Transcriptomic foundation models (TFMs) have recently emerged as powerful tools for analyzing gene expression in cells and tissues, supporting key tasks such as cell-type annotation, batch correction, and perturbation prediction. However, the diversity of model implementations and training strategies across recent TFMs, though promising, makes it challenging to isolate the contribution of individual design choices or evaluate their potential synergies. This hinders the field's ability to converge on best practices and limits the reproducibility of insights across studies. We present BMFM-RNA, an open-source, modular software package that unifies diverse TFM pretraining and fine-tuning objectives within a single framework. Leveraging this capability, we introduce a novel training objective, whole cell expression decoder (WCED), which captures global expression patterns using an autoencoder-like CLS bottleneck representation. In this paper, we describe the framework, supported input representations, and training objectives. We evaluated four model checkpoints pretrained on CELLxGENE using combinations of masked language modeling (MLM), WCED and multitask learning. Using the benchmarking capabilities of BMFM-RNA, we show that WCED-based models achieve performance that matches or exceeds state-of-the-art approaches like scGPT across more than a dozen datasets in both zero-shot and fine-tuning tasks. BMFM-RNA, available as part of the biomed-multi-omics project ( https://github.com/BiomedSciAI/biomed-multi-omic ), offers a reproducible foundation for systematic benchmarking and community-driven exploration of optimal TFM training strategies, enabling the development of more effective tools to leverage the latest advances in AI for understanding cell biology.
Proteins are fundamental to biology, executing diverse functions through complex physicochemical interactions, and they hold transformative potential across medicine, materials science, and environmental applications. Protein Language Models (pLMs) aim to unlock insights from the vast space of unlabeled protein sequences by learning rich, semantic representations from primary sequences via masked language modeling. However, these models typically exhibit limited generative capacity. In this work, we introduce the Diffusion Sequence Model (DSM), a novel pLM trained with masked diffusion to enable both high-quality representation learning and generative protein design. DSM builds upon the ESM2 architecture by incorporating a masked forward diffusion process inspired by the LLaDA framework. After training, DSM is capable of generating diverse, biomimetic sequences that align with expected amino acid compositions, secondary structures, and predicted functions, even with 90\% token corruption. Furthermore, DSM's learned representations match or exceed those of similarly sized pLMs on downstream tasks. We also introduce DSM(ppi), a variant fine-tuned to generate protein binders by attending to target sequences. We demonstrate DSM(ppi)'s effectiveness on the challenging Bench-tested Binder Benchmark (BenchBB), where both DSM and DSM(ppi) produce candidates with superior predicted binding affinity compared to known binders. Our results establish masked diffusion as a powerful paradigm for unifying protein representation and generation in a single framework.
Heterogeneous graph neural networks (HGNNs) excel at capturing structural and semantic information in heterogeneous graphs (HGs), while struggling to generalize across domains and tasks. Recently, some researchers have turned to integrating HGNNs with large language models (LLMs) for more generalizable heterogeneous graph learning. However, these approaches typically extract structural information via HGNNs as HG tokens, and disparities in embedding spaces between HGNNs and LLMs have been shown to bias the LLM's comprehension of HGs. Moreover, as these HG tokens are often derived from node-level tasks, the model's ability to generalize across tasks remains limited. To this end, we propose a simple yet effective Masked Language Modeling-based method, called MLM4HG. MLM4HG introduces metapath-based textual sequences instead of HG tokens to extract structural and semantic information inherent in HGs, and designs customized textual templates to unify different graph tasks into a coherent cloze-style "mask" token prediction paradigm. Specifically, MLM4HG first converts HGs from various domains to texts based on metapaths, and subsequently combines them with the unified task texts to form a HG-based corpus. Moreover, the corpus is fed into a pretrained LM for fine-tuning with a constrained target vocabulary, enabling the fine-tuned LM to generalize to unseen target HGs. Extensive cross-domain and multi-task experiments on four real-world datasets demonstrate the superior generalization performance of MLM4HG over state-of-the-art methods in both few-shot and zero-shot scenarios. Our code is available at https://github.com/BUPT-GAMMA/MLM4HG.
Self-Supervised Learning (SSL) has demonstrated strong performance in speech processing, particularly in automatic speech recognition. In this paper, we explore an SSL pretraining framework that leverages masked language modeling with targets derived from a speech recognition model. We also present chunkwise attention with dynamic chunk size sampling during pretraining to enable both full-context and streaming fine-tuning. Our experiments examine scaling with respect to model size and the amount of data. Using our method, we train the GigaAM family of models, including a state-of-the-art model for Russian speech recognition that outperforms Whisper-large-v3 by 50%. We have released our foundation and ASR models, along with the inference code, under the MIT license as open-source resources to the research community. Available at https://github.com/salute-developers/gigaam.
Target-specific peptides, such as conotoxins, exhibit exceptional binding affinity and selectivity toward ion channels and receptors. However, their therapeutic potential remains underutilized due to the limited diversity of natural variants and the labor-intensive nature of traditional optimization strategies. Here, we present CreoPep, a deep learning-based conditional generative framework that integrates masked language modeling with a progressive masking scheme to design high-affinity peptide mutants while uncovering novel structural motifs. CreoPep employs an integrative augmentation pipeline, combining FoldX-based energy screening with temperature-controlled multinomial sampling, to generate structurally and functionally diverse peptides that retain key pharmacological properties. We validate this approach by designing conotoxin inhibitors targeting the $\alpha$7 nicotinic acetylcholine receptor, achieving submicromolar potency in electrophysiological assays. Structural analysis reveals that CreoPep-generated variants engage in both conserved and novel binding modes, including disulfide-deficient forms, thus expanding beyond conventional design paradigms. Overall, CreoPep offers a robust and generalizable platform that bridges computational peptide design with experimental validation, accelerating the discovery of next-generation peptide therapeutics.
Assembly code analysis and comprehension play critical roles in applications like reverse engineering, yet they face substantial challenges due to low information density and a lack of explicit syntactic structures. While traditional masked language modeling (MLM) approaches do not explicitly focus on natural language interaction, emerging decoder-focused large language models (LLMs) demonstrate partial success in binary analysis yet remain underexplored for holistic comprehension. We present Assembly Augmented Tuning, an end-to-end structural-semantic instruction tuning framework that synergizes encoder architecture with decoder-based LLMs through a projector module, where the assembly encoder extracts hardware-level structural features, the projector bridges representations with the semantic space, and the instruction-tuned LLM preserves natural language capabilities. Experimental results demonstrate three key advantages: (1) State-of-the-art performance in assembly comprehension with +39.7% Recall@1 and +17.8% MRR improvements over GPT-4-Turbo, (2) Consistent enhancements across base models (24.6-107.4% Recall@1 and 15.2-106.3% MRR on Qwen2.5-Coder, Deepseek-Coder and CodeLlama variants), and (3) Superior instruction-following capabilities (41.5%-118% improvements) with controlled code generation degradation (-8.9% to -35% across architectures).
Masked language modeling has become a widely adopted unsupervised technique to pre-train language models. However, the process of selecting tokens for masking is random, and the percentage of masked tokens is typically fixed for the entire training process. In this paper, we propose to adjust the masking ratio and to decide which tokens to mask based on a novel task-informed anti-curriculum learning scheme. First, we harness task-specific knowledge about useful and harmful tokens in order to determine which tokens to mask. Second, we propose a cyclic decaying masking ratio, which corresponds to an anti-curriculum schedule (from hard to easy). We exemplify our novel task-informed anti-curriculum by masking (TIACBM) approach across three diverse downstream tasks: sentiment analysis, text classification by topic, and authorship attribution. Our findings suggest that TIACBM enhances the ability of the model to focus on key task-relevant features, contributing to statistically significant performance gains across tasks. We release our code at https://github.com/JarcaAndrei/TIACBM.
Large Language Models (LLMs) are discovered to suffer from accurately retrieving key information. To address this, we propose Mask-Enhanced Autoregressive Prediction (MEAP), a simple yet effective training paradigm that seamlessly integrates Masked Language Modeling (MLM) into Next-Token Prediction (NTP) to enhance the latter's in-context retrieval capabilities. Specifically, MEAP first randomly masks a small fraction of input tokens and then directly performs the standard next-token prediction autoregressive using a decoder-only Transformer. MEAP eliminates the need for bidirectional attention or encoder-decoder architectures for MLM, incurring no additional computational overhead during pre-training or inference. Intensive experiments demonstrate that MEAP substantially outperforms NTP on key information retrieval and long-context reasoning tasks, while performing on par or better on commonsense reasoning tasks. The benefits of MEAP also extend to supervised fine-tuning, where it shows remarkable advantages in lost-in-the-middle scenarios, outperforming NTP by 11.77 percentage points. Our analysis indicates that MEAP's effectiveness arises from its ability to promote more distinguishable attention scores by concentrating on a reduced set of non-masked tokens. This mechanism improves the model's focus on task-relevant signals while mitigating the influence of peripheral context. These findings position MEAP as a promising training paradigm for large language models.
Establishing the long-context capability of large vision-language models is crucial for video understanding, high-resolution image understanding, multi-modal agents and reasoning. We introduce Long-VITA, a simple yet effective large multi-modal model for long-context visual-language understanding tasks. It is adept at concurrently processing and analyzing modalities of image, video, and text over 4K frames or 1M tokens while delivering advanced performances on short-context multi-modal tasks. We propose an effective multi-modal training schema that starts with large language models and proceeds through vision-language alignment, general knowledge learning, and two sequential stages of long-sequence fine-tuning. We further implement context-parallelism distributed inference and logits-masked language modeling head to scale Long-VITA to infinitely long inputs of images and texts during model inference. Regarding training data, Long-VITA is built on a mix of $17$M samples from public datasets only and demonstrates the state-of-the-art performance on various multi-modal benchmarks, compared against recent cutting-edge models with internal data. Long-VITA is fully reproducible and supports both NPU and GPU platforms for training and testing. We hope Long-VITA can serve as a competitive baseline and offer valuable insights for the open-source community in advancing long-context multi-modal understanding.
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 upon 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, 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 up to 30% and 16% improvements on protein downstream tasks compared to Transformer-based ESM-2 when trained with 100B and 1T tokens, respectively. 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 contexts contained in biological graphs.
We present a simple way to merge masked language modeling with causal language modeling. This hybrid training objective results in a model that combines the strengths of both modeling paradigms within a single transformer stack: GPT-BERT can be transparently used like any standard causal or masked language model. We test the pretraining process that enables this flexible behavior on the BabyLM Challenge 2024. The results show that the hybrid pretraining outperforms masked-only or causal-only models. We openly release the models, training corpora and code.
Curriculum Learning has been a popular strategy to improve the cognitive plausibility of Small-Scale Language Models (SSLMs) in the BabyLM Challenge. However, it has not led to considerable improvements over non-curriculum models. We assess whether theoretical linguistic acquisition theories can be used to specify more fine-grained curriculum learning strategies, creating age-ordered corpora of Child-Directed Speech for four typologically distant language families to implement SSLMs and acquisition-inspired curricula cross-lingually. Comparing the success of three objective curricula (Growing, Inwards and MMM) that precisely replicate the predictions of acquisition theories on a standard SSLM architecture, we find fine-grained acquisition-inspired curricula can outperform non-curriculum baselines and performance benefits of curricula strategies in SSLMs can be derived by specifying fine-grained language-specific curricula that precisely replicate language acquisition theories.
Machine learning (ML) models trained using Empirical Risk Minimization (ERM) often exhibit systematic errors on specific subpopulations of tabular data, known as error slices. Learning robust representation in presence of error slices is challenging, especially in self-supervised settings during the feature reconstruction phase, due to high cardinality features and the complexity of constructing error sets. Traditional robust representation learning methods are largely focused on improving worst group performance in supervised setting in computer vision, leaving a gap in approaches tailored for tabular data. We address this gap by developing a framework to learn robust representation in tabular data during self-supervised pre-training. Our approach utilizes an encoder-decoder model trained with Masked Language Modeling (MLM) loss to learn robust latent representations. This paper applies the Just Train Twice (JTT) and Deep Feature Reweighting (DFR) methods during the pre-training phase for tabular data. These methods fine-tune the ERM pre-trained model by up-weighting error-prone samples or creating balanced datasets for specific categorical features. This results in specialized models for each feature, which are then used in an ensemble approach to enhance downstream classification performance. This methodology improves robustness across slices, thus enhancing overall generalization performance. Extensive experiments across various datasets demonstrate the efficacy of our approach. The code is available: \url{https://github.com/amazon-science/distributionally-robust-self-supervised-learning-for-tabular-data}.
Semantic parsing that translates natural language queries to SPARQL is of great importance for Knowledge Graph Question Answering (KGQA) systems. Although pre-trained language models like T5 have achieved significant success in the Text-to-SPARQL task, their generated outputs still exhibit notable errors specific to the SPARQL language, such as triplet flips. To address this challenge and further improve the performance, we propose an additional pre-training stage with a new objective, Triplet Order Correction (TOC), along with the commonly used Masked Language Modeling (MLM), to collectively enhance the model's sensitivity to triplet order and SPARQL syntax. Our method achieves state-of-the-art performances on three widely-used benchmarks.
Prompt-based fine-tuning has become an essential method for eliciting information encoded in pre-trained language models for a variety of tasks, including text classification. For multi-class classification tasks, prompt-based fine-tuning under low-resource scenarios has resulted in performance levels comparable to those of fully fine-tuning methods. Previous studies have used crafted prompt templates and verbalizers, mapping from the label terms space to the class space, to solve the classification problem as a masked language modeling task. However, cross-domain and fine-grained prompt-based fine-tuning with an automatically enriched verbalizer remains unexplored, mainly due to the difficulty and costs of manually selecting domain label terms for the verbalizer, which requires humans with domain expertise. To address this challenge, we introduce SciPrompt, a framework designed to automatically retrieve scientific topic-related terms for low-resource text classification tasks. To this end, we select semantically correlated and domain-specific label terms within the context of scientific literature for verbalizer augmentation. Furthermore, we propose a new verbalization strategy that uses correlation scores as additional weights to enhance the prediction performance of the language model during model tuning. Our method outperforms state-of-the-art, prompt-based fine-tuning methods on scientific text classification tasks under few and zero-shot settings, especially in classifying fine-grained and emerging scientific topics.
Detecting and classifying suspicious or malicious domain names and URLs is fundamental task in cybersecurity. To leverage such indicators of compromise, cybersecurity vendors and practitioners often maintain and update blacklists of known malicious domains and URLs. However, blacklists frequently fail to identify emerging and obfuscated threats. Over the past few decades, there has been significant interest in developing machine learning models that automatically detect malicious domains and URLs, addressing the limitations of blacklists maintenance and updates. In this paper, we introduce DomURLs_BERT, a pre-trained BERT-based encoder adapted for detecting and classifying suspicious/malicious domains and URLs. DomURLs_BERT is pre-trained using the Masked Language Modeling (MLM) objective on a large multilingual corpus of URLs, domain names, and Domain Generation Algorithms (DGA) dataset. In order to assess the performance of DomURLs_BERT, we have conducted experiments on several binary and multi-class classification tasks involving domain names and URLs, covering phishing, malware, DGA, and DNS tunneling. The evaluations results show that the proposed encoder outperforms state-of-the-art character-based deep learning models and cybersecurity-focused BERT models across multiple tasks and datasets. The pre-training dataset, the pre-trained DomURLs_BERT encoder, and the experiments source code are publicly available.
The vast amount of available medical records has the potential to improve healthcare and biomedical research. However, privacy restrictions make these data accessible for internal use only. Recent works have addressed this problem by generating synthetic data using Causal Language Modeling. Unfortunately, by taking this approach, it is often impossible to guarantee patient privacy while offering the ability to control the diversity of generations without increasing the cost of generating such data. In contrast, we present a system for generating synthetic free-text medical records using Masked Language Modeling. The system preserves critical medical information while introducing diversity in the generations and minimising re-identification risk. The system's size is about 120M parameters, minimising inference cost. The results demonstrate high-quality synthetic data with a HIPAA-compliant PHI recall rate of 96% and a re-identification risk of 3.5%. Moreover, downstream evaluations show that the generated data can effectively train a model with performance comparable to real data.
Understanding the learning process and the embedded computation in transformers is becoming a central goal for the development of interpretable AI. In the present study, we introduce a hierarchical filtering procedure for data models of sequences on trees, allowing us to hand-tune the range of positional correlations in the data. Leveraging this controlled setting, we provide evidence that vanilla encoder-only transformers can approximate the exact inference algorithm when trained on root classification and masked language modeling tasks, and study how this computation is discovered and implemented. We find that correlations at larger distances, corresponding to increasing layers of the hierarchy, are sequentially included by the network during training. By comparing attention maps from models trained with varying degrees of filtering and by probing the different encoder levels, we find clear evidence of a reconstruction of correlations on successive length scales corresponding to the various levels of the hierarchy, which we relate to a plausible implementation of the exact inference algorithm within the same architecture.
Gene transformer models such as Nucleotide Transformer, DNABert, and LOGO are trained to learn optimal gene sequence representations by using the Masked Language Modeling (MLM) training objective over the complete Human Reference Genome. However, the typical tokenization methods employ a basic sliding window of tokens, such as k-mers, that fail to utilize gene-centric semantics. This could result in the (trivial) masking of easily predictable sequences, leading to inefficient MLM training. Time-variant training strategies are known to improve pretraining efficiency in both language and vision tasks. In this work, we focus on using curriculum masking where we systematically increase the difficulty of masked token prediction task by using a Pointwise Mutual Information-based difficulty criterion, as gene sequences lack well-defined semantic units similar to words or sentences of NLP domain. Our proposed Curriculum Masking-based Gene Masking Strategy (CM-GEMS) demonstrates superior representation learning capabilities compared to baseline masking approaches when evaluated on downstream gene sequence classification tasks. We perform extensive evaluation in both few-shot (five datasets) and full dataset settings (Genomic Understanding Evaluation benchmark consisting of 27 tasks). Our findings reveal that CM-GEMS outperforms state-of-the-art models (DNABert-2, Nucleotide transformer, DNABert) trained at 120K steps, achieving similar results in just 10K and 1K steps. We also demonstrate that Curriculum-Learned LOGO (a 2-layer DNABert-like model) can achieve nearly 90% of the state-of-the-art model performance of 120K steps. We will make the models and codes publicly available at https://github.com/roysoumya/curriculum-GeneMask.
Autoregressive language models are the currently dominant paradigm for text generation, but they have some fundamental limitations that cannot be remedied by scale-for example inherently sequential and unidirectional generation. While alternate classes of models have been explored, we have limited mathematical understanding of their fundamental power and limitations. In this paper we focus on Generative Masked Language Models (GMLMs), a non-autoregressive paradigm in which we train a model to fit conditional probabilities of the data distribution via masking, which are subsequently used as inputs to a Markov Chain to draw samples from the model, These models empirically strike a promising speed-quality trade-off as each step can be typically parallelized by decoding the entire sequence in parallel. We develop a mathematical framework for analyzing and improving such models which sheds light on questions of sample complexity and inference speed and quality. Empirically, we adapt the T5 model for iteratively-refined parallel decoding, achieving 2-3x speedup in machine translation with minimal sacrifice in quality compared with autoregressive models. We run careful ablation experiments to give recommendations on key design choices, and make fine-grained observations on the common error modes in connection with our theory. Our mathematical analyses and empirical observations characterize both potentials and limitations of this approach, and can be applied to future works on improving understanding and performance of GMLMs. Our codes are released at https://github.com/google-research/google-research/tree/master/padir