Understanding the irregular electrical activity of atrial fibrillation (AFib) has been a key challenge in electrocardiography. For serious cases of AFib, catheter ablations are performed to collect intracardiac electrograms (EGMs). EGMs offer intricately detailed and localized electrical activity of the heart and are an ideal modality for interpretable cardiac studies. Recent advancements in artificial intelligence (AI) has allowed some works to utilize deep learning frameworks to interpret EGMs during AFib. Additionally, language models (LMs) have shown exceptional performance in being able to generalize to unseen domains, especially in healthcare. In this study, we are the first to leverage pretrained LMs for finetuning of EGM interpolation and AFib classification via masked language modeling. We formulate the EGM as a textual sequence and present competitive performances on AFib classification compared against other representations. Lastly, we provide a comprehensive interpretability study to provide a multi-perspective intuition of the model's behavior, which could greatly benefit the clinical use.
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.
Although BERT-style encoder models are heavily used in NLP research, many researchers do not pretrain their own BERTs from scratch due to the high cost of training. In the past half-decade since BERT first rose to prominence, many advances have been made with other transformer architectures and training configurations that have yet to be systematically incorporated into BERT. Here, we introduce MosaicBERT, a BERT-style encoder architecture and training recipe that is empirically optimized for fast pretraining. This efficient architecture incorporates FlashAttention, Attention with Linear Biases (ALiBi), Gated Linear Units (GLU), a module to dynamically remove padded tokens, and low precision LayerNorm into the classic transformer encoder block. The training recipe includes a 30% masking ratio for the Masked Language Modeling (MLM) objective, bfloat16 precision, and vocabulary size optimized for GPU throughput, in addition to best-practices from RoBERTa and other encoder models. When pretrained from scratch on the C4 dataset, this base model achieves a downstream average GLUE (dev) score of 79.6 in 1.13 hours on 8 A100 80 GB GPUs at a cost of roughly $20. We plot extensive accuracy vs. pretraining speed Pareto curves and show that MosaicBERT base and large are consistently Pareto optimal when compared to a competitive BERT base and large. This empirical speed up in pretraining enables researchers and engineers to pretrain custom BERT-style models at low cost instead of finetune on existing generic models. We open source our model weights and code.
Despite significant advancements in medical vision-language pre-training, existing methods have largely overlooked the inherent entity-specific context within radiology reports and the complex cross-modality contextual relationships between text and images. To close this gap, we propose a novel Entity-centered Context-aware Medical Vision-language Pre-training (ECAMP) framework, which is designed to enable a more entity-centered and context-sensitive interpretation of medical data. Utilizing the recent powerful large language model, we distill entity-centered context from medical reports, which enables ECAMP to gain more effective supervision from the text modality. By further pre-training our model with carefully designed entity-aware, context-enhanced masked language modeling and context-guided super-resolution tasks, ECAMP significantly refines the interplay between text and image modalities, leading to an enhanced ability to extract entity-centered contextual features. Besides, our proposed multi-scale context fusion design also improves the semantic integration of both coarse and fine-level image representations, prompting better performance for multi-scale downstream applications. Combining these components leads to significant performance leaps over current state-of-the-art methods and establishes a new standard for cross-modality learning in medical imaging, whose effectiveness is demonstrated by our extensive experiments on various tasks including classification, segmentation, and detection across several public datasets. Code and models are available at https://github.com/ToniChopp/ECAMP.
In this work we introduce Labrador, a pre-trained Transformer model for laboratory data. Labrador and BERT were pre-trained on a corpus of 100 million lab test results from electronic health records (EHRs) and evaluated on various downstream outcome prediction tasks. Both models demonstrate mastery of the pre-training task but neither consistently outperform XGBoost on downstream supervised tasks. Our ablation studies reveal that transfer learning shows limited effectiveness for BERT and achieves marginal success with Labrador. We explore the reasons for the failure of transfer learning and suggest that the data generating process underlying each patient cannot be characterized sufficiently using labs alone, among other factors. We encourage future work to focus on joint modeling of multiple EHR data categories and to include tree-based baselines in their evaluations.
Recently, prompt-based fine-tuning has garnered considerable interest as a core technique for few-shot text classification task. This approach reformulates the fine-tuning objective to align with the Masked Language Modeling (MLM) objective. Leveraging unlabeled data, prompt-based self-training has shown greater effectiveness in binary and three-class classification. However, prompt-based self-training for multi-class classification has not been adequately investigated, despite its significant applicability to real-world scenarios. Moreover, extending current methods to multi-class classification suffers from the verbalizer that extracts the predicted value of manually pre-defined single label word for each class from MLM predictions. Consequently, we introduce a novel, efficient verbalizer structure, named Mapping-free Automatic Verbalizer (MAV). Comprising two fully connected layers, MAV serves as a trainable verbalizer that automatically extracts the requisite word features for classification by capitalizing on all available information from MLM predictions. Experimental results on five multi-class classification datasets indicate MAV's superior self-training efficacy.
Techniques in causal analysis of language models illuminate how linguistic information is organized in LLMs. We use one such technique, AlterRep, a method of counterfactual probing, to explore the internal structure of multilingual models (mBERT and XLM-R). We train a linear classifier on a binary language identity task, to classify tokens between Language X and Language Y. Applying a counterfactual probing procedure, we use the classifier weights to project the embeddings into the null space and push the resulting embeddings either in the direction of Language X or Language Y. Then we evaluate on a masked language modeling task. We find that, given a template in Language X, pushing towards Language Y systematically increases the probability of Language Y words, above and beyond a third-party control language. But it does not specifically push the model towards translation-equivalent words in Language Y. Pushing towards Language X (the same direction as the template) has a minimal effect, but somewhat degrades these models. Overall, we take these results as further evidence of the rich structure of massive multilingual language models, which include both a language-specific and language-general component. And we show that counterfactual probing can be fruitfully applied to multilingual models.
We present Lil-Bevo, our submission to the BabyLM Challenge. We pretrained our masked language models with three ingredients: an initial pretraining with music data, training on shorter sequences before training on longer ones, and masking specific tokens to target some of the BLiMP subtasks. Overall, our baseline models performed above chance, but far below the performance levels of larger LLMs trained on more data. We found that training on short sequences performed better than training on longer sequences.Pretraining on music may help performance marginally, but, if so, the effect seems small. Our targeted Masked Language Modeling augmentation did not seem to improve model performance in general, but did seem to help on some of the specific BLiMP tasks that we were targeting (e.g., Negative Polarity Items). Training performant LLMs on small amounts of data is a difficult but potentially informative task. While some of our techniques showed some promise, more work is needed to explore whether they can improve performance more than the modest gains here. Our code is available at https://github.com/venkatasg/Lil-Bevo and out models at https://huggingface.co/collections/venkatasg/babylm-653591cdb66f4bf68922873a
We analyze the masked language modeling pretraining objective function from the perspective of the distributional hypothesis. We investigate whether better sample efficiency and the better generalization capability of models pretrained with masked language modeling can be attributed to the semantic similarity encoded in the pretraining data's distributional property. Via a synthetic dataset, our analysis suggests that distributional property indeed leads to the better sample efficiency of pretrained masked language models, but does not fully explain the generalization capability. We also conduct analyses over two real-world datasets and demonstrate that the distributional property does not explain the generalization ability of pretrained natural language models either. Our results illustrate our limited understanding of model pretraining and provide future research directions.
Humans subconsciously engage in geospatial reasoning when reading articles. We recognize place names and their spatial relations in text and mentally associate them with their physical locations on Earth. Although pretrained language models can mimic this cognitive process using linguistic context, they do not utilize valuable geospatial information in large, widely available geographical databases, e.g., OpenStreetMap. This paper introduces GeoLM, a geospatially grounded language model that enhances the understanding of geo-entities in natural language. GeoLM leverages geo-entity mentions as anchors to connect linguistic information in text corpora with geospatial information extracted from geographical databases. GeoLM connects the two types of context through contrastive learning and masked language modeling. It also incorporates a spatial coordinate embedding mechanism to encode distance and direction relations to capture geospatial context. In the experiment, we demonstrate that GeoLM exhibits promising capabilities in supporting toponym recognition, toponym linking, relation extraction, and geo-entity typing, which bridge the gap between natural language processing and geospatial sciences. The code is publicly available at https://github.com/knowledge-computing/geolm.
Numerous debiasing techniques have been proposed to mitigate the gender bias that is prevalent in pretrained language models. These are often evaluated on datasets that check the extent to which the model is gender-neutral in its predictions. Importantly, this evaluation protocol overlooks the possible adverse impact of bias mitigation on useful gender knowledge. To fill this gap, we propose DiFair, a manually curated dataset based on masked language modeling objectives. DiFair allows us to introduce a unified metric, gender invariance score, that not only quantifies a model's biased behavior, but also checks if useful gender knowledge is preserved. We use DiFair as a benchmark for a number of widely-used pretained language models and debiasing techniques. Experimental results corroborate previous findings on the existing gender biases, while also demonstrating that although debiasing techniques ameliorate the issue of gender bias, this improvement usually comes at the price of lowering useful gender knowledge of the model.
Sequential tabular data is one of the most commonly used data types in real-world applications. Different from conventional tabular data, where rows in a table are independent, sequential tabular data contains rich contextual and sequential information, where some fields are dynamically changing over time and others are static. Existing transformer-based approaches analyzing sequential tabular data overlook the differences between dynamic and static fields by replicating and filling static fields into each transformer, and ignore temporal information between rows, which leads to three major disadvantages: (1) computational overhead, (2) artificially simplified data for masked language modeling pre-training task that may yield less meaningful representations, and (3) disregarding the temporal behavioral patterns implied by time intervals. In this work, we propose FATA-Trans, a model with two field transformers for modeling sequential tabular data, where each processes static and dynamic field information separately. FATA-Trans is field- and time-aware for sequential tabular data. The field-type embedding in the method enables FATA-Trans to capture differences between static and dynamic fields. The time-aware position embedding exploits both order and time interval information between rows, which helps the model detect underlying temporal behavior in a sequence. Our experiments on three benchmark datasets demonstrate that the learned representations from FATA-Trans consistently outperform state-of-the-art solutions in the downstream tasks. We also present visualization studies to highlight the insights captured by the learned representations, enhancing our understanding of the underlying data. Our codes are available at https://github.com/zdy93/FATA-Trans.
Language models have become the backbone of today's AI systems. However, their predominant left-to-right generation limits the use of bidirectional context, which is essential for tasks that involve filling text in the middle. We propose the Fill-in Language Model (FiLM), a new language modeling approach that allows for flexible generation at any position without adhering to a specific generation order. Its training extends the masked language modeling objective by adopting varying mask probabilities sampled from the Beta distribution to enhance the generative capabilities of FiLM. During inference, FiLM can seamlessly insert missing phrases, sentences, or paragraphs, ensuring that the outputs are fluent and are coherent with the surrounding context. In both automatic and human evaluations, FiLM outperforms existing infilling methods that rely on left-to-right language models trained on rearranged text segments. FiLM is easy to implement and can be either trained from scratch or fine-tuned from a left-to-right language model. Notably, as the model size grows, FiLM's perplexity approaches that of strong left-to-right language models of similar sizes, indicating FiLM's scalability and potential as a large language model.
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. The computational design of protein-based binders presents unique opportunities to access "undruggable" targets, but have often relied on stable 3D structures or structure-influenced latent spaces for effective binder generation. In this work, we introduce PepMLM, a target sequence-conditioned generator of de novo linear peptide binders. By employing a novel span masking strategy that uniquely positions cognate peptide sequences at the C-terminus of target protein sequences, PepMLM fine-tunes the state-of-the-art ESM-2 pLM to fully reconstruct the binder region, achieving low perplexities matching or improving upon validated peptide-protein sequence pairs. After successful in silico benchmarking with AlphaFold-Multimer, outperforming RFDiffusion on structured targets, we experimentally verify PepMLM's efficacy via fusion of model-derived peptides to E3 ubiquitin ligase domains, demonstrating endogenous degradation of emergent viral phosphoproteins and Huntington's disease-driving proteins. In total, PepMLM enables the generative design of candidate binders to any target protein, without the requirement of target structure, empowering downstream therapeutic applications.
This thesis focuses on improving the pre-training of natural language models using unsupervised raw data to make them more efficient and aligned with downstream applications. In the first part, we introduce three alternative pre-training objectives to BERT's Masked Language Modeling (MLM), namely Random Token Substitution (RTS), Cluster-based Random Token Substitution (C-RTS), and Swapped Language Modeling (SLM). These objectives involve token swapping instead of masking, with RTS and C-RTS aiming to predict token originality and SLM predicting the original token values. Results show that RTS and C-RTS require less pre-training time while maintaining performance comparable to MLM. Surprisingly, SLM outperforms MLM on certain tasks despite using the same computational budget. In the second part, we proposes self-supervised pre-training tasks that align structurally with downstream applications, reducing the need for labeled data. We use large corpora like Wikipedia and CC-News to train models to recognize if text spans originate from the same paragraph or document in several ways. By doing continuous pre-training, starting from existing models like RoBERTa, ELECTRA, DeBERTa, BART, and T5, we demonstrate significant performance improvements in tasks like Fact Verification, Answer Sentence Selection, and Summarization. These improvements are especially pronounced when limited annotation data is available. The proposed objectives also achieve state-of-the-art results on various benchmark datasets, including FEVER (dev set), ASNQ, WikiQA, and TREC-QA, as well as enhancing the quality of summaries. Importantly, these techniques can be easily integrated with other methods without altering the internal structure of Transformer models, making them versatile for various NLP applications.
The objective of few-shot named entity recognition is to identify named entities with limited labeled instances. Previous works have primarily focused on optimizing the traditional token-wise classification framework, while neglecting the exploration of information based on NER data characteristics. To address this issue, we propose a Multi-Task Semantic Decomposition Framework via Joint Task-specific Pre-training (MSDP) for few-shot NER. Drawing inspiration from demonstration-based and contrastive learning, we introduce two novel pre-training tasks: Demonstration-based Masked Language Modeling (MLM) and Class Contrastive Discrimination. These tasks effectively incorporate entity boundary information and enhance entity representation in Pre-trained Language Models (PLMs). In the downstream main task, we introduce a multi-task joint optimization framework with the semantic decomposing method, which facilitates the model to integrate two different semantic information for entity classification. Experimental results of two few-shot NER benchmarks demonstrate that MSDP consistently outperforms strong baselines by a large margin. Extensive analyses validate the effectiveness and generalization of MSDP.
The recent surge of generative AI has been fueled by the generative power of diffusion probabilistic models and the scalable capabilities of large language models. Despite their potential, it remains elusive whether diffusion language models can solve general language tasks comparable to their autoregressive counterparts. This paper demonstrates that scaling diffusion models w.r.t. data, sizes, and tasks can effectively make them strong language learners. We build competent diffusion language models at scale by first acquiring knowledge from massive data via masked language modeling pretraining thanks to their intrinsic connections. We then reprogram pretrained masked language models into diffusion language models via diffusive adaptation, wherein task-specific finetuning and instruction finetuning are explored to unlock their versatility in solving general language tasks. Experiments show that scaling diffusion language models consistently improves performance across downstream language tasks. We further discover that instruction finetuning can elicit zero-shot and few-shot in-context learning abilities that help tackle many unseen tasks by following natural language instructions, and show promise in advanced and challenging abilities such as reasoning.
Grounded on pre-trained language models (PLMs), dense retrieval has been studied extensively on plain text. In contrast, there has been little research on retrieving data with multiple aspects using dense models. In the scenarios such as product search, the aspect information plays an essential role in relevance matching, e.g., category: Electronics, Computers, and Pet Supplies. A common way of leveraging aspect information for multi-aspect retrieval is to introduce an auxiliary classification objective, i.e., using item contents to predict the annotated value IDs of item aspects. However, by learning the value embeddings from scratch, this approach may not capture the various semantic similarities between the values sufficiently. To address this limitation, we leverage the aspect information as text strings rather than class IDs during pre-training so that their semantic similarities can be naturally captured in the PLMs. To facilitate effective retrieval with the aspect strings, we propose mutual prediction objectives between the text of the item aspect and content. In this way, our model makes more sufficient use of aspect information than conducting undifferentiated masked language modeling (MLM) on the concatenated text of aspects and content. Extensive experiments on two real-world datasets (product and mini-program search) show that our approach can outperform competitive baselines both treating aspect values as classes and conducting the same MLM for aspect and content strings. Code and related dataset will be available at the URL \footnote{https://github.com/sunxiaojie99/ATTEMPT}.
The impact of randomness on model training is poorly understood. How do differences in data order and initialization actually manifest in the model, such that some training runs outperform others or converge faster? Furthermore, how can we interpret the resulting training dynamics and the phase transitions that characterize different trajectories? To understand the effect of randomness on the dynamics and outcomes of neural network training, we train models multiple times with different random seeds and compute a variety of metrics throughout training, such as the $L_2$ norm, mean, and variance of the neural network's weights. We then fit a hidden Markov model (HMM) over the resulting sequences of metrics. The HMM represents training as a stochastic process of transitions between latent states, providing an intuitive overview of significant changes during training. Using our method, we produce a low-dimensional, discrete representation of training dynamics on grokking tasks, image classification, and masked language modeling. We use the HMM representation to study phase transitions and identify latent "detour" states that slow down convergence.
In this paper, we investigate the in-context learning ability of retrieval-augmented encoder-decoder language models. We first conduct a comprehensive analysis of existing models and identify their limitations in in-context learning, primarily due to a mismatch between pretraining and inference, as well as a restricted context length. To address these issues, we propose RAVEN, a model that combines retrieval-augmented masked language modeling and prefix language modeling. We further introduce Fusion-in-Context Learning to enhance the few-shot performance by enabling the model to leverage more in-context examples without requiring additional training. Through extensive experiments, we demonstrate that our simple yet effective design significantly improves performance, achieving results comparable to the most advanced language models in certain scenarios, despite having substantially fewer parameters. Our work underscores the potential of retrieval-augmented encoder-decoder language models for in-context learning and encourages further research in this direction.