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Dec 11

Substrate Prediction for RiPP Biosynthetic Enzymes via Masked Language Modeling and Transfer Learning

Ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthetic enzymes often exhibit promiscuous substrate preferences that cannot be reduced to simple rules. Large language models are promising tools for predicting such peptide fitness landscapes. However, state-of-the-art protein language models are trained on relatively few peptide sequences. A previous study comprehensively profiled the peptide substrate preferences of LazBF (a two-component serine dehydratase) and LazDEF (a three-component azole synthetase) from the lactazole biosynthetic pathway. We demonstrated that masked language modeling of LazBF substrate preferences produced language model embeddings that improved downstream classification models of both LazBF and LazDEF substrates. Similarly, masked language modeling of LazDEF substrate preferences produced embeddings that improved the performance of classification models of both LazBF and LazDEF substrates. Our results suggest that the models learned functional forms that are transferable between distinct enzymatic transformations that act within the same biosynthetic pathway. Our transfer learning method improved performance and data efficiency in data-scarce scenarios. We then fine-tuned models on each data set and showed that the fine-tuned models provided interpretable insight that we anticipate will facilitate the design of substrate libraries that are compatible with desired RiPP biosynthetic pathways.

  • 4 authors
·
Feb 23, 2024

Fast, Effective, and Self-Supervised: Transforming Masked Language Models into Universal Lexical and Sentence Encoders

Pretrained Masked Language Models (MLMs) have revolutionised NLP in recent years. However, previous work has indicated that off-the-shelf MLMs are not effective as universal lexical or sentence encoders without further task-specific fine-tuning on NLI, sentence similarity, or paraphrasing tasks using annotated task data. In this work, we demonstrate that it is possible to turn MLMs into effective universal lexical and sentence encoders even without any additional data and without any supervision. We propose an extremely simple, fast and effective contrastive learning technique, termed Mirror-BERT, which converts MLMs (e.g., BERT and RoBERTa) into such encoders in 20-30 seconds without any additional external knowledge. Mirror-BERT relies on fully identical or slightly modified string pairs as positive (i.e., synonymous) fine-tuning examples, and aims to maximise their similarity during identity fine-tuning. We report huge gains over off-the-shelf MLMs with Mirror-BERT in both lexical-level and sentence-level tasks, across different domains and different languages. Notably, in the standard sentence semantic similarity (STS) tasks, our self-supervised Mirror-BERT model even matches the performance of the task-tuned Sentence-BERT models from prior work. Finally, we delve deeper into the inner workings of MLMs, and suggest some evidence on why this simple approach can yield effective universal lexical and sentence encoders.

  • 4 authors
·
Apr 16, 2021

PepMLM: Target Sequence-Conditioned Generation of Peptide Binders via Masked Language Modeling

Target proteins that lack accessible binding pockets and conformational stability have posed increasing challenges for drug development. Induced proximity strategies, such as PROTACs and molecular glues, have thus gained attention as pharmacological alternatives, but still require small molecule docking at binding pockets for targeted protein degradation (TPD). The computational design of protein-based binders presents unique opportunities to access undruggable targets, but have often relied on stable 3D structures or predictions for effective binder generation. Recently, we have leveraged the expressive latent spaces of protein language models (pLMs) for the prioritization of peptide binders from sequence alone, which we have then fused to E3 ubiquitin ligase domains, creating a CRISPR-analogous TPD system for target proteins. However, our methods rely on training discriminator models for ranking heuristically or unconditionally-derived guide peptides for their target binding capability. In this work, we introduce PepMLM, a purely target sequence-conditioned de novo generator of linear peptide binders. By employing a novel masking strategy that uniquely positions cognate peptide sequences at the terminus of target protein sequences, PepMLM tasks the state-of-the-art ESM-2 pLM to fully reconstruct the binder region, achieving low perplexities matching or improving upon previously-validated peptide-protein sequence pairs. After successful in silico benchmarking with AlphaFold-Multimer, we experimentally verify PepMLM's efficacy via fusion of model-derived peptides to E3 ubiquitin ligase domains, demonstrating endogenous degradation of target substrates in cellular models. In total, PepMLM enables the generative design of candidate binders to any target protein, without the requirement of target structure, empowering downstream programmable proteome editing applications.

  • 13 authors
·
Oct 5, 2023

Should We Still Pretrain Encoders with Masked Language Modeling?

Learning high-quality text representations is fundamental to a wide range of NLP tasks. While encoder pretraining has traditionally relied on Masked Language Modeling (MLM), recent evidence suggests that decoder models pretrained with Causal Language Modeling (CLM) can be effectively repurposed as encoders, often surpassing traditional encoders on text representation benchmarks. However, it remains unclear whether these gains reflect an inherent advantage of the CLM objective or arise from confounding factors such as model and data scale. In this paper, we address this question through a series of large-scale, carefully controlled pretraining ablations, training a total of 30 models ranging from 210 million to 1 billion parameters, and conducting over 15,000 fine-tuning and evaluation runs. We find that while training with MLM generally yields better performance across text representation tasks, CLM-trained models are more data-efficient and demonstrate improved fine-tuning stability. Building on these findings, we experimentally show that a biphasic training strategy that sequentially applies CLM and then MLM, achieves optimal performance under a fixed computational training budget. Moreover, we demonstrate that this strategy becomes more appealing when initializing from readily available pretrained CLM models (from the existing LLM ecosystem), reducing the computational burden needed to train best-in-class encoder models. We release all project artifacts at https://hf.co/MLMvsCLM to foster further research.

  • 8 authors
·
Jul 1 9

DrBERT: Unveiling the Potential of Masked Language Modeling Decoder in BERT pretraining

BERT (Bidirectional Encoder Representations from Transformers) has revolutionized the field of natural language processing through its exceptional performance on numerous tasks. Yet, the majority of researchers have mainly concentrated on enhancements related to the model structure, such as relative position embedding and more efficient attention mechanisms. Others have delved into pretraining tricks associated with Masked Language Modeling, including whole word masking. DeBERTa introduced an enhanced decoder adapted for BERT's encoder model for pretraining, proving to be highly effective. We argue that the design and research around enhanced masked language modeling decoders have been underappreciated. In this paper, we propose several designs of enhanced decoders and introduce DrBERT (Decoder-refined BERT), a novel method for modeling training. Typically, a pretrained BERT model is fine-tuned for specific Natural Language Understanding (NLU) tasks. In our approach, we utilize the original BERT model as the encoder, making only changes to the decoder without altering the encoder. This approach does not necessitate extensive modifications to the model's architecture and can be seamlessly integrated into existing fine-tuning pipelines and services, offering an efficient and effective enhancement strategy. Compared to other methods, while we also incur a moderate training cost for the decoder during the pretraining process, our approach does not introduce additional training costs during the fine-tuning phase. We test multiple enhanced decoder structures after pretraining and evaluate their performance on the GLUE benchmark. Our results demonstrate that DrBERT, having only undergone subtle refinements to the model structure during pretraining, significantly enhances model performance without escalating the inference time and serving budget.

  • 2 authors
·
Jan 28, 2024

Pairing interacting protein sequences using masked language modeling

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.

  • 3 authors
·
Aug 14, 2023

W2v-BERT: Combining Contrastive Learning and Masked Language Modeling for Self-Supervised Speech Pre-Training

Motivated by the success of masked language modeling~(MLM) in pre-training natural language processing models, we propose w2v-BERT that explores MLM for self-supervised speech representation learning. w2v-BERT is a framework that combines contrastive learning and MLM, where the former trains the model to discretize input continuous speech signals into a finite set of discriminative speech tokens, and the latter trains the model to learn contextualized speech representations via solving a masked prediction task consuming the discretized tokens. In contrast to existing MLM-based speech pre-training frameworks such as HuBERT, which relies on an iterative re-clustering and re-training process, or vq-wav2vec, which concatenates two separately trained modules, w2v-BERT can be optimized in an end-to-end fashion by solving the two self-supervised tasks~(the contrastive task and MLM) simultaneously. Our experiments show that w2v-BERT achieves competitive results compared to current state-of-the-art pre-trained models on the LibriSpeech benchmarks when using the Libri-Light~60k corpus as the unsupervised data. In particular, when compared to published models such as conformer-based wav2vec~2.0 and HuBERT, our model shows~5\% to~10\% relative WER reduction on the test-clean and test-other subsets. When applied to the Google's Voice Search traffic dataset, w2v-BERT outperforms our internal conformer-based wav2vec~2.0 by more than~30\% relatively.

  • 7 authors
·
Aug 7, 2021

ERNIE-Gram: Pre-Training with Explicitly N-Gram Masked Language Modeling for Natural Language Understanding

Coarse-grained linguistic information, such as named entities or phrases, facilitates adequately representation learning in pre-training. Previous works mainly focus on extending the objective of BERT's Masked Language Modeling (MLM) from masking individual tokens to contiguous sequences of n tokens. We argue that such contiguously masking method neglects to model the intra-dependencies and inter-relation of coarse-grained linguistic information. As an alternative, we propose ERNIE-Gram, an explicitly n-gram masking method to enhance the integration of coarse-grained information into pre-training. In ERNIE-Gram, n-grams are masked and predicted directly using explicit n-gram identities rather than contiguous sequences of n tokens. Furthermore, ERNIE-Gram employs a generator model to sample plausible n-gram identities as optional n-gram masks and predict them in both coarse-grained and fine-grained manners to enable comprehensive n-gram prediction and relation modeling. We pre-train ERNIE-Gram on English and Chinese text corpora and fine-tune on 19 downstream tasks. Experimental results show that ERNIE-Gram outperforms previous pre-training models like XLNet and RoBERTa by a large margin, and achieves comparable results with state-of-the-art methods. The source codes and pre-trained models have been released at https://github.com/PaddlePaddle/ERNIE.

  • 7 authors
·
Oct 22, 2020

It's All in The [MASK]: Simple Instruction-Tuning Enables BERT-like Masked Language Models As Generative Classifiers

While encoder-only models such as BERT and ModernBERT are ubiquitous in real-world NLP applications, their conventional reliance on task-specific classification heads can limit their applicability compared to decoder-based large language models (LLMs). In this work, we introduce ModernBERT-Large-Instruct, a 0.4B-parameter encoder model that leverages its masked language modelling (MLM) head for generative classification. Our approach employs an intentionally simple training loop and inference mechanism that requires no heavy pre-processing, heavily engineered prompting, or architectural modifications. ModernBERT-Large-Instruct exhibits strong zero-shot performance on both classification and knowledge-based tasks, outperforming similarly sized LLMs on MMLU and achieving 93% of Llama3-1B's MMLU performance with 60% less parameters. We also demonstrate that, when fine-tuned, the generative approach using the MLM head matches or even surpasses traditional classification-head methods across diverse NLU tasks.This capability emerges specifically in models trained on contemporary, diverse data mixes, with models trained on lower volume, less-diverse data yielding considerably weaker performance. Although preliminary, these results demonstrate the potential of using the original generative masked language modelling head over traditional task-specific heads for downstream tasks. Our work suggests that further exploration into this area is warranted, highlighting many avenues for future improvements.

  • 3 authors
·
Feb 6

Pre-training Language Model as a Multi-perspective Course Learner

ELECTRA, the generator-discriminator pre-training framework, has achieved impressive semantic construction capability among various downstream tasks. Despite the convincing performance, ELECTRA still faces the challenges of monotonous training and deficient interaction. Generator with only masked language modeling (MLM) leads to biased learning and label imbalance for discriminator, decreasing learning efficiency; no explicit feedback loop from discriminator to generator results in the chasm between these two components, underutilizing the course learning. In this study, a multi-perspective course learning (MCL) method is proposed to fetch a many degrees and visual angles for sample-efficient pre-training, and to fully leverage the relationship between generator and discriminator. Concretely, three self-supervision courses are designed to alleviate inherent flaws of MLM and balance the label in a multi-perspective way. Besides, two self-correction courses are proposed to bridge the chasm between the two encoders by creating a "correction notebook" for secondary-supervision. Moreover, a course soups trial is conducted to solve the "tug-of-war" dynamics problem of MCL, evolving a stronger pre-trained model. Experimental results show that our method significantly improves ELECTRA's average performance by 2.8% and 3.2% absolute points respectively on GLUE and SQuAD 2.0 benchmarks, and overshadows recent advanced ELECTRA-style models under the same settings. The pre-trained MCL model is available at https://huggingface.co/McmanusChen/MCL-base.

  • 9 authors
·
May 6, 2023

Do Not (Always) Look Right: Investigating the Capabilities of Decoder-Based Large Language Models for Sequence Labeling

Pre-trained language models based on masked language modeling (MLM) objective excel in natural language understanding (NLU) tasks. While fine-tuned MLM-based encoders consistently outperform causal language modeling decoders of comparable size, a recent trend of scaling decoder models to multiple billion parameters resulted in large language models (LLMs), making them competitive with MLM-based encoders. Although scale amplifies their prowess in NLU tasks, LLMs fall short of SOTA results in information extraction (IE) tasks, many framed as sequence labeling (SL). However, whether this is an intrinsic limitation of LLMs or whether their SL performance can be improved remains unclear. To address this, we explore strategies to enhance the SL performance of "open" LLMs (Llama2 and Mistral) on IE tasks. We investigate bidirectional information flow within groups of decoder blocks, applying layer-wise removal or enforcement of the causal mask (CM) during LLM fine-tuning. This approach yields performance gains competitive with SOTA SL models, matching or outperforming the results of CM removal from all blocks. Our findings hold for diverse SL tasks, proving that "open" LLMs with layer-dependent CM removal outperform strong MLM-based encoders and instruction-tuned LLMs. However, we observe no effect from CM removal on a small scale when maintaining an equivalent model size, pre-training steps, and pre-training and fine-tuning data.

  • 2 authors
·
Jan 25, 2024

What Language Model Architecture and Pretraining Objective Work Best for Zero-Shot Generalization?

Large pretrained Transformer language models have been shown to exhibit zero-shot generalization, i.e. they can perform a wide variety of tasks that they were not explicitly trained on. However, the architectures and pretraining objectives used across state-of-the-art models differ significantly, and there has been limited systematic comparison of these factors. In this work, we present a large-scale evaluation of modeling choices and their impact on zero-shot generalization. In particular, we focus on text-to-text models and experiment with three model architectures (causal/non-causal decoder-only and encoder-decoder), trained with two different pretraining objectives (autoregressive and masked language modeling), and evaluated with and without multitask prompted finetuning. We train models with over 5 billion parameters for more than 170 billion tokens, thereby increasing the likelihood that our conclusions will transfer to even larger scales. Our experiments show that causal decoder-only models trained on an autoregressive language modeling objective exhibit the strongest zero-shot generalization after purely unsupervised pretraining. However, models with non-causal visibility on their input trained with a masked language modeling objective followed by multitask finetuning perform the best among our experiments. We therefore consider the adaptation of pretrained models across architectures and objectives. We find that pretrained non-causal decoder models can be adapted into performant generative causal decoder models, using autoregressive language modeling as a downstream task. Furthermore, we find that pretrained causal decoder models can be efficiently adapted into non-causal decoder models, ultimately achieving competitive performance after multitask finetuning. Code and checkpoints are available at https://github.com/bigscience-workshop/architecture-objective.

  • 8 authors
·
Apr 12, 2022

Bidirectional Language Models Are Also Few-shot Learners

Large language models such as GPT-3 (Brown et al., 2020) can perform arbitrary tasks without undergoing fine-tuning after being prompted with only a few labeled examples. An arbitrary task can be reformulated as a natural language prompt, and a language model can be asked to generate the completion, indirectly performing the task in a paradigm known as prompt-based learning. To date, emergent prompt-based learning capabilities have mainly been demonstrated for unidirectional language models. However, bidirectional language models pre-trained on denoising objectives such as masked language modeling produce stronger learned representations for transfer learning. This motivates the possibility of prompting bidirectional models, but their pre-training objectives have made them largely incompatible with the existing prompting paradigm. We present SAP (Sequential Autoregressive Prompting), a technique that enables the prompting of bidirectional models. Utilizing the machine translation task as a case study, we prompt the bidirectional mT5 model (Xue et al., 2021) with SAP and demonstrate its few-shot and zero-shot translations outperform the few-shot translations of unidirectional models like GPT-3 and XGLM (Lin et al., 2021), despite mT5's approximately 50% fewer parameters. We further show SAP is effective on question answering and summarization. For the first time, our results demonstrate prompt-based learning is an emergent property of a broader class of language models, rather than only unidirectional models.

  • 6 authors
·
Sep 28, 2022

Biomedical Language Models are Robust to Sub-optimal Tokenization

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.

  • 3 authors
·
Jun 30, 2023

SecureBERT: A Domain-Specific Language Model for Cybersecurity

Natural Language Processing (NLP) has recently gained wide attention in cybersecurity, particularly in Cyber Threat Intelligence (CTI) and cyber automation. Increased connection and automation have revolutionized the world's economic and cultural infrastructures, while they have introduced risks in terms of cyber attacks. CTI is information that helps cybersecurity analysts make intelligent security decisions, that is often delivered in the form of natural language text, which must be transformed to machine readable format through an automated procedure before it can be used for automated security measures. This paper proposes SecureBERT, a cybersecurity language model capable of capturing text connotations in cybersecurity text (e.g., CTI) and therefore successful in automation for many critical cybersecurity tasks that would otherwise rely on human expertise and time-consuming manual efforts. SecureBERT has been trained using a large corpus of cybersecurity text.To make SecureBERT effective not just in retaining general English understanding, but also when applied to text with cybersecurity implications, we developed a customized tokenizer as well as a method to alter pre-trained weights. The SecureBERT is evaluated using the standard Masked Language Model (MLM) test as well as two additional standard NLP tasks. Our evaluation studies show that SecureBERT\url{https://github.com/ehsanaghaei/SecureBERT} outperforms existing similar models, confirming its capability for solving crucial NLP tasks in cybersecurity.

  • 4 authors
·
Apr 6, 2022

Endowing Protein Language Models with Structural Knowledge

Understanding the relationships between protein sequence, structure and function is a long-standing biological challenge with manifold implications from drug design to our understanding of evolution. Recently, protein language models have emerged as the preferred method for this challenge, thanks to their ability to harness large sequence databases. Yet, their reliance on expansive sequence data and parameter sets limits their flexibility and practicality in real-world scenarios. Concurrently, the recent surge in computationally predicted protein structures unlocks new opportunities in protein representation learning. While promising, the computational burden carried by such complex data still hinders widely-adopted practical applications. To address these limitations, we introduce a novel framework that enhances protein language models by integrating protein structural data. Drawing from recent advances in graph transformers, our approach refines the self-attention mechanisms of pretrained language transformers by integrating structural information with structure extractor modules. This refined model, termed Protein Structure Transformer (PST), is further pretrained on a small protein structure database, using the same masked language modeling objective as traditional protein language models. Empirical evaluations of PST demonstrate its superior parameter efficiency relative to protein language models, despite being pretrained on a dataset comprising only 542K structures. Notably, PST consistently outperforms the state-of-the-art foundation model for protein sequences, ESM-2, setting a new benchmark in protein function prediction. Our findings underscore the potential of integrating structural information into protein language models, paving the way for more effective and efficient protein modeling Code and pretrained models are available at https://github.com/BorgwardtLab/PST.

  • 5 authors
·
Jan 26, 2024

Toward Efficient Language Model Pretraining and Downstream Adaptation via Self-Evolution: A Case Study on SuperGLUE

This technical report briefly describes our JDExplore d-team's Vega v2 submission on the SuperGLUE leaderboard. SuperGLUE is more challenging than the widely used general language understanding evaluation (GLUE) benchmark, containing eight difficult language understanding tasks, including question answering, natural language inference, word sense disambiguation, coreference resolution, and reasoning. [Method] Instead of arbitrarily increasing the size of a pretrained language model (PLM), our aim is to 1) fully extract knowledge from the input pretraining data given a certain parameter budget, e.g., 6B, and 2) effectively transfer this knowledge to downstream tasks. To achieve goal 1), we propose self-evolution learning for PLMs to wisely predict the informative tokens that should be masked, and supervise the masked language modeling (MLM) process with rectified smooth labels. For goal 2), we leverage the prompt transfer technique to improve the low-resource tasks by transferring the knowledge from the foundation model and related downstream tasks to the target task. [Results] According to our submission record (Oct. 2022), with our optimized pretraining and fine-tuning strategies, our 6B Vega method achieved new state-of-the-art performance on 4/8 tasks, sitting atop the SuperGLUE leaderboard on Oct. 8, 2022, with an average score of 91.3.

  • 14 authors
·
Dec 4, 2022

L3Cube-HingCorpus and HingBERT: A Code Mixed Hindi-English Dataset and BERT Language Models

Code-switching occurs when more than one language is mixed in a given sentence or a conversation. This phenomenon is more prominent on social media platforms and its adoption is increasing over time. Therefore code-mixed NLP has been extensively studied in the literature. As pre-trained transformer-based architectures are gaining popularity, we observe that real code-mixing data are scarce to pre-train large language models. We present L3Cube-HingCorpus, the first large-scale real Hindi-English code mixed data in a Roman script. It consists of 52.93M sentences and 1.04B tokens, scraped from Twitter. We further present HingBERT, HingMBERT, HingRoBERTa, and HingGPT. The BERT models have been pre-trained on codemixed HingCorpus using masked language modelling objectives. We show the effectiveness of these BERT models on the subsequent downstream tasks like code-mixed sentiment analysis, POS tagging, NER, and LID from the GLUECoS benchmark. The HingGPT is a GPT2 based generative transformer model capable of generating full tweets. We also release L3Cube-HingLID Corpus, the largest code-mixed Hindi-English language identification(LID) dataset and HingBERT-LID, a production-quality LID model to facilitate capturing of more code-mixed data using the process outlined in this work. The dataset and models are available at https://github.com/l3cube-pune/code-mixed-nlp .

  • 2 authors
·
Apr 18, 2022

CM3: A Causal Masked Multimodal Model of the Internet

We introduce CM3, a family of causally masked generative models trained over a large corpus of structured multi-modal documents that can contain both text and image tokens. Our new causally masked approach generates tokens left to right while also masking out a small number of long token spans that are generated at the end of the string, instead of their original positions. The casual masking object provides a type of hybrid of the more common causal and masked language models, by enabling full generative modeling while also providing bidirectional context when generating the masked spans. We train causally masked language-image models on large-scale web and Wikipedia articles, where each document contains all of the text, hypertext markup, hyperlinks, and image tokens (from a VQVAE-GAN), provided in the order they appear in the original HTML source (before masking). The resulting CM3 models can generate rich structured, multi-modal outputs while conditioning on arbitrary masked document contexts, and thereby implicitly learn a wide range of text, image, and cross modal tasks. They can be prompted to recover, in a zero-shot fashion, the functionality of models such as DALL-E, GENRE, and HTLM. We set the new state-of-the-art in zero-shot summarization, entity linking, and entity disambiguation while maintaining competitive performance in the fine-tuning setting. We can generate images unconditionally, conditioned on text (like DALL-E) and do captioning all in a zero-shot setting with a single model.

  • 11 authors
·
Jan 19, 2022

A Survey on Diffusion Language Models

Diffusion Language Models (DLMs) are rapidly emerging as a powerful and promising alternative to the dominant autoregressive (AR) paradigm. By generating tokens in parallel through an iterative denoising process, DLMs possess inherent advantages in reducing inference latency and capturing bidirectional context, thereby enabling fine-grained control over the generation process. While achieving a several-fold speed-up, recent advancements have allowed DLMs to show performance comparable to their autoregressive counterparts, making them a compelling choice for various natural language processing tasks. In this survey, we provide a holistic overview of the current DLM landscape. We trace its evolution and relationship with other paradigms, such as autoregressive and masked language models, and cover both foundational principles and state-of-the-art models. Our work offers an up-to-date, comprehensive taxonomy and an in-depth analysis of current techniques, from pre-training strategies to advanced post-training methods. Another contribution of this survey is a thorough review of DLM inference strategies and optimizations, including improvements in decoding parallelism, caching mechanisms, and generation quality. We also highlight the latest approaches to multimodal extensions of DLMs and delineate their applications across various practical scenarios. Furthermore, our discussion addresses the limitations and challenges of DLMs, including efficiency, long-sequence handling, and infrastructure requirements, while outlining future research directions to sustain progress in this rapidly evolving field. Project GitHub is available at https://github.com/VILA-Lab/Awesome-DLMs.

  • 4 authors
·
Aug 14 2

Linguistic Entity Masking to Improve Cross-Lingual Representation of Multilingual Language Models for Low-Resource Languages

Multilingual Pre-trained Language models (multiPLMs), trained on the Masked Language Modelling (MLM) objective are commonly being used for cross-lingual tasks such as bitext mining. However, the performance of these models is still suboptimal for low-resource languages (LRLs). To improve the language representation of a given multiPLM, it is possible to further pre-train it. This is known as continual pre-training. Previous research has shown that continual pre-training with MLM and subsequently with Translation Language Modelling (TLM) improves the cross-lingual representation of multiPLMs. However, during masking, both MLM and TLM give equal weight to all tokens in the input sequence, irrespective of the linguistic properties of the tokens. In this paper, we introduce a novel masking strategy, Linguistic Entity Masking (LEM) to be used in the continual pre-training step to further improve the cross-lingual representations of existing multiPLMs. In contrast to MLM and TLM, LEM limits masking to the linguistic entity types nouns, verbs and named entities, which hold a higher prominence in a sentence. Secondly, we limit masking to a single token within the linguistic entity span thus keeping more context, whereas, in MLM and TLM, tokens are masked randomly. We evaluate the effectiveness of LEM using three downstream tasks, namely bitext mining, parallel data curation and code-mixed sentiment analysis using three low-resource language pairs English-Sinhala, English-Tamil, and Sinhala-Tamil. Experiment results show that continually pre-training a multiPLM with LEM outperforms a multiPLM continually pre-trained with MLM+TLM for all three tasks.

  • 2 authors
·
Jan 9

CamemBERT 2.0: A Smarter French Language Model Aged to Perfection

French language models, such as CamemBERT, have been widely adopted across industries for natural language processing (NLP) tasks, with models like CamemBERT seeing over 4 million downloads per month. However, these models face challenges due to temporal concept drift, where outdated training data leads to a decline in performance, especially when encountering new topics and terminology. This issue emphasizes the need for updated models that reflect current linguistic trends. In this paper, we introduce two new versions of the CamemBERT base model-CamemBERTav2 and CamemBERTv2-designed to address these challenges. CamemBERTav2 is based on the DeBERTaV3 architecture and makes use of the Replaced Token Detection (RTD) objective for better contextual understanding, while CamemBERTv2 is built on RoBERTa, which uses the Masked Language Modeling (MLM) objective. Both models are trained on a significantly larger and more recent dataset with longer context length and an updated tokenizer that enhances tokenization performance for French. We evaluate the performance of these models on both general-domain NLP tasks and domain-specific applications, such as medical field tasks, demonstrating their versatility and effectiveness across a range of use cases. Our results show that these updated models vastly outperform their predecessors, making them valuable tools for modern NLP systems. All our new models, as well as intermediate checkpoints, are made openly available on Huggingface.

  • 6 authors
·
Nov 13, 2024 9

Lessons learned from the evaluation of Spanish Language Models

Given the impact of language models on the field of Natural Language Processing, a number of Spanish encoder-only masked language models (aka BERTs) have been trained and released. These models were developed either within large projects using very large private corpora or by means of smaller scale academic efforts leveraging freely available data. In this paper we present a comprehensive head-to-head comparison of language models for Spanish with the following results: (i) Previously ignored multilingual models from large companies fare better than monolingual models, substantially changing the evaluation landscape of language models in Spanish; (ii) Results across the monolingual models are not conclusive, with supposedly smaller and inferior models performing competitively. Based on these empirical results, we argue for the need of more research to understand the factors underlying them. In this sense, the effect of corpus size, quality and pre-training techniques need to be further investigated to be able to obtain Spanish monolingual models significantly better than the multilingual ones released by large private companies, specially in the face of rapid ongoing progress in the field. The recent activity in the development of language technology for Spanish is to be welcomed, but our results show that building language models remains an open, resource-heavy problem which requires to marry resources (monetary and/or computational) with the best research expertise and practice.

  • 2 authors
·
Dec 16, 2022

Long-context Protein Language Model

Self-supervised training of language models (LMs) has seen great success for protein sequences in learning meaningful representations and for generative drug design. Most protein LMs are based on the Transformer architecture trained on individual proteins with short context lengths. Such protein LMs cannot extrapolate to longer proteins and protein complexes well. They also fail to account for the underlying biological mechanisms carried out by biomolecular interactions and dynamics i.e., proteins often interact with other proteins, molecules, and pathways in complex biological systems. In this work, we propose LC-PLM based on an alternative protein LM architecture, BiMamba-S, built off selective structured state-space models, to learn high-quality universal protein representations at the amino acid token level using masked language modeling. We also introduce its graph-contextual variant, LC-PLM-G, which contextualizes protein-protein interaction (PPI) graphs for a second stage of training. LC-PLM demonstrates favorable neural scaling laws, better length extrapolation capability, and a 7% to 34% improvement on protein downstream tasks than Transformer-based ESM-2. LC-PLM-G further trained within the context of PPI graphs shows promising results on protein structure and function prediction tasks. Our study demonstrates the benefit of increasing the context size with computationally efficient LM architecture (e.g. structured state space models) in learning universal protein representations and incorporating molecular interaction context contained in biological graphs.

  • 7 authors
·
Oct 29, 2024

Towards Effective Time-Aware Language Representation: Exploring Enhanced Temporal Understanding in Language Models

In the evolving field of Natural Language Processing, understanding the temporal context of text is increasingly crucial. This study investigates methods to incorporate temporal information during pre-training, aiming to achieve effective time-aware language representation for improved performance on time-related tasks. In contrast to common pre-trained models like BERT, which rely on synchronic document collections such as BookCorpus and Wikipedia, our research introduces BiTimeBERT 2.0, a novel language model pre-trained on a temporal news article collection. BiTimeBERT 2.0 utilizes this temporal news collection, focusing on three innovative pre-training objectives: Time-Aware Masked Language Modeling (TAMLM), Document Dating (DD), and Time-Sensitive Entity Replacement (TSER). Each objective targets a unique aspect of temporal information. TAMLM is designed to enhance the understanding of temporal contexts and relations, DD integrates document timestamps as chronological markers, and TSER focuses on the temporal dynamics of "Person" entities, recognizing their inherent temporal significance. The experimental results consistently demonstrate that BiTimeBERT 2.0 outperforms models like BERT and other existing pre-trained models, achieving substantial gains across a variety of downstream NLP tasks and applications where time plays a pivotal role.

  • 3 authors
·
Jun 3, 2024

Advancing Retrieval-Augmented Generation for Persian: Development of Language Models, Comprehensive Benchmarks, and Best Practices for Optimization

This paper examines the specific obstacles of constructing Retrieval-Augmented Generation(RAG) systems in low-resource languages, with a focus on Persian's complicated morphology and versatile syntax. The research aims to improve retrieval and generation accuracy by introducing Persian-specific models, namely MatinaRoberta(a masked language model) and MatinaSRoberta(a fine-tuned Sentence-BERT), along with a comprehensive benchmarking framework. Three datasets-general knowledge(PQuad), scientifically specialized texts, and organizational reports, were used to assess these models after they were trained on a varied corpus of 73.11 billion Persian tokens. The methodology involved extensive pretraining, fine-tuning with tailored loss functions, and systematic evaluations using both traditional metrics and the Retrieval-Augmented Generation Assessment framework. The results show that MatinaSRoberta outperformed previous embeddings, achieving superior contextual relevance and retrieval accuracy across datasets. Temperature tweaking, chunk size modifications, and document summary indexing were explored to enhance RAG setups. Larger models like Llama-3.1 (70B) consistently demonstrated the highest generation accuracy, while smaller models faced challenges with domain-specific and formal contexts. The findings underscore the potential for developing RAG systems in Persian through customized embeddings and retrieval-generation settings and highlight the enhancement of NLP applications such as search engines and legal document analysis in low-resource languages.

  • 5 authors
·
Jan 8

LightCLIP: Learning Multi-Level Interaction for Lightweight Vision-Language Models

Vision-language pre-training like CLIP has shown promising performance on various downstream tasks such as zero-shot image classification and image-text retrieval. Most of the existing CLIP-alike works usually adopt relatively large image encoders like ResNet50 and ViT, while the lightweight counterparts are rarely discussed. In this paper, we propose a multi-level interaction paradigm for training lightweight CLIP models. Firstly, to mitigate the problem that some image-text pairs are not strictly one-to-one correspondence, we improve the conventional global instance-level alignment objective by softening the label of negative samples progressively. Secondly, a relaxed bipartite matching based token-level alignment objective is introduced for finer-grained alignment between image patches and textual words. Moreover, based on the observation that the accuracy of CLIP model does not increase correspondingly as the parameters of text encoder increase, an extra objective of masked language modeling (MLM) is leveraged for maximizing the potential of the shortened text encoder. In practice, an auxiliary fusion module injecting unmasked image embedding into masked text embedding at different network stages is proposed for enhancing the MLM. Extensive experiments show that without introducing additional computational cost during inference, the proposed method achieves a higher performance on multiple downstream tasks.

  • 7 authors
·
Dec 1, 2023

Small Models, Big Impact: Efficient Corpus and Graph-Based Adaptation of Small Multilingual Language Models for Low-Resource Languages

Low-resource languages (LRLs) face significant challenges in natural language processing (NLP) due to limited data. While current state-of-the-art large language models (LLMs) still struggle with LRLs, smaller multilingual models (mLMs) such as mBERT and XLM-R offer greater promise due to a better fit of their capacity to low training data sizes. This study systematically investigates parameter-efficient adapter-based methods for adapting mLMs to LRLs, evaluating three architectures: Sequential Bottleneck, Invertible Bottleneck, and Low-Rank Adaptation. Using unstructured text from GlotCC and structured knowledge from ConceptNet, we show that small adaptation datasets (e.g., up to 1 GB of free-text or a few MB of knowledge graph data) yield gains in intrinsic (masked language modeling) and extrinsic tasks (topic classification, sentiment analysis, and named entity recognition). We find that Sequential Bottleneck adapters excel in language modeling, while Invertible Bottleneck adapters slightly outperform other methods on downstream tasks due to better embedding alignment and larger parameter counts. Adapter-based methods match or outperform full fine-tuning while using far fewer parameters, and smaller mLMs prove more effective for LRLs than massive LLMs like LLaMA-3, GPT-4, and DeepSeek-R1-based distilled models. While adaptation improves performance, pre-training data size remains the dominant factor, especially for languages with extensive pre-training coverage.

  • 4 authors
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Feb 14 2