaluate the proposed method across 6 Indian languages (Bengali, Gujarati, Hindi, Tamil, Telugu and Malayalam) and Spanish for 9 NLP tasks on 17 datasets. The HIT model outperforms state-of-the-art code-mixed representation learning and multilingual language models in all tasks. We further demonstrate the generalizability of the HIT architecture using masked language modeling-based pre-training, zero-shot learning, and transfer learning approaches. Our empirical results show that the pre-training objectives significantly improve the performance on downstream tasks.
Self-supervised pre-training techniques have achieved remarkable progress in Document AI. Most multimodal pre-trained models use a masked language modeling objective to learn bidirectional representations on the text modality, but they differ in pre-training objectives for the image modality. This discrepancy adds difficulty to multimodal representation learning. In this paper, we propose \textbf{LayoutLMv3} to pre-train multimodal Transformers for Document AI with unified text and image masking. Additionally, LayoutLMv3 is pre-trained with a word-patch alignment objective to learn cross-modal alignment by predicting whether the corresponding image patch of a text word is masked. The simple unified architecture and training objectives make LayoutLMv3 a general-purpose pre-trained model for both text-centric and image-centric Document AI tasks. Experimental results show that LayoutLMv3 achieves state-of-the-art performance not only in text-centric tasks, including form understanding, receipt understanding, and document visual question answering, but also in image-centric tasks such as document image classification and document layout analysis. The code and models are publicly available at \url{https://aka.ms/layoutlmv3}.
Text revision refers to a family of natural language generation tasks, where the source and target sequences share moderate resemblance in surface form but differentiate in attributes, such as text formality and simplicity. Current state-of-the-art methods formulate these tasks as sequence-to-sequence learning problems, which rely on large-scale parallel training corpus. In this paper, we present an iterative in-place editing approach for text revision, which requires no parallel data. In this approach, we simply fine-tune a pre-trained Transformer with masked language modeling and attribute classification. During inference, the editing at each iteration is realized by two-step span replacement. At the first step, the distributed representation of the text optimizes on the fly towards an attribute function. At the second step, a text span is masked and another new one is proposed conditioned on the optimized representation. The empirical experiments on two typical and important text revision tasks, text formalization and text simplification, show the effectiveness of our approach. It achieves competitive and even better performance than state-of-the-art supervised methods on text simplification, and gains better performance than strong unsupervised methods on text formalization \footnote{Code and model are available at \url{https://github.com/jingjingli01/OREO}}.