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Dec 8

Reprogramming Pretrained Language Models for Antibody Sequence Infilling

Antibodies comprise the most versatile class of binding molecules, with numerous applications in biomedicine. Computational design of antibodies involves generating novel and diverse sequences, while maintaining structural consistency. Unique to antibodies, designing the complementarity-determining region (CDR), which determines the antigen binding affinity and specificity, creates its own unique challenges. Recent deep learning models have shown impressive results, however the limited number of known antibody sequence/structure pairs frequently leads to degraded performance, particularly lacking diversity in the generated sequences. In our work we address this challenge by leveraging Model Reprogramming (MR), which repurposes pretrained models on a source language to adapt to the tasks that are in a different language and have scarce data - where it may be difficult to train a high-performing model from scratch or effectively fine-tune an existing pre-trained model on the specific task. Specifically, we introduce ReprogBert in which a pretrained English language model is repurposed for protein sequence infilling - thus considers cross-language adaptation using less data. Results on antibody design benchmarks show that our model on low-resourced antibody sequence dataset provides highly diverse CDR sequences, up to more than a two-fold increase of diversity over the baselines, without losing structural integrity and naturalness. The generated sequences also demonstrate enhanced antigen binding specificity and virus neutralization ability. Code is available at https://github.com/IBM/ReprogBERT

  • 7 authors
·
Oct 5, 2022

Assimilation Matters: Model-level Backdoor Detection in Vision-Language Pretrained Models

Vision-language pretrained models (VLPs) such as CLIP have achieved remarkable success, but are also highly vulnerable to backdoor attacks. Given a model fine-tuned by an untrusted third party, determining whether the model has been injected with a backdoor is a critical and challenging problem. Existing detection methods usually rely on prior knowledge of training dataset, backdoor triggers and targets, or downstream classifiers, which may be impractical for real-world applications. To address this, To address this challenge, we introduce Assimilation Matters in DETection (AMDET), a novel model-level detection framework that operates without any such prior knowledge. Specifically, we first reveal the feature assimilation property in backdoored text encoders: the representations of all tokens within a backdoor sample exhibit a high similarity. Further analysis attributes this effect to the concentration of attention weights on the trigger token. Leveraging this insight, AMDET scans a model by performing gradient-based inversion on token embeddings to recover implicit features that capable of activating backdoor behaviors. Furthermore, we identify the natural backdoor feature in the OpenAI's official CLIP model, which are not intentionally injected but still exhibit backdoor-like behaviors. We then filter them out from real injected backdoor by analyzing their loss landscapes. Extensive experiments on 3,600 backdoored and benign-finetuned models with two attack paradigms and three VLP model structures show that AMDET detects backdoors with an F1 score of 89.90%. Besides, it achieves one complete detection in approximately 5 minutes on a RTX 4090 GPU and exhibits strong robustness against adaptive attacks. Code is available at: https://github.com/Robin-WZQ/AMDET

  • 4 authors
·
Nov 29

MIS-FM: 3D Medical Image Segmentation using Foundation Models Pretrained on a Large-Scale Unannotated Dataset

Pretraining with large-scale 3D volumes has a potential for improving the segmentation performance on a target medical image dataset where the training images and annotations are limited. Due to the high cost of acquiring pixel-level segmentation annotations on the large-scale pretraining dataset, pretraining with unannotated images is highly desirable. In this work, we propose a novel self-supervised learning strategy named Volume Fusion (VF) for pretraining 3D segmentation models. It fuses several random patches from a foreground sub-volume to a background sub-volume based on a predefined set of discrete fusion coefficients, and forces the model to predict the fusion coefficient of each voxel, which is formulated as a self-supervised segmentation task without manual annotations. Additionally, we propose a novel network architecture based on parallel convolution and transformer blocks that is suitable to be transferred to different downstream segmentation tasks with various scales of organs and lesions. The proposed model was pretrained with 110k unannotated 3D CT volumes, and experiments with different downstream segmentation targets including head and neck organs, thoracic/abdominal organs showed that our pretrained model largely outperformed training from scratch and several state-of-the-art self-supervised training methods and segmentation models. The code and pretrained model are available at https://github.com/openmedlab/MIS-FM.

  • 6 authors
·
Jun 29, 2023

Geometry-Aware Adaptation for Pretrained Models

Machine learning models -- including prominent zero-shot models -- are often trained on datasets whose labels are only a small proportion of a larger label space. Such spaces are commonly equipped with a metric that relates the labels via distances between them. We propose a simple approach to exploit this information to adapt the trained model to reliably predict new classes -- or, in the case of zero-shot prediction, to improve its performance -- without any additional training. Our technique is a drop-in replacement of the standard prediction rule, swapping argmax with the Fr\'echet mean. We provide a comprehensive theoretical analysis for this approach, studying (i) learning-theoretic results trading off label space diameter, sample complexity, and model dimension, (ii) characterizations of the full range of scenarios in which it is possible to predict any unobserved class, and (iii) an optimal active learning-like next class selection procedure to obtain optimal training classes for when it is not possible to predict the entire range of unobserved classes. Empirically, using easily-available external metrics, our proposed approach, Loki, gains up to 29.7% relative improvement over SimCLR on ImageNet and scales to hundreds of thousands of classes. When no such metric is available, Loki can use self-derived metrics from class embeddings and obtains a 10.5% improvement on pretrained zero-shot models such as CLIP.

  • 7 authors
·
Jul 23, 2023

Expanding Language-Image Pretrained Models for General Video Recognition

Contrastive language-image pretraining has shown great success in learning visual-textual joint representation from web-scale data, demonstrating remarkable "zero-shot" generalization ability for various image tasks. However, how to effectively expand such new language-image pretraining methods to video domains is still an open problem. In this work, we present a simple yet effective approach that adapts the pretrained language-image models to video recognition directly, instead of pretraining a new model from scratch. More concretely, to capture the long-range dependencies of frames along the temporal dimension, we propose a cross-frame attention mechanism that explicitly exchanges information across frames. Such module is lightweight and can be plugged into pretrained language-image models seamlessly. Moreover, we propose a video-specific prompting scheme, which leverages video content information for generating discriminative textual prompts. Extensive experiments demonstrate that our approach is effective and can be generalized to different video recognition scenarios. In particular, under fully-supervised settings, our approach achieves a top-1 accuracy of 87.1% on Kinectics-400, while using 12 times fewer FLOPs compared with Swin-L and ViViT-H. In zero-shot experiments, our approach surpasses the current state-of-the-art methods by +7.6% and +14.9% in terms of top-1 accuracy under two popular protocols. In few-shot scenarios, our approach outperforms previous best methods by +32.1% and +23.1% when the labeled data is extremely limited. Code and models are available at https://aka.ms/X-CLIP

  • 8 authors
·
Aug 4, 2022

CodeRL: Mastering Code Generation through Pretrained Models and Deep Reinforcement Learning

Program synthesis or code generation aims to generate a program that satisfies a problem specification. Recent approaches using large-scale pretrained language models (LMs) have shown promising results, yet they have some critical limitations. In particular, they often follow a standard supervised fine-tuning procedure to train a code generation model only from the pairs of natural-language problem descriptions and ground-truth programs. Such paradigm largely ignores some important but potentially useful signals in the problem specification such as unit tests, which thus often results in poor performance when solving complex unseen coding tasks. To address the limitations, we propose "CodeRL", a new framework for program synthesis tasks through pretrained LMs and deep reinforcement learning (RL). Specifically, during training, we treat the code-generating LM as an actor network, and introduce a critic network that is trained to predict the functional correctness of generated programs and provide dense feedback signals to the actor. During inference, we introduce a new generation procedure with a critical sampling strategy that allows a model to automatically regenerate programs based on feedback from example unit tests and critic scores. For the model backbones, we extended the encoder-decoder architecture of CodeT5 with enhanced learning objectives, larger model sizes, and better pretraining data. Our method not only achieves new SOTA results on the challenging APPS benchmark, but also shows strong zero-shot transfer capability with new SOTA results on the simpler MBPP benchmark.

  • 5 authors
·
Jul 4, 2022

Spectral-Enhanced Transformers: Leveraging Large-Scale Pretrained Models for Hyperspectral Object Tracking

Hyperspectral object tracking using snapshot mosaic cameras is emerging as it provides enhanced spectral information alongside spatial data, contributing to a more comprehensive understanding of material properties. Using transformers, which have consistently outperformed convolutional neural networks (CNNs) in learning better feature representations, would be expected to be effective for Hyperspectral object tracking. However, training large transformers necessitates extensive datasets and prolonged training periods. This is particularly critical for complex tasks like object tracking, and the scarcity of large datasets in the hyperspectral domain acts as a bottleneck in achieving the full potential of powerful transformer models. This paper proposes an effective methodology that adapts large pretrained transformer-based foundation models for hyperspectral object tracking. We propose an adaptive, learnable spatial-spectral token fusion module that can be extended to any transformer-based backbone for learning inherent spatial-spectral features in hyperspectral data. Furthermore, our model incorporates a cross-modality training pipeline that facilitates effective learning across hyperspectral datasets collected with different sensor modalities. This enables the extraction of complementary knowledge from additional modalities, whether or not they are present during testing. Our proposed model also achieves superior performance with minimal training iterations.

  • 5 authors
·
Feb 25

Foundation Model-oriented Robustness: Robust Image Model Evaluation with Pretrained Models

Machine learning has demonstrated remarkable performance over finite datasets, yet whether the scores over the fixed benchmarks can sufficiently indicate the model's performance in the real world is still in discussion. In reality, an ideal robust model will probably behave similarly to the oracle (e.g., the human users), thus a good evaluation protocol is probably to evaluate the models' behaviors in comparison to the oracle. In this paper, we introduce a new robustness measurement that directly measures the image classification model's performance compared with a surrogate oracle (i.e., a foundation model). Besides, we design a simple method that can accomplish the evaluation beyond the scope of the benchmarks. Our method extends the image datasets with new samples that are sufficiently perturbed to be distinct from the ones in the original sets, but are still bounded within the same image-label structure the original test image represents, constrained by a foundation model pretrained with a large amount of samples. As a result, our new method will offer us a new way to evaluate the models' robustness performance, free of limitations of fixed benchmarks or constrained perturbations, although scoped by the power of the oracle. In addition to the evaluation results, we also leverage our generated data to understand the behaviors of the model and our new evaluation strategies.

  • 6 authors
·
Aug 21, 2023

Mug-STAN: Adapting Image-Language Pretrained Models for General Video Understanding

Large-scale image-language pretrained models, e.g., CLIP, have demonstrated remarkable proficiency in acquiring general multi-modal knowledge through web-scale image-text data. Despite the impressive performance of image-language models on various image tasks, how to effectively expand them on general video understanding remains an area of ongoing exploration. In this paper, we investigate the image-to-video transferring from the perspective of the model and the data, unveiling two key obstacles impeding the adaptation of image-language models: non-generalizable temporal modeling and partially misaligned video-text data. To address these challenges, we propose Spatial-Temporal Auxiliary Network with Mutual-guided alignment module (Mug-STAN), a simple yet effective framework extending image-text model to diverse video tasks and video-text data.Specifically, STAN adopts a branch structure with decomposed spatial-temporal modules to enable generalizable temporal modeling, while Mug suppresses misalignment by introducing token-wise feature aggregation of either modality from the other. Extensive experimental results verify Mug-STAN significantly improves adaptation of language-image pretrained models such as CLIP and CoCa at both video-text post-pretraining and finetuning stages. With our solution, state-of-the-art zero-shot and finetuning results on various downstream datasets, including MSR-VTT, DiDeMo, LSMDC, Kinetics-400, Something-Something-2, HMDB-51, UCF- 101, and AVA, are achieved. Moreover, by integrating pretrained Mug-STAN with the emerging multimodal dialogue model, we can realize zero-shot video chatting. Codes are available at https://github.com/farewellthree/STAN

  • 5 authors
·
Nov 25, 2023

Overcoming Knowledge Barriers: Online Imitation Learning from Observation with Pretrained World Models

Incorporating the successful paradigm of pretraining and finetuning from Computer Vision and Natural Language Processing into decision-making has become increasingly popular in recent years. In this paper, we study Imitation Learning from Observation with pretrained models and find existing approaches such as BCO and AIME face knowledge barriers, specifically the Embodiment Knowledge Barrier (EKB) and the Demonstration Knowledge Barrier (DKB), greatly limiting their performance. The EKB arises when pretrained models lack knowledge about unseen observations, leading to errors in action inference. The DKB results from policies trained on limited demonstrations, hindering adaptability to diverse scenarios. We thoroughly analyse the underlying mechanism of these barriers and propose AIME-v2 upon AIME as a solution. AIME-v2 uses online interactions with data-driven regulariser to alleviate the EKB and mitigates the DKB by introducing a surrogate reward function to enhance policy training. Experimental results on tasks from the DeepMind Control Suite and Meta-World benchmarks demonstrate the effectiveness of these modifications in improving both sample-efficiency and converged performance. The study contributes valuable insights into resolving knowledge barriers for enhanced decision-making in pretraining-based approaches. Code will be available at https://github.com/argmax-ai/aime-v2.

  • 4 authors
·
Apr 29, 2024

Contrastive Language-Image Pretrained Models are Zero-Shot Human Scanpath Predictors

Understanding the mechanisms underlying human attention is a fundamental challenge for both vision science and artificial intelligence. While numerous computational models of free-viewing have been proposed, less is known about the mechanisms underlying task-driven image exploration. To address this gap, we present CapMIT1003, a database of captions and click-contingent image explorations collected during captioning tasks. CapMIT1003 is based on the same stimuli from the well-known MIT1003 benchmark, for which eye-tracking data under free-viewing conditions is available, which offers a promising opportunity to concurrently study human attention under both tasks. We make this dataset publicly available to facilitate future research in this field. In addition, we introduce NevaClip, a novel zero-shot method for predicting visual scanpaths that combines contrastive language-image pretrained (CLIP) models with biologically-inspired neural visual attention (NeVA) algorithms. NevaClip simulates human scanpaths by aligning the representation of the foveated visual stimulus and the representation of the associated caption, employing gradient-driven visual exploration to generate scanpaths. Our experimental results demonstrate that NevaClip outperforms existing unsupervised computational models of human visual attention in terms of scanpath plausibility, for both captioning and free-viewing tasks. Furthermore, we show that conditioning NevaClip with incorrect or misleading captions leads to random behavior, highlighting the significant impact of caption guidance in the decision-making process. These findings contribute to a better understanding of mechanisms that guide human attention and pave the way for more sophisticated computational approaches to scanpath prediction that can integrate direct top-down guidance of downstream tasks.

  • 7 authors
·
May 21, 2023

Lift3D Foundation Policy: Lifting 2D Large-Scale Pretrained Models for Robust 3D Robotic Manipulation

3D geometric information is essential for manipulation tasks, as robots need to perceive the 3D environment, reason about spatial relationships, and interact with intricate spatial configurations. Recent research has increasingly focused on the explicit extraction of 3D features, while still facing challenges such as the lack of large-scale robotic 3D data and the potential loss of spatial geometry. To address these limitations, we propose the Lift3D framework, which progressively enhances 2D foundation models with implicit and explicit 3D robotic representations to construct a robust 3D manipulation policy. Specifically, we first design a task-aware masked autoencoder that masks task-relevant affordance patches and reconstructs depth information, enhancing the 2D foundation model's implicit 3D robotic representation. After self-supervised fine-tuning, we introduce a 2D model-lifting strategy that establishes a positional mapping between the input 3D points and the positional embeddings of the 2D model. Based on the mapping, Lift3D utilizes the 2D foundation model to directly encode point cloud data, leveraging large-scale pretrained knowledge to construct explicit 3D robotic representations while minimizing spatial information loss. In experiments, Lift3D consistently outperforms previous state-of-the-art methods across several simulation benchmarks and real-world scenarios.

  • 11 authors
·
Nov 27, 2024

CodeBERTScore: Evaluating Code Generation with Pretrained Models of Code

Since the rise of neural models of code that can generate long expressions and statements rather than a single next-token, one of the major problems has been reliably evaluating their generated output. In this paper, we propose CodeBERTScore: an automatic evaluation metric for code generation, which builds on BERTScore (Zhang et al., 2020). Instead of measuring exact token matching as BLEU, CodeBERTScore computes a soft similarity score between each token in the generated code and in the reference code, using the contextual encodings of large pretrained models. Further, instead of encoding only the generated tokens as in BERTScore, CodeBERTScore also encodes the programmatic context surrounding the generated code. We perform an extensive evaluation of CodeBERTScore across four programming languages. We find that CodeBERTScore achieves a higher correlation with human preference and with functional correctness than all existing metrics. That is, generated code that receives a higher score by CodeBERTScore is more likely to be preferred by humans, as well as to function correctly when executed. Finally, while CodeBERTScore can be used with a multilingual CodeBERT as its base model, we release five language-specific pretrained models to use with our publicly available code at https://github.com/neulab/code-bert-score . Our language-specific models have been downloaded more than 25,000 times from the Huggingface Hub.

  • 4 authors
·
Feb 10, 2023

Fantastic Gains and Where to Find Them: On the Existence and Prospect of General Knowledge Transfer between Any Pretrained Model

Training deep networks requires various design decisions regarding for instance their architecture, data augmentation, or optimization. In this work, we find these training variations to result in networks learning unique feature sets from the data. Using public model libraries comprising thousands of models trained on canonical datasets like ImageNet, we observe that for arbitrary pairings of pretrained models, one model extracts significant data context unavailable in the other -- independent of overall performance. Given any arbitrary pairing of pretrained models and no external rankings (such as separate test sets, e.g. due to data privacy), we investigate if it is possible to transfer such "complementary" knowledge from one model to another without performance degradation -- a task made particularly difficult as additional knowledge can be contained in stronger, equiperformant or weaker models. Yet facilitating robust transfer in scenarios agnostic to pretrained model pairings would unlock auxiliary gains and knowledge fusion from any model repository without restrictions on model and problem specifics - including from weaker, lower-performance models. This work therefore provides an initial, in-depth exploration on the viability of such general-purpose knowledge transfer. Across large-scale experiments, we first reveal the shortcomings of standard knowledge distillation techniques, and then propose a much more general extension through data partitioning for successful transfer between nearly all pretrained models, which we show can also be done unsupervised. Finally, we assess both the scalability and impact of fundamental model properties on successful model-agnostic knowledge transfer.

  • 6 authors
·
Oct 26, 2023

Battle of the Backbones: A Large-Scale Comparison of Pretrained Models across Computer Vision Tasks

Neural network based computer vision systems are typically built on a backbone, a pretrained or randomly initialized feature extractor. Several years ago, the default option was an ImageNet-trained convolutional neural network. However, the recent past has seen the emergence of countless backbones pretrained using various algorithms and datasets. While this abundance of choice has led to performance increases for a range of systems, it is difficult for practitioners to make informed decisions about which backbone to choose. Battle of the Backbones (BoB) makes this choice easier by benchmarking a diverse suite of pretrained models, including vision-language models, those trained via self-supervised learning, and the Stable Diffusion backbone, across a diverse set of computer vision tasks ranging from classification to object detection to OOD generalization and more. Furthermore, BoB sheds light on promising directions for the research community to advance computer vision by illuminating strengths and weakness of existing approaches through a comprehensive analysis conducted on more than 1500 training runs. While vision transformers (ViTs) and self-supervised learning (SSL) are increasingly popular, we find that convolutional neural networks pretrained in a supervised fashion on large training sets still perform best on most tasks among the models we consider. Moreover, in apples-to-apples comparisons on the same architectures and similarly sized pretraining datasets, we find that SSL backbones are highly competitive, indicating that future works should perform SSL pretraining with advanced architectures and larger pretraining datasets. We release the raw results of our experiments along with code that allows researchers to put their own backbones through the gauntlet here: https://github.com/hsouri/Battle-of-the-Backbones

  • 13 authors
·
Oct 30, 2023 1

A Simple Baseline that Questions the Use of Pretrained-Models in Continual Learning

With the success of pretraining techniques in representation learning, a number of continual learning methods based on pretrained models have been proposed. Some of these methods design continual learning mechanisms on the pre-trained representations and only allow minimum updates or even no updates of the backbone models during the training of continual learning. In this paper, we question whether the complexity of these models is needed to achieve good performance by comparing them to a simple baseline that we designed. We argue that the pretrained feature extractor itself can be strong enough to achieve a competitive or even better continual learning performance on Split-CIFAR100 and CoRe 50 benchmarks. To validate this, we conduct a very simple baseline that 1) use the frozen pretrained model to extract image features for every class encountered during the continual learning stage and compute their corresponding mean features on training data, and 2) predict the class of the input based on the nearest neighbor distance between test samples and mean features of the classes; i.e., Nearest Mean Classifier (NMC). This baseline is single-headed, exemplar-free, and can be task-free (by updating the means continually). This baseline achieved 88.53% on 10-Split-CIFAR-100, surpassing most state-of-the-art continual learning methods that are all initialized using the same pretrained transformer model. We hope our baseline may encourage future progress in designing learning systems that can continually add quality to the learning representations even if they started from some pretrained weights.

  • 4 authors
·
Oct 10, 2022

DR-Tune: Improving Fine-tuning of Pretrained Visual Models by Distribution Regularization with Semantic Calibration

The visual models pretrained on large-scale benchmarks encode general knowledge and prove effective in building more powerful representations for downstream tasks. Most existing approaches follow the fine-tuning paradigm, either by initializing or regularizing the downstream model based on the pretrained one. The former fails to retain the knowledge in the successive fine-tuning phase, thereby prone to be over-fitting, and the latter imposes strong constraints to the weights or feature maps of the downstream model without considering semantic drift, often incurring insufficient optimization. To deal with these issues, we propose a novel fine-tuning framework, namely distribution regularization with semantic calibration (DR-Tune). It employs distribution regularization by enforcing the downstream task head to decrease its classification error on the pretrained feature distribution, which prevents it from over-fitting while enabling sufficient training of downstream encoders. Furthermore, to alleviate the interference by semantic drift, we develop the semantic calibration (SC) module to align the global shape and class centers of the pretrained and downstream feature distributions. Extensive experiments on widely used image classification datasets show that DR-Tune consistently improves the performance when combing with various backbones under different pretraining strategies. Code is available at: https://github.com/weeknan/DR-Tune.

  • 3 authors
·
Aug 23, 2023

Aligning Language Models with Observational Data: Opportunities and Risks from a Causal Perspective

Large language models are being widely used across industries to generate content that contributes directly to key performance metrics, such as conversion rates. Pretrained models, however, often fall short when it comes to aligning with human preferences or optimizing for business objectives. As a result, fine-tuning with good-quality labeled data is essential to guide models to generate content that achieves better results. Controlled experiments, like A/B tests, can provide such data, but they are often expensive and come with significant engineering and logistical challenges. Meanwhile, companies have access to a vast amount of historical (observational) data that remains underutilized. In this work, we study the challenges and opportunities of fine-tuning LLMs using observational data. We show that while observational outcomes can provide valuable supervision, directly fine-tuning models on such data can lead them to learn spurious correlations. We present empirical evidence of this issue using various real-world datasets and propose DeconfoundLM, a method that explicitly removes the effect of known confounders from reward signals. Using simulation experiments, we demonstrate that DeconfoundLM improves the recovery of causal relationships and mitigates failure modes found in fine-tuning methods that ignore or naively incorporate confounding variables. Our findings highlight that while observational data presents risks, with the right causal corrections, it can be a powerful source of signal for LLM alignment. Please refer to the project page for code and related resources.

  • 1 authors
·
May 30

Prithvi WxC: Foundation Model for Weather and Climate

Triggered by the realization that AI emulators can rival the performance of traditional numerical weather prediction models running on HPC systems, there is now an increasing number of large AI models that address use cases such as forecasting, downscaling, or nowcasting. While the parallel developments in the AI literature focus on foundation models -- models that can be effectively tuned to address multiple, different use cases -- the developments on the weather and climate side largely focus on single-use cases with particular emphasis on mid-range forecasting. We close this gap by introducing Prithvi WxC, a 2.3 billion parameter foundation model developed using 160 variables from the Modern-Era Retrospective Analysis for Research and Applications, Version 2 (MERRA-2). Prithvi WxC employs an encoder-decoder-based architecture, incorporating concepts from various recent transformer models to effectively capture both regional and global dependencies in the input data. The model has been designed to accommodate large token counts to model weather phenomena in different topologies at fine resolutions. Furthermore, it is trained with a mixed objective that combines the paradigms of masked reconstruction with forecasting. We test the model on a set of challenging downstream tasks namely: Autoregressive rollout forecasting, Downscaling, Gravity wave flux parameterization, and Extreme events estimation. The pretrained model with 2.3 billion parameters, along with the associated fine-tuning workflows, has been publicly released as an open-source contribution via Hugging Face.

  • 29 authors
·
Sep 20, 2024 4

EEGFormer: Towards Transferable and Interpretable Large-Scale EEG Foundation Model

Self-supervised learning has emerged as a highly effective approach in the fields of natural language processing and computer vision. It is also applicable to brain signals such as electroencephalography (EEG) data, given the abundance of available unlabeled data that exist in a wide spectrum of real-world medical applications ranging from seizure detection to wave analysis. The existing works leveraging self-supervised learning on EEG modeling mainly focus on pretraining upon each individual dataset corresponding to a single downstream task, which cannot leverage the power of abundant data, and they may derive sub-optimal solutions with a lack of generalization. Moreover, these methods rely on end-to-end model learning which is not easy for humans to understand. In this paper, we present a novel EEG foundation model, namely EEGFormer, pretrained on large-scale compound EEG data. The pretrained model cannot only learn universal representations on EEG signals with adaptable performance on various downstream tasks but also provide interpretable outcomes of the useful patterns within the data. To validate the effectiveness of our model, we extensively evaluate it on various downstream tasks and assess the performance under different transfer settings. Furthermore, we demonstrate how the learned model exhibits transferable anomaly detection performance and provides valuable interpretability of the acquired patterns via self-supervised learning.

  • 7 authors
·
Jan 11, 2024

netFound: Foundation Model for Network Security

Developing generalizable ML-based solutions for disparate learning problems in network security is highly desired. However, despite a rich history of applying ML to network security, most existing solutions lack generalizability. This lack of progress can be attributed to an overreliance on supervised learning techniques and the associated challenges of curating well-specified labeled training data. This paper addresses a fundamental gap by introducing a novel transformer-based network foundation model, netFound. We employ self-supervised learning techniques on abundant, unlabeled network telemetry data for pre-training. This pretrained model can subsequently be fine-tuned to create generalizable learning artifacts for disparate learning tasks, even when using commonly available but challenging labeled datasets that are sparse, noisy, and skewed. To realize this goal, netFound leverages various domain-specific attributes and constraints unique to network data (packet traces) by developing multi-modal embeddings, protocol-aware tokenization, data-driven token composition, and hierarchical transformers. Our results demonstrate that netFound's domain-specific design choices ensure that it (1) effectively captures the hidden networking context in production settings, (2) outperforms four different SOTA methods on five different learning tasks, and (3) is robust to both noisy labels and learning shortcuts -- critical for developing generalizable ML models in practical settings.

  • 5 authors
·
Oct 25, 2023

Layer Swapping for Zero-Shot Cross-Lingual Transfer in Large Language Models

Model merging, such as model souping, is the practice of combining different models with the same architecture together without further training. In this work, we present a model merging methodology that addresses the difficulty of fine-tuning Large Language Models (LLMs) for target tasks in non-English languages, where task-specific data is often unavailable. We focus on mathematical reasoning and without in-language math data, facilitate cross-lingual transfer by composing language and math capabilities. Starting from the same pretrained model, we fine-tune separate "experts" on math instruction data in English and on generic instruction data in the target language. We then replace the top and bottom transformer layers of the math expert directly with layers from the language expert, which consequently enhances math performance in the target language. The resulting merged models outperform the individual experts and other merging methods on the math benchmark, MGSM, by 10% across four major languages where math instruction data is scarce. In addition, this layer swapping is simple, inexpensive, and intuitive, as it is based on an interpretative analysis of the most important parameter changes during the fine-tuning of each expert. The ability to successfully re-compose LLMs for cross-lingual transfer in this manner opens up future possibilities to combine model expertise, create modular solutions, and transfer reasoning capabilities across languages all post hoc.

  • 7 authors
·
Oct 2, 2024 3

Towards Open Respiratory Acoustic Foundation Models: Pretraining and Benchmarking

Respiratory audio, such as coughing and breathing sounds, has predictive power for a wide range of healthcare applications, yet is currently under-explored. The main problem for those applications arises from the difficulty in collecting large labeled task-specific data for model development. Generalizable respiratory acoustic foundation models pretrained with unlabeled data would offer appealing advantages and possibly unlock this impasse. However, given the safety-critical nature of healthcare applications, it is pivotal to also ensure openness and replicability for any proposed foundation model solution. To this end, we introduce OPERA, an OPEn Respiratory Acoustic foundation model pretraining and benchmarking system, as the first approach answering this need. We curate large-scale respiratory audio datasets (~136K samples, 440 hours), pretrain three pioneering foundation models, and build a benchmark consisting of 19 downstream respiratory health tasks for evaluation. Our pretrained models demonstrate superior performance (against existing acoustic models pretrained with general audio on 16 out of 19 tasks) and generalizability (to unseen datasets and new respiratory audio modalities). This highlights the great promise of respiratory acoustic foundation models and encourages more studies using OPERA as an open resource to accelerate research on respiratory audio for health. The system is accessible from https://github.com/evelyn0414/OPERA.

  • 9 authors
·
Jun 23, 2024

Efficient Language Model Training through Cross-Lingual and Progressive Transfer Learning

Most Transformer language models are primarily pretrained on English text, limiting their use for other languages. As the model sizes grow, the performance gap between English and other languages with fewer compute and data resources increases even further. Consequently, more resource-efficient training methods are needed to bridge the gap for languages with fewer resources available. To address this problem, we introduce a cross-lingual and progressive transfer learning approach, called CLP-Transfer, that transfers models from a source language, for which pretrained models are publicly available, like English, to a new target language. As opposed to prior work, which focused on the cross-lingual transfer between two languages, we extend the transfer to the model size. Given a pretrained model in a source language, we aim for a same-sized model in a target language. Instead of training a model from scratch, we exploit a smaller model that is in the target language but requires much fewer resources. Both small and source models are then used to initialize the token embeddings of the larger model based on the overlapping vocabulary of the source and target language. All remaining weights are reused from the model in the source language. This approach outperforms the sole cross-lingual transfer and can save up to 80% of the training steps compared to the random initialization.

  • 2 authors
·
Jan 23, 2023

Generative Pretrained Autoregressive Transformer Graph Neural Network applied to the Analysis and Discovery of Novel Proteins

We report a flexible language-model based deep learning strategy, applied here to solve complex forward and inverse problems in protein modeling, based on an attention neural network that integrates transformer and graph convolutional architectures in a causal multi-headed graph mechanism, to realize a generative pretrained model. The model is applied to predict secondary structure content (per-residue level and overall content), protein solubility, and sequencing tasks. Further trained on inverse tasks, the model is rendered capable of designing proteins with these properties as target features. The model is formulated as a general framework, completely prompt-based, and can be adapted for a variety of downstream tasks. We find that adding additional tasks yields emergent synergies that the model exploits in improving overall performance, beyond what would be possible by training a model on each dataset alone. Case studies are presented to validate the method, yielding protein designs specifically focused on structural proteins, but also exploring the applicability in the design of soluble, antimicrobial biomaterials. While our model is trained to ultimately perform 8 distinct tasks, with available datasets it can be extended to solve additional problems. In a broader sense, this work illustrates a form of multiscale modeling that relates a set of ultimate building blocks (here, byte-level utf8 characters) to complex output. This materiomic scheme captures complex emergent relationships between universal building block and resulting properties via a synergizing learning capacity to express a set of potentialities embedded in the knowledge used in training, via the interplay of universality and diversity.

  • 1 authors
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May 7, 2023

TunBERT: Pretrained Contextualized Text Representation for Tunisian Dialect

Pretrained contextualized text representation models learn an effective representation of a natural language to make it machine understandable. After the breakthrough of the attention mechanism, a new generation of pretrained models have been proposed achieving good performances since the introduction of the Transformer. Bidirectional Encoder Representations from Transformers (BERT) has become the state-of-the-art model for language understanding. Despite their success, most of the available models have been trained on Indo-European languages however similar research for under-represented languages and dialects remains sparse. In this paper, we investigate the feasibility of training monolingual Transformer-based language models for under represented languages, with a specific focus on the Tunisian dialect. We evaluate our language model on sentiment analysis task, dialect identification task and reading comprehension question-answering task. We show that the use of noisy web crawled data instead of structured data (Wikipedia, articles, etc.) is more convenient for such non-standardized language. Moreover, results indicate that a relatively small web crawled dataset leads to performances that are as good as those obtained using larger datasets. Finally, our best performing TunBERT model reaches or improves the state-of-the-art in all three downstream tasks. We release the TunBERT pretrained model and the datasets used for fine-tuning.

  • 9 authors
·
Nov 25, 2021

Pretraining Language Models for Diachronic Linguistic Change Discovery

Large language models (LLMs) have shown potential as tools for scientific discovery. This has engendered growing interest in their use in humanistic disciplines, such as historical linguistics and literary studies. These fields often construct arguments on the basis of delineations like genre, or more inflexibly, time period. Although efforts have been made to restrict inference to specific domains via fine-tuning or model editing, we posit that the only true guarantee is domain-restricted pretraining -- typically, a data- and compute-expensive proposition. We show that efficient pretraining techniques can produce useful models over corpora too large for easy manual inspection but too small for "typical" LLM approaches. We employ a novel date-attribution pipeline in order to obtain a temporally-segmented dataset of five 10-million-word slices. We train two corresponding five-model batteries over these corpus segments, efficient pretraining and Llama3-8B parameter efficiently finetuned. We find that the pretrained models are faster to train than the finetuned baselines and that they better respect the historical divisions of our corpus. Emphasizing speed and precision over a-historical comprehensiveness enables a number of novel approaches to hypothesis discovery and testing in our target fields. Taking up diachronic linguistics as a testbed, we show that our method enables the detection of a diverse set of phenomena, including en masse lexical change, non-lexical (grammatical and morphological) change, and word sense introduction/obsolescence. We provide a ready-to-use pipeline that allows extension of our approach to other target fields with only minimal adaptation.

  • 5 authors
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Apr 7 2

INF-LLaVA: Dual-perspective Perception for High-Resolution Multimodal Large Language Model

With advancements in data availability and computing resources, Multimodal Large Language Models (MLLMs) have showcased capabilities across various fields. However, the quadratic complexity of the vision encoder in MLLMs constrains the resolution of input images. Most current approaches mitigate this issue by cropping high-resolution images into smaller sub-images, which are then processed independently by the vision encoder. Despite capturing sufficient local details, these sub-images lack global context and fail to interact with one another. To address this limitation, we propose a novel MLLM, INF-LLaVA, designed for effective high-resolution image perception. INF-LLaVA incorporates two innovative components. First, we introduce a Dual-perspective Cropping Module (DCM), which ensures that each sub-image contains continuous details from a local perspective and comprehensive information from a global perspective. Second, we introduce Dual-perspective Enhancement Module (DEM) to enable the mutual enhancement of global and local features, allowing INF-LLaVA to effectively process high-resolution images by simultaneously capturing detailed local information and comprehensive global context. Extensive ablation studies validate the effectiveness of these components, and experiments on a diverse set of benchmarks demonstrate that INF-LLaVA outperforms existing MLLMs. Code and pretrained model are available at https://github.com/WeihuangLin/INF-LLaVA.

  • 7 authors
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Jul 23, 2024 3

RedDino: A foundation model for red blood cell analysis

Red blood cells (RBCs) are essential to human health, and their precise morphological analysis is important for diagnosing hematological disorders. Despite the promise of foundation models in medical diagnostics, comprehensive AI solutions for RBC analysis remain scarce. We present RedDino, a self-supervised foundation model designed for RBC image analysis. RedDino uses an RBC-specific adaptation of the DINOv2 self-supervised learning framework and is trained on a curated dataset of 1.25 million RBC images from diverse acquisition modalities and sources. Extensive evaluations show that RedDino outperforms existing state-of-the-art models on RBC shape classification. Through assessments including linear probing and nearest neighbor classification, we confirm its strong feature representations and generalization ability. Our main contributions are: (1) a foundation model tailored for RBC analysis, (2) ablation studies exploring DINOv2 configurations for RBC modeling, and (3) a detailed evaluation of generalization performance. RedDino addresses key challenges in computational hematology by capturing nuanced morphological features, advancing the development of reliable diagnostic tools. The source code and pretrained models for RedDino are available at https://github.com/Snarci/RedDino, and the pretrained models can be downloaded from our Hugging Face collection at https://huggingface.co/collections/Snarcy/reddino-689a13e29241d2e5690202fc

  • 4 authors
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Aug 11 2

A Fully Open and Generalizable Foundation Model for Ultrasound Clinical Applications

Artificial intelligence (AI) that can effectively learn ultrasound representations by integrating multi-source data holds significant promise for advancing clinical care. However, the scarcity of large labeled datasets in real-world clinical environments and the limited generalizability of task-specific models have hindered the development of generalizable clinical AI models for ultrasound applications. In this study, we present EchoCare, a novel ultrasound foundation model for generalist clinical use, developed via self-supervised learning on our curated, publicly available, large-scale dataset EchoCareData. EchoCareData comprises 4.5 million ultrasound images, sourced from over 23 countries across 5 continents and acquired via a diverse range of distinct imaging devices, thus encompassing global cohorts that are multi-center, multi-device, and multi-ethnic. Unlike prior studies that adopt off-the-shelf vision foundation model architectures, we introduce a hierarchical classifier into EchoCare to enable joint learning of pixel-level and representation-level features, capturing both global anatomical contexts and local ultrasound characteristics. With minimal training, EchoCare outperforms state-of-the-art comparison models across 10 representative ultrasound benchmarks of varying diagnostic difficulties, spanning disease diagnosis, lesion segmentation, organ detection, landmark prediction, quantitative regression, imaging enhancement and report generation. The code and pretrained model are publicly released, rendering EchoCare accessible for fine-tuning and local adaptation, supporting extensibility to additional applications. EchoCare provides a fully open and generalizable foundation model to boost the development of AI technologies for diverse clinical ultrasound applications.

  • 25 authors
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Sep 15

Parameter Competition Balancing for Model Merging

While fine-tuning pretrained models has become common practice, these models often underperform outside their specific domains. Recently developed model merging techniques enable the direct integration of multiple models, each fine-tuned for distinct tasks, into a single model. This strategy promotes multitasking capabilities without requiring retraining on the original datasets. However, existing methods fall short in addressing potential conflicts and complex correlations between tasks, especially in parameter-level adjustments, posing a challenge in effectively balancing parameter competition across various tasks. This paper introduces an innovative technique named PCB-Merging (Parameter Competition Balancing), a lightweight and training-free technique that adjusts the coefficients of each parameter for effective model merging. PCB-Merging employs intra-balancing to gauge parameter significance within individual tasks and inter-balancing to assess parameter similarities across different tasks. Parameters with low importance scores are dropped, and the remaining ones are rescaled to form the final merged model. We assessed our approach in diverse merging scenarios, including cross-task, cross-domain, and cross-training configurations, as well as out-of-domain generalization. The experimental results reveal that our approach achieves substantial performance enhancements across multiple modalities, domains, model sizes, number of tasks, fine-tuning forms, and large language models, outperforming existing model merging methods. The code is publicly available at: https://github.com/duguodong7/pcb-merging.

  • 11 authors
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Oct 3, 2024

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

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

  • 8 authors
·
Apr 12, 2022

eP-ALM: Efficient Perceptual Augmentation of Language Models

Large Language Models (LLMs) have so far impressed the world, with unprecedented capabilities that emerge in models at large scales. On the vision side, transformer models (i.e., ViT) are following the same trend, achieving the best performance on challenging benchmarks. With the abundance of such unimodal models, a natural question arises; do we need also to follow this trend to tackle multimodal tasks? In this work, we propose to rather direct effort to efficient adaptations of existing models, and propose to augment Language Models with perception. Existing approaches for adapting pretrained models for vision-language tasks still rely on several key components that hinder their efficiency. In particular, they still train a large number of parameters, rely on large multimodal pretraining, use encoders (e.g., CLIP) trained on huge image-text datasets, and add significant inference overhead. In addition, most of these approaches have focused on Zero-Shot and In Context Learning, with little to no effort on direct finetuning. We investigate the minimal computational effort needed to adapt unimodal models for multimodal tasks and propose a new challenging setup, alongside different approaches, that efficiently adapts unimodal pretrained models. We show that by freezing more than 99\% of total parameters, training only one linear projection layer, and prepending only one trainable token, our approach (dubbed eP-ALM) significantly outperforms other baselines on VQA and Captioning across Image, Video, and Audio modalities, following the proposed setup. The code will be available here: https://github.com/mshukor/eP-ALM.

  • 3 authors
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Mar 20, 2023

RoMA: Scaling up Mamba-based Foundation Models for Remote Sensing

Recent advances in self-supervised learning for Vision Transformers (ViTs) have fueled breakthroughs in remote sensing (RS) foundation models. However, the quadratic complexity of self-attention poses a significant barrier to scalability, particularly for large models and high-resolution images. While the linear-complexity Mamba architecture offers a promising alternative, existing RS applications of Mamba remain limited to supervised tasks on small, domain-specific datasets. To address these challenges, we propose RoMA, a framework that enables scalable self-supervised pretraining of Mamba-based RS foundation models using large-scale, diverse, unlabeled data. RoMA enhances scalability for high-resolution images through a tailored auto-regressive learning strategy, incorporating two key innovations: 1) a rotation-aware pretraining mechanism combining adaptive cropping with angular embeddings to handle sparsely distributed objects with arbitrary orientations, and 2) multi-scale token prediction objectives that address the extreme variations in object scales inherent to RS imagery. Systematic empirical studies validate that Mamba adheres to RS data and parameter scaling laws, with performance scaling reliably as model and data size increase. Furthermore, experiments across scene classification, object detection, and semantic segmentation tasks demonstrate that RoMA-pretrained Mamba models consistently outperform ViT-based counterparts in both accuracy and computational efficiency. The source code and pretrained models will be released at https://github.com/MiliLab/RoMA.

  • 11 authors
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Mar 13

EoS-FM: Can an Ensemble of Specialist Models act as a Generalist Feature Extractor?

Recent advances in foundation models have shown great promise in domains such as natural language processing and computer vision, and similar efforts are now emerging in the Earth Observation community. These models aim to generalize across tasks with limited supervision, reducing the need for training separate models for each task. However, current strategies, which largely focus on scaling model size and dataset volume, require prohibitive computational and data resources, limiting accessibility to only a few large institutions. Moreover, this paradigm of ever-larger models stands in stark contrast with the principles of sustainable and environmentally responsible AI, as it leads to immense carbon footprints and resource inefficiency. In this work, we present a novel and efficient alternative: an Ensemble-of-Specialists framework for building Remote Sensing Foundation Models (RSFMs). Our method decomposes the training process into lightweight, task-specific ConvNeXtV2 specialists that can be frozen and reused. This modular approach offers strong advantages in efficiency, interpretability, and extensibility. Moreover, it naturally supports federated training, pruning, and continuous specialist integration, making it particularly well-suited for collaborative and resource-constrained settings. Our framework sets a new direction for building scalable and efficient RSFMs. All codes and pretrained models are available at https://github.com/pierreadorni/EoS-FM.

  • 4 authors
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Nov 26

PeftCD: Leveraging Vision Foundation Models with Parameter-Efficient Fine-Tuning for Remote Sensing Change Detection

To tackle the prevalence of pseudo changes, the scarcity of labeled samples, and the difficulty of cross-domain generalization in multi-temporal and multi-source remote sensing imagery, we propose PeftCD, a change detection framework built upon Vision Foundation Models (VFMs) with Parameter-Efficient Fine-Tuning (PEFT). At its core, PeftCD employs a weight-sharing Siamese encoder derived from a VFM, into which LoRA and Adapter modules are seamlessly integrated. This design enables highly efficient task adaptation by training only a minimal set of additional parameters. To fully unlock the potential of VFMs, we investigate two leading backbones: the Segment Anything Model v2 (SAM2), renowned for its strong segmentation priors, and DINOv3, a state-of-the-art self-supervised representation learner. The framework is complemented by a deliberately lightweight decoder, ensuring the focus remains on the powerful feature representations from the backbones. Extensive experiments demonstrate that PeftCD achieves state-of-the-art performance across multiple public datasets, including SYSU-CD (IoU 73.81%), WHUCD (92.05%), MSRSCD (64.07%), MLCD (76.89%), CDD (97.01%), S2Looking (52.25%) and LEVIR-CD (85.62%), with notably precise boundary delineation and strong suppression of pseudo-changes. In summary, PeftCD presents an optimal balance of accuracy, efficiency, and generalization. It offers a powerful and scalable paradigm for adapting large-scale VFMs to real-world remote sensing change detection applications. The code and pretrained models will be released at https://github.com/dyzy41/PeftCD.

  • 5 authors
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Sep 11

Representing Part-Whole Hierarchies in Foundation Models by Learning Localizability, Composability, and Decomposability from Anatomy via Self-Supervision

Humans effortlessly interpret images by parsing them into part-whole hierarchies; deep learning excels in learning multi-level feature spaces, but they often lack explicit coding of part-whole relations, a prominent property of medical imaging. To overcome this limitation, we introduce Adam-v2, a new self-supervised learning framework extending Adam [79] by explicitly incorporating part-whole hierarchies into its learning objectives through three key branches: (1) Localizability, acquiring discriminative representations to distinguish different anatomical patterns; (2) Composability, learning each anatomical structure in a parts-to-whole manner; and (3) Decomposability, comprehending each anatomical structure in a whole-to-parts manner. Experimental results across 10 tasks, compared to 11 baselines in zero-shot, few-shot transfer, and full fine-tuning settings, showcase Adam-v2's superior performance over large-scale medical models and existing SSL methods across diverse downstream tasks. The higher generality and robustness of Adam-v2's representations originate from its explicit construction of hierarchies for distinct anatomical structures from unlabeled medical images. Adam-v2 preserves a semantic balance of anatomical diversity and harmony in its embedding, yielding representations that are both generic and semantically meaningful, yet overlooked in existing SSL methods. All code and pretrained models are available at https://github.com/JLiangLab/Eden.

  • 3 authors
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Apr 24, 2024

T2V-DDPM: Thermal to Visible Face Translation using Denoising Diffusion Probabilistic Models

Modern-day surveillance systems perform person recognition using deep learning-based face verification networks. Most state-of-the-art facial verification systems are trained using visible spectrum images. But, acquiring images in the visible spectrum is impractical in scenarios of low-light and nighttime conditions, and often images are captured in an alternate domain such as the thermal infrared domain. Facial verification in thermal images is often performed after retrieving the corresponding visible domain images. This is a well-established problem often known as the Thermal-to-Visible (T2V) image translation. In this paper, we propose a Denoising Diffusion Probabilistic Model (DDPM) based solution for T2V translation specifically for facial images. During training, the model learns the conditional distribution of visible facial images given their corresponding thermal image through the diffusion process. During inference, the visible domain image is obtained by starting from Gaussian noise and performing denoising repeatedly. The existing inference process for DDPMs is stochastic and time-consuming. Hence, we propose a novel inference strategy for speeding up the inference time of DDPMs, specifically for the problem of T2V image translation. We achieve the state-of-the-art results on multiple datasets. The code and pretrained models are publically available at http://github.com/Nithin-GK/T2V-DDPM

  • 2 authors
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Sep 19, 2022