Pre-trained protein models (PTPMs) represent a protein with one fixed embedding and thus are not capable for diverse tasks. For example, protein structures can shift, namely protein folding, between several conformations in various biological processes. To enable PTPMs to produce task-aware representations, we propose to learn interpretable, pluggable and extensible protein prompts as a way of injecting task-related knowledge into PTPMs. In this regard, prior PTPM optimization with the masked language modeling task can be interpreted as learning a sequence prompt (Seq prompt) that enables PTPMs to capture the sequential dependency between amino acids. To incorporate conformational knowledge to PTPMs, we propose an interaction-conformation prompt (IC prompt) that is learned through back-propagation with the protein-protein interaction task. As an instantiation, we present a conformation-aware pre-trained protein model that learns both sequence and interaction-conformation prompts in a multi-task setting. We conduct comprehensive experiments on nine protein datasets. Results confirm our expectation that using the sequence prompt does not hurt PTPMs' performance on sequence-related tasks while incorporating the interaction-conformation prompt significantly improves PTPMs' performance on tasks where conformational knowledge counts. We also show the learned prompts can be combined and extended to deal with new complex tasks.
相關內容
Vision-and-language Navigation (VLN) task requires an embodied agent to navigate to a remote location following a natural language instruction. Previous methods usually adopt a sequence model (e.g., Transformer and LSTM) as the navigator. In such a paradigm, the sequence model predicts action at each step through a maintained navigation state, which is generally represented as a one-dimensional vector. However, the crucial navigation clues (i.e., object-level environment layout) for embodied navigation task is discarded since the maintained vector is essentially unstructured. In this paper, we propose a novel Structured state-Evolution (SEvol) model to effectively maintain the environment layout clues for VLN. Specifically, we utilise the graph-based feature to represent the navigation state instead of the vector-based state. Accordingly, we devise a Reinforced Layout clues Miner (RLM) to mine and detect the most crucial layout graph for long-term navigation via a customised reinforcement learning strategy. Moreover, the Structured Evolving Module (SEM) is proposed to maintain the structured graph-based state during navigation, where the state is gradually evolved to learn the object-level spatial-temporal relationship. The experiments on the R2R and R4R datasets show that the proposed SEvol model improves VLN models' performance by large margins, e.g., +3% absolute SPL accuracy for NvEM and +8% for EnvDrop on the R2R test set.
The latest biological findings discover that the motionless 'lock-and-key' theory is no longer applicable and the flexibility of both the receptor and ligand plays a significant role in helping understand the principles of the binding affinity prediction. Based on this mechanism, molecular dynamics (MD) simulations have been invented as a useful tool to investigate the dynamical properties of this molecular system. However, the computational expenditure prohibits the growth of reported protein trajectories. To address this insufficiency, we present a novel spatial-temporal pre-training protocol, PretrainMD, to grant the protein encoder the capacity to capture the time-dependent geometric mobility along MD trajectories. Specifically, we introduce two sorts of self-supervised learning tasks: an atom-level denoising generative task and a protein-level snapshot ordering task. We validate the effectiveness of PretrainMD through the PDBbind dataset for both linear-probing and fine-tuning. Extensive experiments show that our PretrainMD exceeds most state-of-the-art methods and achieves comparable performance. More importantly, through visualization we discover that the learned representations by pre-training on MD trajectories without any label from the downstream task follow similar patterns of the magnitude of binding affinities. This strongly aligns with the fact that the motion of the interactions of protein and ligand maintains the key information of their binding. Our work provides a promising perspective of self-supervised pre-training for protein representations with very fine temporal resolutions and hopes to shed light on the further usage of MD simulations for the biomedical deep learning community.
With the increasing adoption of NLP models in real-world products, it becomes more and more important to protect these models from privacy leakage. Because private information in language data is sparse, previous research formalized a Selective-Differential-Privacy (SDP) notion to provide protection for sensitive tokens detected by policy functions, and prove its effectiveness on RNN-based models. But the previous mechanism requires separating the private and public model parameters and thus cannot be applied on large attention-based models. In this paper, we propose a simple yet effective just-fine-tune-twice privacy mechanism to first fine-tune on in-domain redacted data and then on in-domain private data, to achieve SDP for large Transformer-based language models. We also design explicit and contextual policy functions to provide protections at different levels. Experiments show that our models achieve strong performance while staying robust to the canary insertion attack. We further show that even under low-resource settings with a small amount of in-domain data, SDP can still improve the model utility. We will release the code, data and models to facilitate future research.
Due to the superior performance, large-scale pre-trained language models (PLMs) have been widely adopted in many aspects of human society. However, we still lack effective tools to understand the potential bias embedded in the black-box models. Recent advances in prompt tuning show the possibility to explore the internal mechanism of the PLMs. In this work, we propose two token-level sentiment tests: Sentiment Association Test (SAT) and Sentiment Shift Test (SST) which utilize the prompt as a probe to detect the latent bias in the PLMs. Our experiments on the collection of sentiment datasets show that both SAT and SST can identify sentiment bias in PLMs and SST is able to quantify the bias. The results also suggest that fine-tuning can possibly augment the existing bias in PLMs.
A recent study by Ahmed and Devanbu reported that using a corpus of code written in multilingual datasets to fine-tune multilingual Pre-trained Language Models (PLMs) achieves higher performance as opposed to using a corpus of code written in just one programming language. However, no analysis was made with respect to fine-tuning monolingual PLMs. Furthermore, some programming languages are inherently different and code written in one language usually cannot be interchanged with the others, i.e., Ruby and Java code possess very different structure. To better understand how monolingual and multilingual PLMs affect different programming languages, we investigate 1) the performance of PLMs on Ruby for two popular Software Engineering tasks: Code Summarization and Code Search, 2) the strategy (to select programming languages) that works well on fine-tuning multilingual PLMs for Ruby, and 3) the performance of the fine-tuned PLMs on Ruby given different code lengths. In this work, we analyze over a hundred of pre-trained and fine-tuned models. Our results show that 1) multilingual PLMs have a lower Performance-to-Time Ratio (the BLEU, METEOR, or MRR scores over the fine-tuning duration) as compared to monolingual PLMs, 2) our proposed strategy to select target programming languages to fine-tune multilingual PLMs is effective: it reduces the time to fine-tune yet achieves higher performance in Code Summarization and Code Search tasks, and 3) our proposed strategy consistently shows good performance on different code lengths.
Pre-trained models learn contextualized word representations on large-scale text corpus through a self-supervised learning method, which has achieved promising performance after fine-tuning. These models, however, suffer from poor robustness and lack of interpretability. Pre-trained models with knowledge injection, which we call knowledge enhanced pre-trained models (KEPTMs), possess deep understanding and logical reasoning and introduce interpretability to some extent. In this survey, we provide a comprehensive overview of KEPTMs for natural language processing. We first introduce the progress of pre-trained models and knowledge representation learning. Then we systematically categorize existing KEPTMs from three different perspectives. Finally, we outline some potential directions of KEPTMs for future research.
Recently pre-trained language representation models such as BERT have shown great success when fine-tuned on downstream tasks including information retrieval (IR). However, pre-training objectives tailored for ad-hoc retrieval have not been well explored. In this paper, we propose Pre-training with Representative wOrds Prediction (PROP) for ad-hoc retrieval. PROP is inspired by the classical statistical language model for IR, specifically the query likelihood model, which assumes that the query is generated as the piece of text representative of the "ideal" document. Based on this idea, we construct the representative words prediction (ROP) task for pre-training. Given an input document, we sample a pair of word sets according to the document language model, where the set with higher likelihood is deemed as more representative of the document. We then pre-train the Transformer model to predict the pairwise preference between the two word sets, jointly with the Masked Language Model (MLM) objective. By further fine-tuning on a variety of representative downstream ad-hoc retrieval tasks, PROP achieves significant improvements over baselines without pre-training or with other pre-training methods. We also show that PROP can achieve exciting performance under both the zero- and low-resource IR settings. The code and pre-trained models are available at //github.com/Albert-Ma/PROP.
Most object recognition approaches predominantly focus on learning discriminative visual patterns while overlooking the holistic object structure. Though important, structure modeling usually requires significant manual annotations and therefore is labor-intensive. In this paper, we propose to "look into object" (explicitly yet intrinsically model the object structure) through incorporating self-supervisions into the traditional framework. We show the recognition backbone can be substantially enhanced for more robust representation learning, without any cost of extra annotation and inference speed. Specifically, we first propose an object-extent learning module for localizing the object according to the visual patterns shared among the instances in the same category. We then design a spatial context learning module for modeling the internal structures of the object, through predicting the relative positions within the extent. These two modules can be easily plugged into any backbone networks during training and detached at inference time. Extensive experiments show that our look-into-object approach (LIO) achieves large performance gain on a number of benchmarks, including generic object recognition (ImageNet) and fine-grained object recognition tasks (CUB, Cars, Aircraft). We also show that this learning paradigm is highly generalizable to other tasks such as object detection and segmentation (MS COCO). Project page: //github.com/JDAI-CV/LIO.
In this paper, we propose Latent Relation Language Models (LRLMs), a class of language models that parameterizes the joint distribution over the words in a document and the entities that occur therein via knowledge graph relations. This model has a number of attractive properties: it not only improves language modeling performance, but is also able to annotate the posterior probability of entity spans for a given text through relations. Experiments demonstrate empirical improvements over both a word-based baseline language model and a previous approach that incorporates knowledge graph information. Qualitative analysis further demonstrates the proposed model's ability to learn to predict appropriate relations in context.
Image-to-image translation aims to learn the mapping between two visual domains. There are two main challenges for many applications: 1) the lack of aligned training pairs and 2) multiple possible outputs from a single input image. In this work, we present an approach based on disentangled representation for producing diverse outputs without paired training images. To achieve diversity, we propose to embed images onto two spaces: a domain-invariant content space capturing shared information across domains and a domain-specific attribute space. Our model takes the encoded content features extracted from a given input and the attribute vectors sampled from the attribute space to produce diverse outputs at test time. To handle unpaired training data, we introduce a novel cross-cycle consistency loss based on disentangled representations. Qualitative results show that our model can generate diverse and realistic images on a wide range of tasks without paired training data. For quantitative comparisons, we measure realism with user study and diversity with a perceptual distance metric. We apply the proposed model to domain adaptation and show competitive performance when compared to the state-of-the-art on the MNIST-M and the LineMod datasets.
注冊地址： 北京市海淀區羊坊店路18號2幢3層301-191