Predicting which proteins interact together from amino-acid sequences is an important task. We develop a method to pair interacting protein sequences which leverages the power of protein language models trained on multiple sequence alignments, such as MSA Transformer and the EvoFormer module of AlphaFold. We formulate the problem of pairing interacting partners among the paralogs of two protein families in a differentiable way. We introduce a method called DiffPALM that solves it by exploiting the ability of MSA Transformer to fill in masked amino acids in multiple sequence alignments using the surrounding context. MSA Transformer encodes coevolution between functionally or structurally coupled amino acids. We show that it captures inter-chain coevolution, while it was trained on single-chain data, which means that it can be used out-of-distribution. Relying on MSA Transformer without fine-tuning, DiffPALM outperforms existing coevolution-based pairing methods on difficult benchmarks of shallow multiple sequence alignments extracted from ubiquitous prokaryotic protein datasets. It also outperforms an alternative method based on a state-of-the-art protein language model trained on single sequences. Paired alignments of interacting protein sequences are a crucial ingredient of supervised deep learning methods to predict the three-dimensional structure of protein complexes. DiffPALM substantially improves the structure prediction of some eukaryotic protein complexes by AlphaFold-Multimer, without significantly deteriorating any of those we tested. It also achieves competitive performance with using orthology-based pairing.
Masked Image Modeling (MIM) is a promising self-supervised learning approach that enables learning from unlabeled images. Despite its recent success, learning good representations through MIM remains challenging because it requires predicting the right semantic content in accurate locations. For example, given an incomplete picture of a dog, we can guess that there is a tail, but we cannot determine its exact location. In this work, we propose to incorporate location uncertainty into MIM by using stochastic positional embeddings (StoP). Specifically, we condition the model on stochastic masked token positions drawn from a Gaussian distribution. StoP reduces overfitting to location features and guides the model toward learning features that are more robust to location uncertainties. Quantitatively, StoP improves downstream MIM performance on a variety of downstream tasks, including $+1.7\%$ on ImageNet linear probing using ViT-B, and $+2.5\%$ for ViT-H using $1\%$ of the data.
Large-scale language models such as DNABert and LOGO aim to learn optimal gene representations and are trained on the entire Human Reference Genome. However, standard tokenization schemes involve a simple sliding window of tokens like k-mers that do not leverage any gene-based semantics and thus may lead to (trivial) masking of easily predictable sequences and subsequently inefficient Masked Language Modeling (MLM) training. Therefore, we propose a novel masking algorithm, GeneMask, for MLM training of gene sequences, where we randomly identify positions in a gene sequence as mask centers and locally select the span around the mask center with the highest Normalized Pointwise Mutual Information (NPMI) to mask. We observe that in the absence of human-understandable semantics in the genomics domain (in contrast, semantic units like words and phrases are inherently available in NLP), GeneMask-based models substantially outperform the SOTA models (DNABert and LOGO) over four benchmark gene sequence classification datasets in five few-shot settings (10 to 1000-shot). More significantly, the GeneMask-based DNABert model is trained for less than one-tenth of the number of epochs of the original SOTA model. We also observe a strong correlation between top-ranked PMI tokens and conserved DNA sequence motifs, which may indicate the incorporation of latent genomic information. The codes (including trained models) and datasets are made publicly available at https://github.com/roysoumya/GeneMask.
As opposed to general English, many concepts in biomedical terminology have been designed in recent history by biomedical professionals with the goal of being precise and concise. This is often achieved by concatenating meaningful biomedical morphemes to create new semantic units. Nevertheless, most modern biomedical language models (LMs) are pre-trained using standard domain-specific tokenizers derived from large scale biomedical corpus statistics without explicitly leveraging the agglutinating nature of biomedical language. In this work, we first find that standard open-domain and biomedical tokenizers are largely unable to segment biomedical terms into meaningful components. Therefore, we hypothesize that using a tokenizer which segments biomedical terminology more accurately would enable biomedical LMs to improve their performance on downstream biomedical NLP tasks, especially ones which involve biomedical terms directly such as named entity recognition (NER) and entity linking. Surprisingly, we find that pre-training a biomedical LM using a more accurate biomedical tokenizer does not improve the entity representation quality of a language model as measured by several intrinsic and extrinsic measures such as masked language modeling prediction (MLM) accuracy as well as NER and entity linking performance. These quantitative findings, along with a case study which explores entity representation quality more directly, suggest that the biomedical pre-training process is quite robust to instances of sub-optimal tokenization.
Superconductivity allows electrical current to flow without any energy loss, and thus making solids superconducting is a grand goal of physics, material science, and electrical engineering. More than 16 Nobel Laureates have been awarded for their contribution to superconductivity research. Superconductors are valuable for sustainable development goals (SDGs), such as climate change mitigation, affordable and clean energy, industry, innovation and infrastructure, and so on. However, a unified physics theory explaining all superconductivity mechanism is still unknown. It is believed that superconductivity is microscopically due to not only molecular compositions but also the geometric crystal structure. Hence a new dataset, S2S, containing both crystal structures and superconducting critical temperature, is built upon SuperCon and Material Project. Based on this new dataset, we propose a novel model, S2SNet, which utilizes the attention mechanism for superconductivity prediction. To overcome the shortage of data, S2SNet is pre-trained on the whole Material Project dataset with Masked-Language Modeling (MLM). S2SNet makes a new state-of-the-art, with out-of-sample accuracy of 92% and Area Under Curve (AUC) of 0.92. To the best of our knowledge, S2SNet is the first work to predict superconductivity with only information of crystal structures. This work is beneficial to superconductivity discovery and further SDGs. Code and datasets are available in https://github.com/zjuKeLiu/S2SNet
In recent years, a significant number of high-quality pretrained models have emerged, greatly impacting Natural Language Understanding (NLU), Natural Language Generation (NLG), and Text Representation tasks. Traditionally, these models are pretrained on custom domain corpora and finetuned for specific tasks, resulting in high costs related to GPU usage and labor. Unfortunately, recent trends in language modeling have shifted towards enhancing performance through scaling, further exacerbating the associated costs. Introducing GUR: a pretraining framework that combines language modeling and contrastive learning objectives in a single training step. We select similar text pairs based on their Longest Common Substring (LCS) from raw unlabeled documents and train the model using masked language modeling and unsupervised contrastive learning. The resulting model, GUR, achieves impressive results without any labeled training data, outperforming all other pretrained baselines as a retriever at the recall benchmark in a zero-shot setting. Additionally, GUR maintains its language modeling ability, as demonstrated in our ablation experiment. Our code is available at \url{https://github.com/laohur/GUR}.
We address personalized image enhancement in this study, where we enhance input images for each user based on the user's preferred images. Previous methods apply the same preferred style to all input images (i.e., only one style for each user); in contrast to these methods, we aim to achieve content-aware personalization by applying different styles to each image considering the contents. For content-aware personalization, we make two contributions. First, we propose a method named masked style modeling, which can predict a style for an input image considering the contents by using the framework of masked language modeling. Second, to allow this model to consider the contents of images, we propose a novel training scheme where we download images from Flickr and create pseudo input and retouched image pairs using a degrading model. We conduct quantitative evaluations and a user study, and our method trained using our training scheme successfully achieves content-aware personalization; moreover, our method outperforms other previous methods in this field. Our source code is available at https://github.com/satoshi-kosugi/masked-style-modeling.
Cross-modal alignment plays a crucial role in vision-language pre-training (VLP) models, enabling them to capture meaningful associations across different modalities. For this purpose, numerous masked modeling tasks have been proposed for VLP to further promote cross-modal interactions. The core idea of previous masked modeling tasks is to focus on reconstructing the masked tokens based on visible context for learning local-local alignment. However, most of them pay little attention to the global semantic features generated for the masked data, resulting in a limited cross-modal alignment ability of global representations to local features of the other modality. Therefore, in this paper, we propose a novel Global and Local Semantic Completion Learning (GLSCL) task to facilitate global-local alignment and local-local alignment simultaneously. Specifically, the GLSCL task complements the missing semantics of masked data and recovers global and local features by cross-modal interactions. Our GLSCL consists of masked global semantic completion (MGSC) and masked local token completion (MLTC). MGSC promotes learning more representative global features, which have a great impact on the performance of downstream tasks, while MLTC reconstructs modal-fusion local tokens, further enhancing accurate comprehension of multimodal data. To evaluate the proposed approaches on cross-modal alignment, we develop a validation benchmark called ALIGN-BENCH. Moreover, we present a flexible vision encoder, enabling our model to simultaneously perform image-text and video-text multimodal tasks. Experimental results show that our proposed method obtains state-of-the-art performance on various vision-language benchmarks, such as visual question answering, image-text retrieval, and video-text retrieval.
Dialogue response selection aims to select an appropriate response from several candidates based on a given user and system utterance history. Most existing works primarily focus on post-training and fine-tuning tailored for cross-encoders. However, there are no post-training methods tailored for dense encoders in dialogue response selection. We argue that when the current language model, based on dense dialogue systems (such as BERT), is employed as a dense encoder, it separately encodes dialogue context and response, leading to a struggle to achieve the alignment of both representations. Thus, we propose Dial-MAE (Dialogue Contextual Masking Auto-Encoder), a straightforward yet effective post-training technique tailored for dense encoders in dialogue response selection. Dial-MAE uses an asymmetric encoder-decoder architecture to compress the dialogue semantics into dense vectors, which achieves better alignment between the features of the dialogue context and response. Our experiments have demonstrated that Dial-MAE is highly effective, achieving state-of-the-art performance on two commonly evaluated benchmarks.
Masked language modeling (MLM) has been one of the most popular pretraining recipes in natural language processing, e.g., BERT, one of the representative models. Recently, contrastive language-image pretraining (CLIP) has also attracted attention, especially its vision models that achieve excellent performance on a broad range of vision tasks. However, few studies are dedicated to studying the text encoders learned by CLIP. In this paper, we analyze the difference between BERT-style and CLIP-style text encoders from three experiments: (i) general text understanding, (ii) vision-centric text understanding, and (iii) text-to-image generation. Experimental analyses show that although CLIP-style text encoders underperform BERT-style ones for general text understanding tasks, they are equipped with a unique ability, i.e., synesthesia, for the cross-modal association, which is more similar to the senses of humans.
This paper presents a novel design of the system aimed at supporting the Wikipedia community in addressing vandalism on the platform. To achieve this, we collected a massive dataset of 47 languages, and applied advanced filtering and feature engineering techniques, including multilingual masked language modeling to build the training dataset from human-generated data. The performance of the system was evaluated through comparison with the one used in production in Wikipedia, known as ORES. Our research results in a significant increase in the number of languages covered, making Wikipedia patrolling more efficient to a wider range of communities. Furthermore, our model outperforms ORES, ensuring that the results provided are not only more accurate but also less biased against certain groups of contributors.
Learned sparse retrieval (LSR) is a family of neural retrieval methods that transform queries and documents into sparse weight vectors aligned with a vocabulary. While LSR approaches like Splade work well for short passages, it is unclear how well they handle longer documents. We investigate existing aggregation approaches for adapting LSR to longer documents and find that proximal scoring is crucial for LSR to handle long documents. To leverage this property, we proposed two adaptations of the Sequential Dependence Model (SDM) to LSR: ExactSDM and SoftSDM. ExactSDM assumes only exact query term dependence, while SoftSDM uses potential functions that model the dependence of query terms and their expansion terms (i.e., terms identified using a transformer's masked language modeling head). Experiments on the MSMARCO Document and TREC Robust04 datasets demonstrate that both ExactSDM and SoftSDM outperform existing LSR aggregation approaches for different document length constraints. Surprisingly, SoftSDM does not provide any performance benefits over ExactSDM. This suggests that soft proximity matching is not necessary for modeling term dependence in LSR. Overall, this study provides insights into handling long documents with LSR, proposing adaptations that improve its performance.
Large pre-trained language models (PLMs) have demonstrated strong performance on natural language understanding (NLU) tasks through fine-tuning. However, fine-tuned models still suffer from overconfident predictions, especially in out-of-domain settings. In this paper, we tackle the problem of calibrating fine-tuned language models. We demonstrate that the PLMs are well-calibrated on the masked language modeling task with robust predictive confidence under domain shift, yet the fine-tuned models fail to retain such property due to catastrophic forgetting, which impacts the calibration on the downstream classification task. In light of these observations, we evaluate the calibration of several methods that preserve pre-trained features and show that preserving pre-trained features can improve the calibration of fine-tuned language models. Among these methods, our proposed method that encourages the fine-tuned model to learn generative representations with auxiliary language modeling objective achieves competitive accuracy and the lowest expected calibration error compared to several strong baselines under both in-domain and out-of-domain settings on three downstream NLU tasks.
In this paper, we study Chinese Spelling Correction (CSC) as a joint decision made by two separate models: a language model and an error model. Through empirical analysis, we find that fine-tuning BERT tends to over-fit the error model while under-fit the language model, resulting in poor generalization to out-of-distribution error patterns. Given that BERT is the backbone of most CSC models, this phenomenon has a significant negative impact. To address this issue, we are releasing a multi-domain benchmark LEMON, with higher quality and diversity than existing benchmarks, to allow a comprehensive assessment of the open domain generalization of CSC models. Then, we demonstrate that a very simple strategy, randomly masking 20\% non-error tokens from the input sequence during fine-tuning is sufficient for learning a much better language model without sacrificing the error model. This technique can be applied to any model architecture and achieves new state-of-the-art results on SIGHAN, ECSpell, and LEMON.
In recent years, language models have drastically grown in size, and the abilities of these models have been shown to improve with scale. The majority of recent scaling laws studies focused on high-compute high-parameter count settings, leaving the question of when these abilities begin to emerge largely unanswered. In this paper, we investigate whether the effects of pre-training can be observed when the problem size is reduced, modeling a smaller, reduced-vocabulary language. We show the benefits of pre-training with masked language modeling (MLM) objective in models as small as 1.25M parameters, and establish a strong correlation between pre-training perplexity and downstream performance (GLUE benchmark). We examine downscaling effects, extending scaling laws to models as small as ~1M parameters. At this scale, we observe a break of the power law for compute-optimal models and show that the MLM loss does not scale smoothly with compute-cost (FLOPs) below $2.2 \times 10^{15}$ FLOPs. We also find that adding layers does not always benefit downstream performance.
With a growing focus on morphological inflection systems for languages where high-quality data is scarce, training data noise is a serious but so far largely ignored concern. We aim at closing this gap by investigating the types of noise encountered within a pipeline for truly unsupervised morphological paradigm completion and its impact on morphological inflection systems: First, we propose an error taxonomy and annotation pipeline for inflection training data. Then, we compare the effect of different types of noise on multiple state-of-the-art inflection models. Finally, we propose a novel character-level masked language modeling (CMLM) pretraining objective and explore its impact on the models' resistance to noise. Our experiments show that various architectures are impacted differently by separate types of noise, but encoder-decoders tend to be more robust to noise than models trained with a copy bias. CMLM pretraining helps transformers, but has lower impact on LSTMs.
Scene Text Recognition (STR) is difficult because of the variations in text styles, shapes, and backgrounds. Though the integration of linguistic information enhances models' performance, existing methods based on either permuted language modeling (PLM) or masked language modeling (MLM) have their pitfalls. PLM's autoregressive decoding lacks foresight into subsequent characters, while MLM overlooks inter-character dependencies. Addressing these problems, we propose a masked and permuted implicit context learning network for STR, which unifies PLM and MLM within a single decoder, inheriting the advantages of both approaches. We utilize the training procedure of PLM, and to integrate MLM, we incorporate word length information into the decoding process and replace the undetermined characters with mask tokens. Besides, perturbation training is employed to train a more robust model against potential length prediction errors. Our empirical evaluations demonstrate the performance of our model. It not only achieves superior performance on the common benchmarks but also achieves a substantial improvement of $9.1\%$ on the more challenging Union14M-Benchmark.
Masked language modeling, widely used in discriminative language model (e.g., BERT) pretraining, commonly adopts a random masking strategy. However, random masking does not consider the importance of the different words in the sentence meaning, where some of them are more worthy to be predicted. Therefore, various masking strategies (e.g., entity-level masking) are proposed, but most of them require expensive prior knowledge and generally train from scratch without reusing existing model weights. In this paper, we present Self-Evolution learning (SE), a simple and effective token masking and learning method to fully and wisely exploit the knowledge from data. SE focuses on learning the informative yet under-explored tokens and adaptively regularizes the training by introducing a novel Token-specific Label Smoothing approach. Experiments on 10 tasks show that our SE brings consistent and significant improvements (+1.43~2.12 average scores) upon different PLMs. In-depth analyses demonstrate that SE improves linguistic knowledge learning and generalization.
Despite their successes in NLP, Transformer-based language models still require extensive computing resources and suffer in low-resource or low-compute settings. In this paper, we present AxomiyaBERTa, a novel BERT model for Assamese, a morphologically-rich low-resource language (LRL) of Eastern India. AxomiyaBERTa is trained only on the masked language modeling (MLM) task, without the typical additional next sentence prediction (NSP) objective, and our results show that in resource-scarce settings for very low-resource languages like Assamese, MLM alone can be successfully leveraged for a range of tasks. AxomiyaBERTa achieves SOTA on token-level tasks like Named Entity Recognition and also performs well on "longer-context" tasks like Cloze-style QA and Wiki Title Prediction, with the assistance of a novel embedding disperser and phonological signals respectively. Moreover, we show that AxomiyaBERTa can leverage phonological signals for even more challenging tasks, such as a novel cross-document coreference task on a translated version of the ECB+ corpus, where we present a new SOTA result for an LRL. Our source code and evaluation scripts may be found at https://github.com/csu-signal/axomiyaberta.
Event detection is a crucial information extraction task in many domains, such as Wikipedia or news. The task typically relies on trigger detection (TD) -- identifying token spans in the text that evoke specific events. While the notion of triggers should ideally be universal across domains, domain transfer for TD from high- to low-resource domains results in significant performance drops. We address the problem of negative transfer in TD by coupling triggers between domains using subject-object relations obtained from a rule-based open information extraction (OIE) system. We demonstrate that OIE relations injected through multi-task training can act as mediators between triggers in different domains, enhancing zero- and few-shot TD domain transfer and reducing performance drops, in particular when transferring from a high-resource source domain (Wikipedia) to a low(er)-resource target domain (news). Additionally, we combine this improved transfer with masked language modeling on the target domain, observing further TD transfer gains. Finally, we demonstrate that the gains are robust to the choice of the OIE system.