Antibodies are vital proteins offering robust protection for the human body from pathogens. The development of general protein and antibody-specific pre-trained language models both facilitate antibody prediction tasks. However, few studies comprehensively explore the representation capability of distinct pre-trained language models on different antibody problems. Here, to investigate the problem, we aim to answer the following key questions: (1) How do pre-trained language models perform in antibody tasks with different specificity? (2) How many benefits will the model gain if we introduce the specific biological mechanism to the pre-training process? (3) Do the learned antibody pre-trained representations make sense in real-world antibody problems, like drug discovery and immune process understanding? Previously, no benchmark available largely hindered the study to answer these questions. To facilitate the investigation, we provide an AnTibody Understanding Evaluation (ATUE) benchmark. We comprehensively evaluate the performance of protein pre-trained language models by empirical study along with conclusions and new insights. Our ATUE and code are released at //github.com/dqwang122/EATLM.
相關內容
Language models have demonstrated strong performance on various natural language understanding tasks. Similar to humans, language models could also have their own bias that is learned from the training data. As more and more downstream tasks integrate language models as part of the pipeline, it is necessary to understand the internal stereotypical representation and the methods to mitigate the negative effects. In this paper, we proposed a simple method to test the internal stereotypical representation in pre-trained language models using counterexamples. We mainly focused on gender bias, but the method can be extended to other types of bias. We evaluated models on 9 different cloze-style prompts consisting of knowledge and base prompts. Our results indicate that pre-trained language models show a certain amount of robustness when using unrelated knowledge, and prefer shallow linguistic cues, such as word position and syntactic structure, to alter the internal stereotypical representation. Such findings shed light on how to manipulate language models in a neutral approach for both finetuning and evaluation.
Denoising Diffusion Models (DDMs) have emerged as a strong competitor to Generative Adversarial Networks (GANs). However, despite their widespread use in image synthesis and editing applications, their latent space is still not as well understood. Recently, a semantic latent space for DDMs, coined `$h$-space', was shown to facilitate semantic image editing in a way reminiscent of GANs. The $h$-space is comprised of the bottleneck activations in the DDM's denoiser across all timesteps of the diffusion process. In this paper, we explore the properties of h-space and propose several novel methods for finding meaningful semantic directions within it. We start by studying unsupervised methods for revealing interpretable semantic directions in pretrained DDMs. Specifically, we show that global latent directions emerge as the principal components in the latent space. Additionally, we provide a novel method for discovering image-specific semantic directions by spectral analysis of the Jacobian of the denoiser w.r.t. the latent code. Next, we extend the analysis by finding directions in a supervised fashion in unconditional DDMs. We demonstrate how such directions can be found by relying on either a labeled data set of real images or by annotating generated samples with a domain-specific attribute classifier. We further show how to semantically disentangle the found direction by simple linear projection. Our approaches are applicable without requiring any architectural modifications, text-based guidance, CLIP-based optimization, or model fine-tuning.
Link prediction aims to identify potential missing triples in knowledge graphs. To get better results, some recent studies have introduced multimodal information to link prediction. However, these methods utilize multimodal information separately and neglect the complicated interaction between different modalities. In this paper, we aim at better modeling the inter-modality information and thus introduce a novel Interactive Multimodal Fusion (IMF) model to integrate knowledge from different modalities. To this end, we propose a two-stage multimodal fusion framework to preserve modality-specific knowledge as well as take advantage of the complementarity between different modalities. Instead of directly projecting different modalities into a unified space, our multimodal fusion module limits the representations of different modalities independent while leverages bilinear pooling for fusion and incorporates contrastive learning as additional constraints. Furthermore, the decision fusion module delivers the learned weighted average over the predictions of all modalities to better incorporate the complementarity of different modalities. Our approach has been demonstrated to be effective through empirical evaluations on several real-world datasets. The implementation code is available online at //github.com/HestiaSky/IMF-Pytorch.
Large-scale pre-trained language models (PLMs) such as BERT have recently achieved great success and become a milestone in natural language processing (NLP). It is now the consensus of the NLP community to adopt PLMs as the backbone for downstream tasks. In recent works on knowledge graph question answering (KGQA), BERT or its variants have become necessary in their KGQA models. However, there is still a lack of comprehensive research and comparison of the performance of different PLMs in KGQA. To this end, we summarize two basic KGQA frameworks based on PLMs without additional neural network modules to compare the performance of nine PLMs in terms of accuracy and efficiency. In addition, we present three benchmarks for larger-scale KGs based on the popular SimpleQuestions benchmark to investigate the scalability of PLMs. We carefully analyze the results of all PLMs-based KGQA basic frameworks on these benchmarks and two other popular datasets, WebQuestionSP and FreebaseQA, and find that knowledge distillation techniques and knowledge enhancement methods in PLMs are promising for KGQA. Furthermore, we test ChatGPT, which has drawn a great deal of attention in the NLP community, demonstrating its impressive capabilities and limitations in zero-shot KGQA. We have released the code and benchmarks to promote the use of PLMs on KGQA.
We study the application of large language models to zero-shot and few-shot classification of tabular data. We prompt the large language model with a serialization of the tabular data to a natural-language string, together with a short description of the classification problem. In the few-shot setting, we fine-tune the large language model using some labeled examples. We evaluate several serialization methods including templates, table-to-text models, and large language models. Despite its simplicity, we find that this technique outperforms prior deep-learning-based tabular classification methods on several benchmark datasets. In most cases, even zero-shot classification obtains non-trivial performance, illustrating the method's ability to exploit prior knowledge encoded in large language models. Unlike many deep learning methods for tabular datasets, this approach is also competitive with strong traditional baselines like gradient-boosted trees, especially in the very-few-shot setting.
With the rise of powerful pre-trained vision-language models like CLIP, it becomes essential to investigate ways to adapt these models to downstream datasets. A recently proposed method named Context Optimization (CoOp) introduces the concept of prompt learning -- a recent trend in NLP -- to the vision domain for adapting pre-trained vision-language models. Specifically, CoOp turns context words in a prompt into a set of learnable vectors and, with only a few labeled images for learning, can achieve huge improvements over intensively-tuned manual prompts. In our study we identify a critical problem of CoOp: the learned context is not generalizable to wider unseen classes within the same dataset, suggesting that CoOp overfits base classes observed during training. To address the problem, we propose Conditional Context Optimization (CoCoOp), which extends CoOp by further learning a lightweight neural network to generate for each image an input-conditional token (vector). Compared to CoOp's static prompts, our dynamic prompts adapt to each instance and are thus less sensitive to class shift. Extensive experiments show that CoCoOp generalizes much better than CoOp to unseen classes, even showing promising transferability beyond a single dataset; and yields stronger domain generalization performance as well. Code is available at //github.com/KaiyangZhou/CoOp.
Large-scale pre-trained models (PTMs) such as BERT and GPT have recently achieved great success and become a milestone in the field of artificial intelligence (AI). Owing to sophisticated pre-training objectives and huge model parameters, large-scale PTMs can effectively capture knowledge from massive labeled and unlabeled data. By storing knowledge into huge parameters and fine-tuning on specific tasks, the rich knowledge implicitly encoded in huge parameters can benefit a variety of downstream tasks, which has been extensively demonstrated via experimental verification and empirical analysis. It is now the consensus of the AI community to adopt PTMs as backbone for downstream tasks rather than learning models from scratch. In this paper, we take a deep look into the history of pre-training, especially its special relation with transfer learning and self-supervised learning, to reveal the crucial position of PTMs in the AI development spectrum. Further, we comprehensively review the latest breakthroughs of PTMs. These breakthroughs are driven by the surge of computational power and the increasing availability of data, towards four important directions: designing effective architectures, utilizing rich contexts, improving computational efficiency, and conducting interpretation and theoretical analysis. Finally, we discuss a series of open problems and research directions of PTMs, and hope our view can inspire and advance the future study of PTMs.
Generative models are now capable of producing highly realistic images that look nearly indistinguishable from the data on which they are trained. This raises the question: if we have good enough generative models, do we still need datasets? We investigate this question in the setting of learning general-purpose visual representations from a black-box generative model rather than directly from data. Given an off-the-shelf image generator without any access to its training data, we train representations from the samples output by this generator. We compare several representation learning methods that can be applied to this setting, using the latent space of the generator to generate multiple "views" of the same semantic content. We show that for contrastive methods, this multiview data can naturally be used to identify positive pairs (nearby in latent space) and negative pairs (far apart in latent space). We find that the resulting representations rival those learned directly from real data, but that good performance requires care in the sampling strategy applied and the training method. Generative models can be viewed as a compressed and organized copy of a dataset, and we envision a future where more and more "model zoos" proliferate while datasets become increasingly unwieldy, missing, or private. This paper suggests several techniques for dealing with visual representation learning in such a future. Code is released on our project page: //ali-design.github.io/GenRep/
Recently, the emergence of pre-trained models (PTMs) has brought natural language processing (NLP) to a new era. In this survey, we provide a comprehensive review of PTMs for NLP. We first briefly introduce language representation learning and its research progress. Then we systematically categorize existing PTMs based on a taxonomy with four perspectives. Next, we describe how to adapt the knowledge of PTMs to the downstream tasks. Finally, we outline some potential directions of PTMs for future research. This survey is purposed to be a hands-on guide for understanding, using, and developing PTMs for various NLP tasks.
Language model based pre-trained models such as BERT have provided significant gains across different NLP tasks. In this paper, we study different types of pre-trained transformer based models such as auto-regressive models (GPT-2), auto-encoder models (BERT), and seq2seq models (BART) for conditional data augmentation. We show that prepending the class labels to text sequences provides a simple yet effective way to condition the pre-trained models for data augmentation. On three classification benchmarks, pre-trained Seq2Seq model outperforms other models. Further, we explore how different pre-trained model based data augmentation differs in-terms of data diversity, and how well such methods preserve the class-label information.
小貼士
登錄享
注冊地址： 北京市海淀區羊坊店路18號2幢3層301-191