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Jul 9

Pretrain like Your Inference: Masked Tuning Improves Zero-Shot Composed Image Retrieval

Zero-shot composed image retrieval (ZS-CIR), which takes a textual modification and a reference image as a query to retrieve a target image without triplet labeling, has gained more and more attention in data mining. Current ZS-CIR research mainly relies on the generalization ability of pre-trained vision-language models, e.g., CLIP. However, the pre-trained vision-language models and CIR tasks have substantial discrepancies, where the vision-language models focus on learning the similarities but CIR aims to learn the modifications of the image guided by text. In this paper, we introduce a novel unlabeled and pre-trained masked tuning approach, which reduces the gap between the pre-trained vision-language model and the downstream CIR task. First, to reduce the gap, we reformulate the contrastive learning of the vision-language model as the CIR task, where we randomly mask input image patches to generate langlemasked image, text, imagerangle triplet from an image-text pair. Then, we propose a simple but novel pre-trained masked tuning method, which uses the text and the masked image to learn the modifications of the original image. With such a simple design, the proposed masked tuning can learn to better capture fine-grained text-guided modifications. Extensive experimental results demonstrate the significant superiority of our approach over the baseline models on four ZS-CIR datasets, including FashionIQ, CIRR, CIRCO, and GeneCIS. Our codes are available at https://github.com/Chen-Junyang-cn/PLI

  • 2 authors
·
Nov 12, 2023

Diffusion-Inspired Masked Fine-Tuning for Knowledge Injection in Autoregressive LLMs

Large language models (LLMs) are often used in environments where facts evolve, yet factual knowledge updates via fine-tuning on unstructured text often suffers from 1) reliance on compute-heavy paraphrase augmentation and 2) the reversal curse. Recent studies show diffusion large language models (dLLMs) require fewer training samples to achieve lower loss in pre-training and are more resistant to the reversal curse, suggesting dLLMs may learn new knowledge more easily than autoregressive LLMs (arLLMs). We test this hypothesis in controlled knowledge fine-tuning experiments and find that while arLLMs rely on paraphrase augmentation to generalize knowledge text into question-answering (QA) capability, dLLMs do not require paraphrases to achieve high QA accuracy. To further investigate whether the demasking objective alone can induce such a knowledge injection advantage in dLLMs regardless of their diffusion denoising paradigm, we propose masked fine-tuning for arLLMs, which prompts an arLLM to reconstruct the original text given a masked version in context. The masked fine-tuning for arLLMs substantially improves the efficacy of knowledge injection, i.e. no paraphrase needed and resistant to the reversal curse, closing the gap between arLLMs and dLLMs. We also demonstrate that the same demasking objective improves supervised fine-tuning (SFT) on math tasks over standard SFT, suggesting broader applicability of the demasking objective.

  • 5 authors
·
Oct 10, 2025

Regularized Mask Tuning: Uncovering Hidden Knowledge in Pre-trained Vision-Language Models

Prompt tuning and adapter tuning have shown great potential in transferring pre-trained vision-language models (VLMs) to various downstream tasks. In this work, we design a new type of tuning method, termed as regularized mask tuning, which masks the network parameters through a learnable selection. Inspired by neural pathways, we argue that the knowledge required by a downstream task already exists in the pre-trained weights but just gets concealed in the upstream pre-training stage. To bring the useful knowledge back into light, we first identify a set of parameters that are important to a given downstream task, then attach a binary mask to each parameter, and finally optimize these masks on the downstream data with the parameters frozen. When updating the mask, we introduce a novel gradient dropout strategy to regularize the parameter selection, in order to prevent the model from forgetting old knowledge and overfitting the downstream data. Experimental results on 11 datasets demonstrate the consistent superiority of our method over previous alternatives. It is noteworthy that we manage to deliver 18.73% performance improvement compared to the zero-shot CLIP via masking an average of only 2.56% parameters. Furthermore, our method is synergistic with most existing parameter-efficient tuning methods and can boost the performance on top of them. Project page can be found here (https://wuw2019.github.io/R-AMT/).

  • 9 authors
·
Jul 27, 2023

Thinking with Frames: Generative Video Distortion Evaluation via Frame Reward Model

Recent advances in video reward models and post-training strategies have improved text-to-video (T2V) generation. While these models typically assess visual quality, motion quality, and text alignment, they often overlook key structural distortions, such as abnormal object appearances and interactions, which can degrade the overall quality of the generative video. To address this gap, we introduce REACT, a frame-level reward model designed specifically for structural distortions evaluation in generative videos. REACT assigns point-wise scores and attribution labels by reasoning over video frames, focusing on recognizing distortions. To support this, we construct a large-scale human preference dataset, annotated based on our proposed taxonomy of structural distortions, and generate additional data using a efficient Chain-of-Thought (CoT) synthesis pipeline. REACT is trained with a two-stage framework: (1) supervised fine-tuning with masked loss for domain knowledge injection, followed by (2) reinforcement learning with Group Relative Policy Optimization (GRPO) and pairwise rewards to enhance reasoning capability and align output scores with human preferences. During inference, a dynamic sampling mechanism is introduced to focus on frames most likely to exhibit distortion. We also present REACT-Bench, a benchmark for generative video distortion evaluation. Experimental results demonstrate that REACT complements existing reward models in assessing structutal distortion, achieving both accurate quantitative evaluations and interpretable attribution analysis.

  • 8 authors
·
Jan 7

Think Thrice Before You Act: Progressive Thought Refinement in Large Language Models

Recent advancements in large language models (LLMs) have demonstrated that progressive refinement, rather than providing a single answer, results in more accurate and thoughtful outputs. However, existing methods often rely heavily on supervision signals to evaluate previous responses, making it difficult to assess output quality in more open-ended scenarios effectively. Additionally, these methods are typically designed for specific tasks, which limits their generalization to new domains. To address these limitations, we propose Progressive Thought Refinement (PTR), a framework that enables LLMs to refine their responses progressively. PTR operates in two phases: (1) Thought data construction stage: We propose a weak and strong model collaborative selection strategy to build a high-quality progressive refinement dataset to ensure logical consistency from thought to answers, and the answers are gradually refined in each round. (2) Thought-Mask Fine-Tuning Phase: We design a training structure to mask the "thought" and adjust loss weights to encourage LLMs to refine prior thought, teaching them to implicitly understand "how to improve" rather than "what is correct." Experimental results show that PTR significantly enhances LLM performance across ten diverse tasks (avg. from 49.6% to 53.5%) without task-specific fine-tuning. Notably, in more open-ended tasks, LLMs also demonstrate substantial improvements in the quality of responses beyond mere accuracy, suggesting that PTR truly teaches LLMs to self-improve over time.

  • 12 authors
·
Oct 17, 2024

PathReasoner-R1: Instilling Structured Reasoning into Pathology Vision-Language Model via Knowledge-Guided Policy Optimization

Vision-Language Models (VLMs) are advancing computational pathology with superior visual understanding capabilities. However, current systems often reduce diagnosis to directly output conclusions without verifiable evidence-linked reasoning, which severely limits clinical trust and hinders expert error rectification. To address these barriers, we construct PathReasoner, the first large-scale dataset of whole-slide image (WSI) reasoning. Unlike previous work reliant on unverified distillation, we develop a rigorous knowledge-guided generation pipeline. By leveraging medical knowledge graphs, we explicitly align structured pathological findings and clinical reasoning with diagnoses, generating over 20K high-quality instructional samples. Based on the database, we propose PathReasoner-R1, which synergizes trajectory-masked supervised fine-tuning with reasoning-oriented reinforcement learning to instill structured chain-of-thought capabilities. To ensure medical rigor, we engineer a knowledge-aware multi-granular reward function incorporating an Entity Reward mechanism strictly aligned with knowledge graphs. This effectively guides the model to optimize for logical consistency rather than mere outcome matching, thereby enhancing robustness. Extensive experiments demonstrate that PathReasoner-R1 achieves state-of-the-art performance on both PathReasoner and public benchmarks across various image scales, equipping pathology models with transparent, clinically grounded reasoning capabilities. Dataset and code are available at https://github.com/cyclexfy/PathReasoner-R1.

  • 5 authors
·
Jan 29

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, 2025

Composable Sparse Fine-Tuning for Cross-Lingual Transfer

Fine-tuning the entire set of parameters of a large pretrained model has become the mainstream approach for transfer learning. To increase its efficiency and prevent catastrophic forgetting and interference, techniques like adapters and sparse fine-tuning have been developed. Adapters are modular, as they can be combined to adapt a model towards different facets of knowledge (e.g., dedicated language and/or task adapters). Sparse fine-tuning is expressive, as it controls the behavior of all model components. In this work, we introduce a new fine-tuning method with both these desirable properties. In particular, we learn sparse, real-valued masks based on a simple variant of the Lottery Ticket Hypothesis. Task-specific masks are obtained from annotated data in a source language, and language-specific masks from masked language modeling in a target language. Both these masks can then be composed with the pretrained model. Unlike adapter-based fine-tuning, this method neither increases the number of parameters at inference time nor alters the original model architecture. Most importantly, it outperforms adapters in zero-shot cross-lingual transfer by a large margin in a series of multilingual benchmarks, including Universal Dependencies, MasakhaNER, and AmericasNLI. Based on an in-depth analysis, we additionally find that sparsity is crucial to prevent both 1) interference between the fine-tunings to be composed and 2) overfitting. We release the code and models at https://github.com/cambridgeltl/composable-sft.

  • 4 authors
·
Oct 14, 2021

Can Masked Autoencoders Also Listen to Birds?

Masked Autoencoders (MAEs) have shown competitive results in audio classification by learning rich semantic representations through an efficient self-supervised reconstruction task. However, general-purpose models fail to generalize well when applied directly to fine-grained audio domains. Specifically, bird-sound classification requires distinguishing subtle inter-species differences and managing high intra-species acoustic variability, thereby revealing the performance limitations of general-domain Audio-MAE models. This work demonstrates that bridging this domain gap requires more than domain-specific pretraining data; adapting the entire training pipeline is crucial. We systematically revisit and adapt the pretraining recipe, fine-tuning methods, and frozen feature utilization to bird sounds using BirdSet, a large-scale bioacoustic dataset comparable to AudioSet. Our resulting Bird-MAE achieves new state-of-the-art results in BirdSet's multi-label classification benchmark. Additionally, we introduce the parameter-efficient prototypical probing, enhancing the utility of frozen MAE representations and closely approaching fine-tuning performance in low-resource settings. Bird-MAE's prototypical probes outperform linear probing by up to 37%_p in MAP and narrow the gap to fine-tuning to approximately 3.3%_p on average across BirdSet downstream tasks. Bird-MAE also demonstrates robust few-shot capabilities with prototypical probing in our newly established few-shot benchmark on BirdSet, highlighting the potential of tailored self-supervised learning pipelines for fine-grained audio domains.

  • 6 authors
·
Apr 17, 2025

Stare at What You See: Masked Image Modeling without Reconstruction

Masked Autoencoders (MAE) have been prevailing paradigms for large-scale vision representation pre-training. By reconstructing masked image patches from a small portion of visible image regions, MAE forces the model to infer semantic correlation within an image. Recently, some approaches apply semantic-rich teacher models to extract image features as the reconstruction target, leading to better performance. However, unlike the low-level features such as pixel values, we argue the features extracted by powerful teacher models already encode rich semantic correlation across regions in an intact image.This raises one question: is reconstruction necessary in Masked Image Modeling (MIM) with a teacher model? In this paper, we propose an efficient MIM paradigm named MaskAlign. MaskAlign simply learns the consistency of visible patch features extracted by the student model and intact image features extracted by the teacher model. To further advance the performance and tackle the problem of input inconsistency between the student and teacher model, we propose a Dynamic Alignment (DA) module to apply learnable alignment. Our experimental results demonstrate that masked modeling does not lose effectiveness even without reconstruction on masked regions. Combined with Dynamic Alignment, MaskAlign can achieve state-of-the-art performance with much higher efficiency. Code and models will be available at https://github.com/OpenPerceptionX/maskalign.

  • 7 authors
·
Nov 16, 2022

Masked Thought: Simply Masking Partial Reasoning Steps Can Improve Mathematical Reasoning Learning of Language Models

In reasoning tasks, even a minor error can cascade into inaccurate results, leading to suboptimal performance of large language models in such domains. Earlier fine-tuning approaches sought to mitigate this by leveraging more precise supervisory signals from human labeling, larger models, or self-sampling, although at a high cost. Conversely, we develop a method that avoids external resources, relying instead on introducing perturbations to the input. Our training approach randomly masks certain tokens within the chain of thought, a technique we found to be particularly effective for reasoning tasks. When applied to fine-tuning with GSM8K, this method achieved a 5% improvement in accuracy over standard supervised fine-tuning with a few codes modified and no additional labeling effort. Furthermore, it is complementary to existing methods. When integrated with related data augmentation methods, it leads to an average improvement of 3% improvement in GSM8K accuracy and 1% improvement in MATH accuracy across five datasets of various quality and size, as well as two base models. We further investigate the mechanisms behind this improvement through case studies and quantitative analysis, suggesting that our approach may provide superior support for the model in capturing long-distance dependencies, especially those related to questions. This enhancement could deepen understanding of premises in questions and prior steps. Our code is available at Github.

  • 9 authors
·
Mar 4, 2024

Not All Parameters Matter: Masking Diffusion Models for Enhancing Generation Ability

The diffusion models, in early stages focus on constructing basic image structures, while the refined details, including local features and textures, are generated in later stages. Thus the same network layers are forced to learn both structural and textural information simultaneously, significantly differing from the traditional deep learning architectures (e.g., ResNet or GANs) which captures or generates the image semantic information at different layers. This difference inspires us to explore the time-wise diffusion models. We initially investigate the key contributions of the U-Net parameters to the denoising process and identify that properly zeroing out certain parameters (including large parameters) contributes to denoising, substantially improving the generation quality on the fly. Capitalizing on this discovery, we propose a simple yet effective method-termed ``MaskUNet''- that enhances generation quality with negligible parameter numbers. Our method fully leverages timestep- and sample-dependent effective U-Net parameters. To optimize MaskUNet, we offer two fine-tuning strategies: a training-based approach and a training-free approach, including tailored networks and optimization functions. In zero-shot inference on the COCO dataset, MaskUNet achieves the best FID score and further demonstrates its effectiveness in downstream task evaluations. Project page: https://gudaochangsheng.github.io/MaskUnet-Page/

NankaiUniversity Nankai University
·
May 5, 2025

Fine-Tuning Language Models with Just Forward Passes

Fine-tuning language models (LMs) has yielded success on diverse downstream tasks, but as LMs grow in size, backpropagation requires a prohibitively large amount of memory. Zeroth-order (ZO) methods can in principle estimate gradients using only two forward passes but are theorized to be catastrophically slow for optimizing large models. In this work, we propose a memory-efficient zerothorder optimizer (MeZO), adapting the classical ZO-SGD method to operate in-place, thereby fine-tuning LMs with the same memory footprint as inference. For example, with a single A100 80GB GPU, MeZO can train a 30-billion parameter model, whereas fine-tuning with backpropagation can train only a 2.7B LM with the same budget. We conduct comprehensive experiments across model types (masked and autoregressive LMs), model scales (up to 66B), and downstream tasks (classification, multiple-choice, and generation). Our results demonstrate that (1) MeZO significantly outperforms in-context learning and linear probing; (2) MeZO achieves comparable performance to fine-tuning with backpropagation across multiple tasks, with up to 12x memory reduction; (3) MeZO is compatible with both full-parameter and parameter-efficient tuning techniques such as LoRA and prefix tuning; (4) MeZO can effectively optimize non-differentiable objectives (e.g., maximizing accuracy or F1). We support our empirical findings with theoretical insights, highlighting how adequate pre-training and task prompts enable MeZO to fine-tune huge models, despite classical ZO analyses suggesting otherwise.

  • 7 authors
·
May 26, 2023 2

Multimodal Masked Autoencoder Pre-training for 3D MRI-Based Brain Tumor Analysis with Missing Modalities

Multimodal magnetic resonance imaging (MRI) constitutes the first line of investigation for clinicians in the care of brain tumors, providing crucial insights for surgery planning, treatment monitoring, and biomarker identification. Pre-training on large datasets have been shown to help models learn transferable representations and adapt with minimal labeled data. This behavior is especially valuable in medical imaging, where annotations are often scarce. However, applying this paradigm to multimodal medical data introduces a challenge: most existing approaches assume that all imaging modalities are available during both pre-training and fine-tuning. In practice, missing modalities often occur due to acquisition issues, specialist unavailability, or specific experimental designs on small in-house datasets. Consequently, a common approach involves training a separate model for each desired modality combination, making the process both resource-intensive and impractical for clinical use. Therefore, we introduce BM-MAE, a masked image modeling pre-training strategy tailored for multimodal MRI data. The same pre-trained model seamlessly adapts to any combination of available modalities, extracting rich representations that capture both intra- and inter-modal information. This allows fine-tuning on any subset of modalities without requiring architectural changes, while still benefiting from a model pre-trained on the full set of modalities. Extensive experiments show that the proposed pre-training strategy outperforms or remains competitive with baselines that require separate pre-training for each modality subset, while substantially surpassing training from scratch on several downstream tasks. Additionally, it can quickly and efficiently reconstruct missing modalities, highlighting its practical value. Code and trained models are available at: https://github.com/Lucas-rbnt/BM-MAE

  • 3 authors
·
May 1, 2025

Delving into Masked Autoencoders for Multi-Label Thorax Disease Classification

Vision Transformer (ViT) has become one of the most popular neural architectures due to its great scalability, computational efficiency, and compelling performance in many vision tasks. However, ViT has shown inferior performance to Convolutional Neural Network (CNN) on medical tasks due to its data-hungry nature and the lack of annotated medical data. In this paper, we pre-train ViTs on 266,340 chest X-rays using Masked Autoencoders (MAE) which reconstruct missing pixels from a small part of each image. For comparison, CNNs are also pre-trained on the same 266,340 X-rays using advanced self-supervised methods (e.g., MoCo v2). The results show that our pre-trained ViT performs comparably (sometimes better) to the state-of-the-art CNN (DenseNet-121) for multi-label thorax disease classification. This performance is attributed to the strong recipes extracted from our empirical studies for pre-training and fine-tuning ViT. The pre-training recipe signifies that medical reconstruction requires a much smaller proportion of an image (10% vs. 25%) and a more moderate random resized crop range (0.5~1.0 vs. 0.2~1.0) compared with natural imaging. Furthermore, we remark that in-domain transfer learning is preferred whenever possible. The fine-tuning recipe discloses that layer-wise LR decay, RandAug magnitude, and DropPath rate are significant factors to consider. We hope that this study can direct future research on the application of Transformers to a larger variety of medical imaging tasks.

  • 4 authors
·
Oct 23, 2022

Activating Visual Context and Commonsense Reasoning through Masked Prediction in VLMs

Recent breakthroughs in reasoning models have markedly advanced the reasoning capabilities of large language models, particularly via training on tasks with verifiable rewards. Yet, a significant gap persists in their adaptation to real world multimodal scenarios, most notably, vision language tasks, due to a heavy focus on single modal language settings. While efforts to transplant reinforcement learning techniques from NLP to VLMs have emerged, these approaches often remain confined to perception centric tasks or reduce images to textual summaries, failing to fully exploit visual context and commonsense knowledge, ultimately constraining the generalization of reasoning capabilities across diverse multimodal environments. To address this limitation, we introduce a novel fine tuning task, Masked Prediction via Context and Commonsense, which forces models to integrate visual context and commonsense reasoning by reconstructing semantically meaningful content from occluded images, thereby laying the foundation for generalized reasoning. To systematically evaluate the model performance in generalized reasoning, we developed a specialized evaluation benchmark, MPCC Eval, and employed various fine tuning strategies to guide reasoning. Among these, we introduced an innovative training method, Reinforcement Fine tuning with Prior Sampling, which not only enhances model performance but also improves its generalized reasoning capabilities in OOD and cross task scenarios.

  • 7 authors
·
Oct 21, 2025

Ask2Mask: Guided Data Selection for Masked Speech Modeling

Masked speech modeling (MSM) methods such as wav2vec2 or w2v-BERT learn representations over speech frames which are randomly masked within an utterance. While these methods improve performance of Automatic Speech Recognition (ASR) systems, they have one major limitation. They treat all unsupervised speech samples with equal weight, which hinders learning as not all samples have relevant information to learn meaningful representations. In this work, we address this limitation. We propose ask2mask (ATM), a novel approach to focus on specific samples during MSM pre-training. ATM employs an external ASR model or scorer to weight unsupervised input samples in two different ways: 1) A fine-grained data selection is performed by masking over the highly confident input frames as chosen by the scorer. This allows the model to learn meaningful representations. 2) ATM is further extended to focus at utterance-level by weighting the final MSM loss with the utterance-level confidence score. We conduct fine-tuning experiments on two well-benchmarked corpora: LibriSpeech (matching the pre-training data) and Commonvoice, TED-LIUM, AMI and CHiME-6 (not matching the pre-training data). The results substantiate the efficacy of ATM on significantly improving the recognition performance under mismatched conditions (up to 11.6\% relative over published results and upto 4.46\% relative over our internal baseline) while still yielding modest improvements under matched conditions.

  • 5 authors
·
Feb 24, 2022

DLLM-JEPA: Joint Embedding Predictive Architectures for Masked Diffusion Language Models

Joint Embedding Predictive Architectures (JEPAs) have reshaped self-supervised representation learning in vision. The recent LLM-JEPA ported JEPA to autoregressive language models but inherited two steep costs from the causal-attention substrate: it demands explicit multi-view data (e.g., text-code pairs), and it requires two gradient-carrying forward passes per step. We introduce DLLM-JEPA, which pairs JEPA with masked-diffusion language models to eliminate both costs at once. The bidirectional attention of diffusion models yields two semantically distinct views of the same input via different masking rates -- no explicit pairs needed -- and supports a single gradient-carrying forward pass, cutting training FLOPs by 33% relative to LLM-JEPA. DLLM-JEPA improves over diffusion-only fine-tuning in every (task, architecture) combination we evaluate: up to +18.7 pp on LLaDA-8B GSM8K and +11.4 pp on Dream-7B GSM8K, with consistent positive gains on Spider, NL-RX-SYNTH, and Django. Beyond accuracy, DLLM-JEPA exhibits a dual-win property: on LLaDA-8B with the Wide-t configuration, it simultaneously raises GSM8K accuracy (67.1 vs. 65.2, +1.8 pp), drives held-out Wikitext loss below the pre-trained base, and preserves MMLU accuracy at base level across three fine-tuning seeds -- whereas an L2-to-base parameter anchor matches baseline accuracy with no task gain. Layer-wise probing reveals the mechanism: a geometric-functional drift dissociation in which the fine-tuned backbone moves further from the pre-trained weights than the baseline yet forgets less on held-out Wikitext, with the amplification concentrated in middle transformer layers. The pattern appears on Dream-7B as well, indicating the phenomenon is not specific to a single backbone.

  • 1 authors
·
May 23

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

Particle Trajectory Representation Learning with Masked Point Modeling

Effective self-supervised learning (SSL) techniques have been key to unlocking large datasets for representation learning. While many promising methods have been developed using online corpora and captioned photographs, their application to scientific domains, where data encodes highly specialized knowledge, remains a challenge. Liquid Argon Time Projection Chambers (LArTPCs) provide high-resolution 3D imaging for fundamental physics, but analysis of their sparse, complex point cloud data often relies on supervised methods trained on large simulations, introducing potential biases. We introduce the Point-based Liquid Argon Masked Autoencoder (PoLAr-MAE), applying masked point modeling to unlabeled LArTPC images using domain-specific volumetric tokenization and energy prediction. We show this SSL approach learns physically meaningful trajectory representations directly from data. This yields remarkable data efficiency: fine-tuning on just 100 labeled events achieves track/shower semantic segmentation performance comparable to the state-of-the-art supervised baseline trained on >100,000 events. Furthermore, internal attention maps exhibit emergent instance segmentation of particle trajectories. While challenges remain, particularly for fine-grained features, we make concrete SSL's potential for building a foundation model for LArTPC image analysis capable of serving as a common base for all data reconstruction tasks. To facilitate further progress, we release PILArNet-M, a large dataset of 1M LArTPC events. Project site: https://youngsm.com/polarmae.

  • 3 authors
·
Feb 4, 2025

Masked Scene Modeling: Narrowing the Gap Between Supervised and Self-Supervised Learning in 3D Scene Understanding

Self-supervised learning has transformed 2D computer vision by enabling models trained on large, unannotated datasets to provide versatile off-the-shelf features that perform similarly to models trained with labels. However, in 3D scene understanding, self-supervised methods are typically only used as a weight initialization step for task-specific fine-tuning, limiting their utility for general-purpose feature extraction. This paper addresses this shortcoming by proposing a robust evaluation protocol specifically designed to assess the quality of self-supervised features for 3D scene understanding. Our protocol uses multi-resolution feature sampling of hierarchical models to create rich point-level representations that capture the semantic capabilities of the model and, hence, are suitable for evaluation with linear probing and nearest-neighbor methods. Furthermore, we introduce the first self-supervised model that performs similarly to supervised models when only off-the-shelf features are used in a linear probing setup. In particular, our model is trained natively in 3D with a novel self-supervised approach based on a Masked Scene Modeling objective, which reconstructs deep features of masked patches in a bottom-up manner and is specifically tailored to hierarchical 3D models. Our experiments not only demonstrate that our method achieves competitive performance to supervised models, but also surpasses existing self-supervised approaches by a large margin. The model and training code can be found at our Github repository (https://github.com/phermosilla/msm).

  • 3 authors
·
Apr 9, 2025 2

Attention, Please! Revisiting Attentive Probing for Masked Image Modeling

As fine-tuning (FT) becomes increasingly impractical at scale, probing is emerging as the preferred evaluation protocol for self-supervised learning (SSL). Yet, the standard linear probing (LP) fails to adequately reflect the potential of models trained with Masked Image Modeling (MIM), due to the distributed nature of patch tokens. This motivates the need for attentive probing, an alternative that uses attention to selectively aggregate patch-level features. Despite its growing adoption, attentive probing remains under-explored, with existing methods suffering from excessive parameterization and poor computational efficiency. In this work, we revisit attentive probing through the lens of the accuracy-efficiency trade-off. We conduct a systematic study of existing methods, analyzing their mechanisms and benchmarking their performance. We introduce efficient probing (EP), a multi-query cross-attention mechanism that eliminates redundant projections, reduces the number of trainable parameters, and achieves up to a 10times speed-up over conventional multi-head attention. Despite its simplicity, EP outperforms LP and prior attentive probing approaches across seven benchmarks, generalizes well beyond MIM to diverse pre-training paradigms, produces interpretable attention maps, and achieves strong gains in low-shot and layer-wise settings. Code available at https://github.com/billpsomas/efficient-probing.

  • 9 authors
·
Jun 11, 2025 2

Masked-and-Reordered Self-Supervision for Reinforcement Learning from Verifiable Rewards

Test-time scaling has been shown to substantially improve large language models' (LLMs) mathematical reasoning. However, for a large portion of mathematical corpora, especially theorem proving, RLVR's scalability is limited: intermediate reasoning is crucial, while final answers are difficult to directly and reliably verify. Meanwhile, token-level SFT often degenerates into rote memorization rather than inducing longer chains of thought. Inspired by BERT's self-supervised tasks, we propose MR-RLVR (Masked-and-Reordered RLVR), which constructs process-level self-supervised rewards via "masked-then-fill" and "step reordering" to extract learnable signals from intermediate reasoning. Our training pipeline comprises two stages: we first perform self-supervised training on sampled mathematical calculation and proof data; we then conduct RLVR fine-tuning on mathematical calculation datasets where only outcomes are verifiable. We implement MR-RLVR on Qwen2.5-3B and DeepSeek-R1-Distill-Qwen-1.5B, and evaluate on AIME24, AIME25, AMC23, and MATH500. Under a fixed sampling and decoding budget, MR-RLVR achieves average relative gains over the original RLVR of +9.86% Pass@1, +5.27% Pass@5, and +4.00% Pass@8. These results indicate that incorporating process-aware self-supervised signals can effectively enhance RLVR's scalability and performance in only outcome-verifiable settings.

  • 3 authors
·
Nov 21, 2025

MMCLIP: Cross-modal Attention Masked Modelling for Medical Language-Image Pre-Training

Vision-and-language pretraining (VLP) in the medical field utilizes contrastive learning on image-text pairs to achieve effective transfer across tasks. Yet, current VLP approaches with the masked modeling strategy face two challenges when applied to the medical domain. First, current models struggle to accurately reconstruct key pathological features due to the scarcity of medical data. Second, most methods only adopt either paired image-text or image-only data, failing to exploit the combination of both paired and unpaired data. To this end, this paper proposes the MMCLIP (Masked Medical Contrastive Language-Image Pre-Training) framework to enhance pathological learning and feature learning via unpaired data. First, we introduce the attention-masked image modeling (AttMIM) and entity-driven masked language modeling module (EntMLM), which learns to reconstruct pathological visual and textual tokens via multi-modal feature interaction, thus improving medical-enhanced features. The AttMIM module masks a portion of the image features that are highly responsive to textual features. This allows MMCLIP to improve the reconstruction of highly similar image data in medicine efficiency. Second, our MMCLIP capitalizes unpaired data to enhance multimodal learning by introducing disease-kind prompts. The experimental results show that MMCLIP achieves SOTA for zero-shot and fine-tuning classification performance on five datasets. Our code will be available at https://github.com/AIGeeksGroup/MMCLIP.

  • 7 authors
·
Jul 28, 2024

Self-Supervised Pre-Training with Contrastive and Masked Autoencoder Methods for Dealing with Small Datasets in Deep Learning for Medical Imaging

Deep learning in medical imaging has the potential to minimize the risk of diagnostic errors, reduce radiologist workload, and accelerate diagnosis. Training such deep learning models requires large and accurate datasets, with annotations for all training samples. However, in the medical imaging domain, annotated datasets for specific tasks are often small due to the high complexity of annotations, limited access, or the rarity of diseases. To address this challenge, deep learning models can be pre-trained on large image datasets without annotations using methods from the field of self-supervised learning. After pre-training, small annotated datasets are sufficient to fine-tune the models for a specific task. The most popular self-supervised pre-training approaches in medical imaging are based on contrastive learning. However, recent studies in natural image processing indicate a strong potential for masked autoencoder approaches. Our work compares state-of-the-art contrastive learning methods with the recently introduced masked autoencoder approach "SparK" for convolutional neural networks (CNNs) on medical images. Therefore we pre-train on a large unannotated CT image dataset and fine-tune on several CT classification tasks. Due to the challenge of obtaining sufficient annotated training data in medical imaging, it is of particular interest to evaluate how the self-supervised pre-training methods perform when fine-tuning on small datasets. By experimenting with gradually reducing the training dataset size for fine-tuning, we find that the reduction has different effects depending on the type of pre-training chosen. The SparK pre-training method is more robust to the training dataset size than the contrastive methods. Based on our results, we propose the SparK pre-training for medical imaging tasks with only small annotated datasets.

  • 7 authors
·
Aug 12, 2023

Model-tuning Via Prompts Makes NLP Models Adversarially Robust

In recent years, NLP practitioners have converged on the following practice: (i) import an off-the-shelf pretrained (masked) language model; (ii) append a multilayer perceptron atop the CLS token's hidden representation (with randomly initialized weights); and (iii) fine-tune the entire model on a downstream task (MLP-FT). This procedure has produced massive gains on standard NLP benchmarks, but these models remain brittle, even to mild adversarial perturbations. In this work, we demonstrate surprising gains in adversarial robustness enjoyed by Model-tuning Via Prompts (MVP), an alternative method of adapting to downstream tasks. Rather than appending an MLP head to make output prediction, MVP appends a prompt template to the input, and makes prediction via text infilling/completion. Across 5 NLP datasets, 4 adversarial attacks, and 3 different models, MVP improves performance against adversarial substitutions by an average of 8% over standard methods and even outperforms adversarial training-based state-of-art defenses by 3.5%. By combining MVP with adversarial training, we achieve further improvements in adversarial robustness while maintaining performance on unperturbed examples. Finally, we conduct ablations to investigate the mechanism underlying these gains. Notably, we find that the main causes of vulnerability of MLP-FT can be attributed to the misalignment between pre-training and fine-tuning tasks, and the randomly initialized MLP parameters.

  • 5 authors
·
Mar 13, 2023

Learning 3D Representations from 2D Pre-trained Models via Image-to-Point Masked Autoencoders

Pre-training by numerous image data has become de-facto for robust 2D representations. In contrast, due to the expensive data acquisition and annotation, a paucity of large-scale 3D datasets severely hinders the learning for high-quality 3D features. In this paper, we propose an alternative to obtain superior 3D representations from 2D pre-trained models via Image-to-Point Masked Autoencoders, named as I2P-MAE. By self-supervised pre-training, we leverage the well learned 2D knowledge to guide 3D masked autoencoding, which reconstructs the masked point tokens with an encoder-decoder architecture. Specifically, we first utilize off-the-shelf 2D models to extract the multi-view visual features of the input point cloud, and then conduct two types of image-to-point learning schemes on top. For one, we introduce a 2D-guided masking strategy that maintains semantically important point tokens to be visible for the encoder. Compared to random masking, the network can better concentrate on significant 3D structures and recover the masked tokens from key spatial cues. For another, we enforce these visible tokens to reconstruct the corresponding multi-view 2D features after the decoder. This enables the network to effectively inherit high-level 2D semantics learned from rich image data for discriminative 3D modeling. Aided by our image-to-point pre-training, the frozen I2P-MAE, without any fine-tuning, achieves 93.4% accuracy for linear SVM on ModelNet40, competitive to the fully trained results of existing methods. By further fine-tuning on on ScanObjectNN's hardest split, I2P-MAE attains the state-of-the-art 90.11% accuracy, +3.68% to the second-best, demonstrating superior transferable capacity. Code will be available at https://github.com/ZrrSkywalker/I2P-MAE.

  • 5 authors
·
Dec 13, 2022

MV-JAR: Masked Voxel Jigsaw and Reconstruction for LiDAR-Based Self-Supervised Pre-Training

This paper introduces the Masked Voxel Jigsaw and Reconstruction (MV-JAR) method for LiDAR-based self-supervised pre-training and a carefully designed data-efficient 3D object detection benchmark on the Waymo dataset. Inspired by the scene-voxel-point hierarchy in downstream 3D object detectors, we design masking and reconstruction strategies accounting for voxel distributions in the scene and local point distributions within the voxel. We employ a Reversed-Furthest-Voxel-Sampling strategy to address the uneven distribution of LiDAR points and propose MV-JAR, which combines two techniques for modeling the aforementioned distributions, resulting in superior performance. Our experiments reveal limitations in previous data-efficient experiments, which uniformly sample fine-tuning splits with varying data proportions from each LiDAR sequence, leading to similar data diversity across splits. To address this, we propose a new benchmark that samples scene sequences for diverse fine-tuning splits, ensuring adequate model convergence and providing a more accurate evaluation of pre-training methods. Experiments on our Waymo benchmark and the KITTI dataset demonstrate that MV-JAR consistently and significantly improves 3D detection performance across various data scales, achieving up to a 6.3% increase in mAPH compared to training from scratch. Codes and the benchmark will be available at https://github.com/SmartBot-PJLab/MV-JAR .

  • 7 authors
·
Mar 23, 2023

Fixed-Point Masked Generative Modeling

Masked Generative Models (MGMs) enable parallel decoding and achieve strong performance across modalities, but require full-sequence bidirectional transformers at every step, making training costly and degrading quality under low sampling budgets. Existing work improves efficiency via better samplers or cheaper fixed-depth denoisers, but they still allocate a fixed amount of denoiser computation to each refinement step. We introduce Fixed-Point Masked Generative Models (FP-MGMs), which replace part of the denoiser with a fixed-point solver over shared attention layers to enable adaptive depth with fewer parameters. To make it more effective for masked generation, we first introduce a cross-step consistency loss, which aligns hidden representations at neighboring denoising steps and, second, three-state reuse (3SR) which warm-starts the solver using the previous solution by treating differently unchanged, still-masked, and newly revealed tokens respectively. Together, these components define our complete training-to-inference framework for fixed-point masked generation, CoFRe. We also show that pre-trained MGMs can be converted into FP-MGMs with short fine-tuning, avoiding full retraining. Across modalities, CoFRe improves the quality and cost trade-off. On OpenWebText, CoFRe reduces parameters by 38.8\%, training time by 11.5\%, and VRAM by 16.9\%, while improving generative perplexity from 830.8 to 101.8 at a budget of 96 transformer-block forward passes, compared to MDLM. In ImageNette, CoFRe reduces training time by 48.6\% and VRAM by 50.7\%, while improving FID in all sample budgets tested. Overall, CoFRe offers a practical framework for cheaper training and stronger low-budget masked generation.

  • 5 authors
·
May 29

Uni4Eye: Unified 2D and 3D Self-supervised Pre-training via Masked Image Modeling Transformer for Ophthalmic Image Classification

A large-scale labeled dataset is a key factor for the success of supervised deep learning in computer vision. However, a limited number of annotated data is very common, especially in ophthalmic image analysis, since manual annotation is time-consuming and labor-intensive. Self-supervised learning (SSL) methods bring huge opportunities for better utilizing unlabeled data, as they do not need massive annotations. With an attempt to use as many as possible unlabeled ophthalmic images, it is necessary to break the dimension barrier, simultaneously making use of both 2D and 3D images. In this paper, we propose a universal self-supervised Transformer framework, named Uni4Eye, to discover the inherent image property and capture domain-specific feature embedding in ophthalmic images. Uni4Eye can serve as a global feature extractor, which builds its basis on a Masked Image Modeling task with a Vision Transformer (ViT) architecture. We employ a Unified Patch Embedding module to replace the origin patch embedding module in ViT for jointly processing both 2D and 3D input images. Besides, we design a dual-branch multitask decoder module to simultaneously perform two reconstruction tasks on the input image and its gradient map, delivering discriminative representations for better convergence. We evaluate the performance of our pre-trained Uni4Eye encoder by fine-tuning it on six downstream ophthalmic image classification tasks. The superiority of Uni4Eye is successfully established through comparisons to other state-of-the-art SSL pre-training methods.

  • 4 authors
·
Mar 9, 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

Probabilistic Hyper-Graphs using Multiple Randomly Masked Autoencoders for Semi-supervised Multi-modal Multi-task Learning

The computer vision domain has greatly benefited from an abundance of data across many modalities to improve on various visual tasks. Recently, there has been a lot of focus on self-supervised pre-training methods through Masked Autoencoders (MAE) he2022masked,bachmann2022multimae, usually used as a first step before optimizing for a downstream task, such as classification or regression. This is very useful as it doesn't require any manually labeled data. In this work, we introduce Probabilistic Hyper-Graphs using Masked Autoencoders (PHG-MAE): a novel model that unifies the classical work on neural graphs leordeanu2021semi with the modern approach of masked autoencoders under a common theoretical framework. Through random masking of entire modalities, not just patches, the model samples from the distribution of hyper-edges on each forward pass. Additionally, the model adapts the standard MAE algorithm by combining pre-training and fine-tuning into a single training loop. Moreover, our approach enables the creation of inference-time ensembles which, through aggregation, boost the final prediction performance and consistency. Lastly, we show that we can apply knowledge distillation on top of the ensembles with little loss in performance, even with models that have fewer than 1M parameters. While our work mostly focuses on outdoor UAV scenes that contain multiple world interpretations and modalities, the same steps can be followed in other similar domains, such as autonomous driving or indoor robotics. In order to streamline the process of integrating external pre-trained experts for computer vision multi-modal multi-task learning (MTL) scenarios, we developed a data-pipeline software. Using this tool, we have created and released a fully-automated extension of the Dronescapes dataset. All the technical details, code and reproduction steps are publicly released.

  • 2 authors
·
Oct 11, 2025

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

Beyond ViT Tokens: Masked-Diffusion Pretrained Convolutional Pathology Foundation Model for Cell-Level Dense Prediction

Cell-level dense prediction is central to computational pathology, but remains challenging due to fine-grained histological structures, strong domain shifts, and costly dense annotations. Existing ViT-based pathology foundation models rely on patch tokenization, which can disrupt spatial continuity and weaken local morphological details needed for cell-level prediction. To address this, we propose Masked-Diffusion Convolutional Foundation Models, termed ConvNeXt Masked-Diffusion (CMD), a self-supervised convolutional generative pretraining framework for dense pathology representation learning. CMD uses a fully convolutional ConvNeXt-UNet backbone, performs masked-diffusion pretraining in pixel space, and incorporates frozen pathology foundation model features through adaptive normalization. Experimental results demonstrate that CMD consistently outperforms existing ViT-based pathology foundation models and even surpasses state-of-the-art end-to-end segmentation methods while fine-tuning only a small number of task-specific parameters across multiple pathology dense prediction tasks. The advantage is particularly pronounced under limited annotation settings, where CMD exhibits stronger robustness and generalization ability. Our findings suggest that purely convolutional architectures can also serve as competitive pathology foundation models for cell-level dense prediction, achieving leading performance within the current ViT-dominated paradigm and providing a scalable, high-performance solution that better preserves histological structural priors for fine-grained pathology understanding.

  • 8 authors
·
May 7

Mimic before Reconstruct: Enhancing Masked Autoencoders with Feature Mimicking

Masked Autoencoders (MAE) have been popular paradigms for large-scale vision representation pre-training. However, MAE solely reconstructs the low-level RGB signals after the decoder and lacks supervision upon high-level semantics for the encoder, thus suffering from sub-optimal learned representations and long pre-training epochs. To alleviate this, previous methods simply replace the pixel reconstruction targets of 75% masked tokens by encoded features from pre-trained image-image (DINO) or image-language (CLIP) contrastive learning. Different from those efforts, we propose to Mimic before Reconstruct for Masked Autoencoders, named as MR-MAE, which jointly learns high-level and low-level representations without interference during pre-training. For high-level semantics, MR-MAE employs a mimic loss over 25% visible tokens from the encoder to capture the pre-trained patterns encoded in CLIP and DINO. For low-level structures, we inherit the reconstruction loss in MAE to predict RGB pixel values for 75% masked tokens after the decoder. As MR-MAE applies high-level and low-level targets respectively at different partitions, the learning conflicts between them can be naturally overcome and contribute to superior visual representations for various downstream tasks. On ImageNet-1K, the MR-MAE base pre-trained for only 400 epochs achieves 85.8% top-1 accuracy after fine-tuning, surpassing the 1600-epoch MAE base by +2.2% and the previous state-of-the-art BEiT V2 base by +0.3%. Code and pre-trained models will be released at https://github.com/Alpha-VL/ConvMAE.

  • 7 authors
·
Mar 9, 2023

SimMIM: A Simple Framework for Masked Image Modeling

This paper presents SimMIM, a simple framework for masked image modeling. We simplify recently proposed related approaches without special designs such as block-wise masking and tokenization via discrete VAE or clustering. To study what let the masked image modeling task learn good representations, we systematically study the major components in our framework, and find that simple designs of each component have revealed very strong representation learning performance: 1) random masking of the input image with a moderately large masked patch size (e.g., 32) makes a strong pre-text task; 2) predicting raw pixels of RGB values by direct regression performs no worse than the patch classification approaches with complex designs; 3) the prediction head can be as light as a linear layer, with no worse performance than heavier ones. Using ViT-B, our approach achieves 83.8% top-1 fine-tuning accuracy on ImageNet-1K by pre-training also on this dataset, surpassing previous best approach by +0.6%. When applied on a larger model of about 650 million parameters, SwinV2-H, it achieves 87.1% top-1 accuracy on ImageNet-1K using only ImageNet-1K data. We also leverage this approach to facilitate the training of a 3B model (SwinV2-G), that by 40times less data than that in previous practice, we achieve the state-of-the-art on four representative vision benchmarks. The code and models will be publicly available at https://github.com/microsoft/SimMIM.

  • 8 authors
·
Nov 18, 2021

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, 2025 9

Light-PEFT: Lightening Parameter-Efficient Fine-Tuning via Early Pruning

Parameter-efficient fine-tuning (PEFT) has emerged as the predominant technique for fine-tuning in the era of large language models. However, existing PEFT methods still have inadequate training efficiency. Firstly, the utilization of large-scale foundation models during the training process is excessively redundant for certain fine-tuning tasks. Secondly, as the model size increases, the growth in trainable parameters of empirically added PEFT modules becomes non-negligible and redundant, leading to inefficiency. To achieve task-specific efficient fine-tuning, we propose the Light-PEFT framework, which includes two methods: Masked Early Pruning of the Foundation Model and Multi-Granularity Early Pruning of PEFT. The Light-PEFT framework allows for the simultaneous estimation of redundant parameters in both the foundation model and PEFT modules during the early stage of training. These parameters can then be pruned for more efficient fine-tuning. We validate our approach on GLUE, SuperGLUE, QA tasks, and various models. With Light-PEFT, parameters of the foundation model can be pruned by up to over 40%, while still controlling trainable parameters to be only 25% of the original PEFT method. Compared to utilizing the PEFT method directly, Light-PEFT achieves training and inference speedup, reduces memory usage, and maintains comparable performance and the plug-and-play feature of PEFT.

  • 6 authors
·
Jun 6, 2024

OpenUS: A Fully Open-Source Foundation Model for Ultrasound Image Analysis via Self-Adaptive Masked Contrastive Learning

Ultrasound (US) is one of the most widely used medical imaging modalities, thanks to its low cost, portability, real-time feedback, and absence of ionizing radiation. However, US image interpretation remains highly operator-dependent and varies significantly across anatomical regions, acquisition protocols, and device types. These variations, along with unique challenges such as speckle, low contrast, and limited standardized annotations, hinder the development of generalizable, label-efficient ultrasound AI models. In this paper, we propose OpenUS, the first reproducible, open-source ultrasound foundation model built on a large collection of public data. OpenUS employs a vision Mamba backbone, capturing both local and global long-range dependencies across the image. To extract rich features during pre-training, we introduce a novel self-adaptive masking framework that combines contrastive learning with masked image modeling. This strategy integrates the teacher's attention map with student reconstruction loss, adaptively refining clinically-relevant masking to enhance pre-training effectiveness. OpenUS also applies a dynamic learning schedule to progressively adjust the difficulty of the pre-training process. To develop the foundation model, we compile the largest to-date public ultrasound dataset comprising over 308K images from 42 publicly available datasets, covering diverse anatomical regions, institutions, imaging devices, and disease types. Our pre-trained OpenUS model can be easily adapted to specific downstream tasks by serving as a backbone for label-efficient fine-tuning. Code is available at https://github.com/XZheng0427/OpenUS.

Urban In-Context Learning: Bridging Pretraining and Inference through Masked Diffusion for Urban Profiling

Urban profiling aims to predict urban profiles in unknown regions and plays a critical role in economic and social censuses. Existing approaches typically follow a two-stage paradigm: first, learning representations of urban areas; second, performing downstream prediction via linear probing, which originates from the BERT era. Inspired by the development of GPT style models, recent studies have shown that novel self-supervised pretraining schemes can endow models with direct applicability to downstream tasks, thereby eliminating the need for task-specific fine-tuning. This is largely because GPT unifies the form of pretraining and inference through next-token prediction. However, urban data exhibit structural characteristics that differ fundamentally from language, making it challenging to design a one-stage model that unifies both pretraining and inference. In this work, we propose Urban In-Context Learning, a framework that unifies pretraining and inference via a masked autoencoding process over urban regions. To capture the distribution of urban profiles, we introduce the Urban Masked Diffusion Transformer, which enables each region' s prediction to be represented as a distribution rather than a deterministic value. Furthermore, to stabilize diffusion training, we propose the Urban Representation Alignment Mechanism, which regularizes the model's intermediate features by aligning them with those from classical urban profiling methods. Extensive experiments on three indicators across two cities demonstrate that our one-stage method consistently outperforms state-of-the-art two-stage approaches. Ablation studies and case studies further validate the effectiveness of each proposed module, particularly the use of diffusion modeling.

  • 5 authors
·
Aug 4, 2025

Dynamic Proxy-Mixing: Transferring Replay Controllers from Small to Large Models for Continual Instruction Tuning

Continual instruction tuning updates a language model through a sequence of new domains, yet each update can progressively erode previously learned capabilities and alignment behavior. Replay is the standard mitigation, but fixed replay ratios are inherently limited because the optimal mixture varies with the current domain, the training stage, and the evolving vulnerability of prior behaviors. We propose PROX-YMIX, a framework that learns a dynamic replay controller on a small proxy model and transfers the frozen controller to a larger target. The controller never observes future tasks and constructs its state from normalized validation losses and their temporal dynamics, producing a masked mixture over the current task and accessible replay buffers. Our core empirical hypothesis is forgetting mirroring: task vulnerability rankings remain largely consistent across model scales even when absolute loss magnitudes differ. We validate this assumption empirically before transferring controllers across scales. On LLaMA-3-8B across five continual instruction tuning sequences, PROXYMIX improves average accuracy by 3.4 points, reduces final forgetting by 3.5 points, and raises safety score by 5.8 points over the strongest non-oracle baseline, at roughly 50x lower policy learning cost than Oracle Target RL. The framework is leakage free and architecture independent at the interface level, and we also identify settings where the proxy assumption breaks down, highlighting limitations for robust deployment.

  • 3 authors
·
May 28

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

Benign Fine-Tuning Breaks Safety Alignment in Audio LLMs

Prior work shows that fine-tuning aligned models on benign data degrades safety in text and vision modalities, and that proximity to harmful content in representation space predicts which samples cause the most damage. However, existing analyses operate within a single, undifferentiated embedding space -- leaving open whether distinct input properties drive the vulnerability differently. Audio introduces a structurally richer problem: a benign sample can neighbor harmful content not only through what is said but through how it sounds, even when its words are entirely innocuous. We present the first systematic study of benign fine-tuning safety in Audio LLMs, evaluating three state-of-the-art models with a proximity-based filtering framework that selects benign audio by embedding-space distance to harmful content. By decomposing proximity into semantic, acoustic, and mixed axes using external reference encoders alongside each model's own internal encoder, we show that benign fine-tuning elevates Jailbreak Success Rate (JSR) from single digits to as high as 87.12%. Crucially, the dominant vulnerability axis and the relative risk of audio versus text fine-tuning are both architecture-conditioned -- determined by how each model's encoder and projector transform audio into the LLM's input space. We propose two defenses: filtering training data to maximize distance from harmful embeddings, and a textual system prompt at inference, both reducing JSR to near-zero without architectural modification. Our mechanistic analysis on two architectures reveals that fine-tuning selectively suppresses the late-layer refusal circuit while the frozen encoder preserves representations, and that even the suppression pattern is architecture-conditioned, mirroring the behavioral asymmetries across modalities. Safety degradation from benign fine-tuning is a qualitatively distinct risk in Audio LLMs.

  • 2 authors
·
Apr 16 2

Tuning Language Models by Proxy

Despite the general capabilities of large pretrained language models, they consistently benefit from further adaptation to better achieve desired behaviors. However, tuning these models has become increasingly resource-intensive, or impossible when model weights are private. We introduce proxy-tuning, a lightweight decoding-time algorithm that operates on top of black-box LMs to achieve the result of directly tuning the model, but by accessing only its prediction over the output vocabulary. Our method instead tunes a smaller LM, then applies the difference between the predictions of the small tuned and untuned LMs to shift the original predictions of the base model in the direction of tuning, while retaining the benefits of larger scale pretraining. In experiments, when we apply proxy-tuning to Llama2-70B using proxies of only 7B size, we can close 88% of the gap between Llama2-70B and its truly-tuned chat version, when evaluated across knowledge, reasoning, and safety benchmarks. Interestingly, when tested on TruthfulQA, proxy-tuned models are actually more truthful than directly tuned models, possibly because decoding-time guidance better retains the model's factual knowledge. We then demonstrate the generality of proxy-tuning by applying it for domain adaptation on code, and task-specific finetuning on question-answering and math problems. Our work demonstrates the promise of using small tuned LMs to efficiently customize large, potentially proprietary LMs through decoding-time guidance.

  • 6 authors
·
Jan 16, 2024 2