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Dec 10

Foresight -- Generative Pretrained Transformer (GPT) for Modelling of Patient Timelines using EHRs

Background: Electronic Health Records hold detailed longitudinal information about each patient's health status and general clinical history, a large portion of which is stored within the unstructured text. Existing approaches focus mostly on structured data and a subset of single-domain outcomes. We explore how temporal modelling of patients from free text and structured data, using deep generative transformers can be used to forecast a wide range of future disorders, substances, procedures or findings. Methods: We present Foresight, a novel transformer-based pipeline that uses named entity recognition and linking tools to convert document text into structured, coded concepts, followed by providing probabilistic forecasts for future medical events such as disorders, substances, procedures and findings. We processed the entire free-text portion from three different hospital datasets totalling 811336 patients covering both physical and mental health. Findings: On tests in two UK hospitals (King's College Hospital, South London and Maudsley) and the US MIMIC-III dataset precision@10 0.68, 0.76 and 0.88 was achieved for forecasting the next disorder in a patient timeline, while precision@10 of 0.80, 0.81 and 0.91 was achieved for forecasting the next biomedical concept. Foresight was also validated on 34 synthetic patient timelines by five clinicians and achieved relevancy of 97% for the top forecasted candidate disorder. As a generative model, it can forecast follow-on biomedical concepts for as many steps as required. Interpretation: Foresight is a general-purpose model for biomedical concept modelling that can be used for real-world risk forecasting, virtual trials and clinical research to study the progression of disorders, simulate interventions and counterfactuals, and educational purposes.

  • 12 authors
·
Dec 13, 2022

ACTRESS: Active Retraining for Semi-supervised Visual Grounding

Semi-Supervised Visual Grounding (SSVG) is a new challenge for its sparse labeled data with the need for multimodel understanding. A previous study, RefTeacher, makes the first attempt to tackle this task by adopting the teacher-student framework to provide pseudo confidence supervision and attention-based supervision. However, this approach is incompatible with current state-of-the-art visual grounding models, which follow the Transformer-based pipeline. These pipelines directly regress results without region proposals or foreground binary classification, rendering them unsuitable for fitting in RefTeacher due to the absence of confidence scores. Furthermore, the geometric difference in teacher and student inputs, stemming from different data augmentations, induces natural misalignment in attention-based constraints. To establish a compatible SSVG framework, our paper proposes the ACTive REtraining approach for Semi-Supervised Visual Grounding, abbreviated as ACTRESS. Initially, the model is enhanced by incorporating an additional quantized detection head to expose its detection confidence. Building upon this, ACTRESS consists of an active sampling strategy and a selective retraining strategy. The active sampling strategy iteratively selects high-quality pseudo labels by evaluating three crucial aspects: Faithfulness, Robustness, and Confidence, optimizing the utilization of unlabeled data. The selective retraining strategy retrains the model with periodic re-initialization of specific parameters, facilitating the model's escape from local minima. Extensive experiments demonstrates our superior performance on widely-used benchmark datasets.

  • 4 authors
·
Jul 3, 2024

Interpreting Key Mechanisms of Factual Recall in Transformer-Based Language Models

In this paper, we delve into several mechanisms employed by Transformer-based language models (LLMs) for factual recall tasks. We outline a pipeline consisting of three major steps: (1) Given a prompt ``The capital of France is,'' task-specific attention heads extract the topic token, such as ``France,'' from the context and pass it to subsequent MLPs. (2) As attention heads' outputs are aggregated with equal weight and added to the residual stream, the subsequent MLP acts as an ``activation,'' which either erases or amplifies the information originating from individual heads. As a result, the topic token ``France'' stands out in the residual stream. (3) A deep MLP takes ``France'' and generates a component that redirects the residual stream towards the direction of the correct answer, i.e., ``Paris.'' This procedure is akin to applying an implicit function such as ``get\_capital(X),'' and the argument X is the topic token information passed by attention heads. To achieve the above quantitative and qualitative analysis for MLPs, we proposed a novel analytic method aimed at decomposing the outputs of the MLP into components understandable by humans. Additionally, we observed a universal anti-overconfidence mechanism in the final layer of models, which suppresses correct predictions. We mitigate this suppression by leveraging our interpretation to improve factual recall confidence. The above interpretations are evaluated across diverse tasks spanning various domains of factual knowledge, using various language models from the GPT-2 families, 1.3B OPT, up to 7B Llama-2, and in both zero- and few-shot setups.

  • 8 authors
·
Mar 28, 2024

Cross-Domain Evaluation of Transformer-Based Vulnerability Detection on Open & Industry Data

Deep learning solutions for vulnerability detection proposed in academic research are not always accessible to developers, and their applicability in industrial settings is rarely addressed. Transferring such technologies from academia to industry presents challenges related to trustworthiness, legacy systems, limited digital literacy, and the gap between academic and industrial expertise. For deep learning in particular, performance and integration into existing workflows are additional concerns. In this work, we first evaluate the performance of CodeBERT for detecting vulnerable functions in industrial and open-source software. We analyse its cross-domain generalisation when fine-tuned on open-source data and tested on industrial data, and vice versa, also exploring strategies for handling class imbalance. Based on these results, we develop AI-DO(Automating vulnerability detection Integration for Developers' Operations), a Continuous Integration-Continuous Deployment (CI/CD)-integrated recommender system that uses fine-tuned CodeBERT to detect and localise vulnerabilities during code review without disrupting workflows. Finally, we assess the tool's perceived usefulness through a survey with the company's IT professionals. Our results show that models trained on industrial data detect vulnerabilities accurately within the same domain but lose performance on open-source code, while a deep learner fine-tuned on open data, with appropriate undersampling techniques, improves the detection of vulnerabilities.

  • 3 authors
·
Sep 11 2

Statistical Depth for Ranking and Characterizing Transformer-Based Text Embeddings

The popularity of transformer-based text embeddings calls for better statistical tools for measuring distributions of such embeddings. One such tool would be a method for ranking texts within a corpus by centrality, i.e. assigning each text a number signifying how representative that text is of the corpus as a whole. However, an intrinsic center-outward ordering of high-dimensional text representations is not trivial. A statistical depth is a function for ranking k-dimensional objects by measuring centrality with respect to some observed k-dimensional distribution. We adopt a statistical depth to measure distributions of transformer-based text embeddings, transformer-based text embedding (TTE) depth, and introduce the practical use of this depth for both modeling and distributional inference in NLP pipelines. We first define TTE depth and an associated rank sum test for determining whether two corpora differ significantly in embedding space. We then use TTE depth for the task of in-context learning prompt selection, showing that this approach reliably improves performance over statistical baseline approaches across six text classification tasks. Finally, we use TTE depth and the associated rank sum test to characterize the distributions of synthesized and human-generated corpora, showing that five recent synthetic data augmentation processes cause a measurable distributional shift away from associated human-generated text.

  • 2 authors
·
Oct 23, 2023

GenCAD: Image-Conditioned Computer-Aided Design Generation with Transformer-Based Contrastive Representation and Diffusion Priors

The creation of manufacturable and editable 3D shapes through Computer-Aided Design (CAD) remains a highly manual and time-consuming task, hampered by the complex topology of boundary representations of 3D solids and unintuitive design tools. While most work in the 3D shape generation literature focuses on representations like meshes, voxels, or point clouds, practical engineering applications demand the modifiability and manufacturability of CAD models and the ability for multi-modal conditional CAD model generation. This paper introduces GenCAD, a generative model that employs autoregressive transformers with a contrastive learning framework and latent diffusion models to transform image inputs into parametric CAD command sequences, resulting in editable 3D shape representations. Extensive evaluations demonstrate that GenCAD significantly outperforms existing state-of-the-art methods in terms of the unconditional and conditional generations of CAD models. Additionally, the contrastive learning framework of GenCAD facilitates the retrieval of CAD models using image queries from large CAD databases, which is a critical challenge within the CAD community. Our results provide a significant step forward in highlighting the potential of generative models to expedite the entire design-to-production pipeline and seamlessly integrate different design modalities.

  • 2 authors
·
Sep 8, 2024 1

Target Specific De Novo Design of Drug Candidate Molecules with Graph Transformer-based Generative Adversarial Networks

Discovering novel drug candidate molecules is one of the most fundamental and critical steps in drug development. Generative deep learning models, which create synthetic data given a probability distribution, offer a high potential for designing de novo molecules. However, to be utilisable in real life drug development pipelines, these models should be able to design drug like and target centric molecules. In this study, we propose an end to end generative system, DrugGEN, for the de novo design of drug candidate molecules that interact with intended target proteins. The proposed method represents molecules as graphs and processes them via a generative adversarial network comprising graph transformer layers. The system is trained using a large dataset of drug like compounds and target specific bioactive molecules to design effective inhibitory molecules against the AKT1 protein, which is critically important in developing treatments for various types of cancer. We conducted molecular docking and dynamics to assess the target centric generation performance of the model, as well as attention score visualisation to examine model interpretability. In parallel, selected compounds were chemically synthesised and evaluated in the context of in vitro enzymatic assays, which identified two bioactive molecules that inhibited AKT1 at low micromolar concentrations. These results indicate that DrugGEN's de novo molecules have a high potential for interacting with the AKT1 protein at the level of its native ligands. Using the open access DrugGEN codebase, it is possible to easily train models for other druggable proteins, given a dataset of experimentally known bioactive molecules.

  • 10 authors
·
Feb 15, 2023

Balancing Pipeline Parallelism with Vocabulary Parallelism

Pipeline parallelism is widely used to scale the training of transformer-based large language models, various works have been done to improve its throughput and memory footprint. In this paper, we address a frequently overlooked issue: the vocabulary layers can cause imbalanced computation and memory usage across pipeline stages, worsening pipeline bubbles and the memory bottleneck. To tackle this, we partition the vocabulary layers evenly across pipeline devices and group the computation into pipeline passes. To reduce the activation memory overhead, we propose several algorithms to reduce communication barriers within vocabulary layers. Additionally, we utilize a generalizable method to integrate Vocabulary Parallelism with existing pipeline schedules. By combining these techniques, our methods effectively balance the computation and parameter memory, with only a small constant activation memory overhead. Notably, when combined with activation memory-balanced schedules like V-Half, our approach achieves perfect balance in both memory and computation. Extensive evaluations demonstrate that our method achieves computation and memory balance regardless of the vocabulary size, resulting in a 5% to 51% improvement in throughput compared to naive approaches, meanwhile significantly reducing peak memory usage especially for large vocabulary scenarios. Our implementation is open-sourced at https://github.com/sail-sg/VocabularyParallelism .

  • 4 authors
·
Nov 7, 2024 3

ACE: All-round Creator and Editor Following Instructions via Diffusion Transformer

Diffusion models have emerged as a powerful generative technology and have been found to be applicable in various scenarios. Most existing foundational diffusion models are primarily designed for text-guided visual generation and do not support multi-modal conditions, which are essential for many visual editing tasks. This limitation prevents these foundational diffusion models from serving as a unified model in the field of visual generation, like GPT-4 in the natural language processing field. In this work, we propose ACE, an All-round Creator and Editor, which achieves comparable performance compared to those expert models in a wide range of visual generation tasks. To achieve this goal, we first introduce a unified condition format termed Long-context Condition Unit (LCU), and propose a novel Transformer-based diffusion model that uses LCU as input, aiming for joint training across various generation and editing tasks. Furthermore, we propose an efficient data collection approach to address the issue of the absence of available training data. It involves acquiring pairwise images with synthesis-based or clustering-based pipelines and supplying these pairs with accurate textual instructions by leveraging a fine-tuned multi-modal large language model. To comprehensively evaluate the performance of our model, we establish a benchmark of manually annotated pairs data across a variety of visual generation tasks. The extensive experimental results demonstrate the superiority of our model in visual generation fields. Thanks to the all-in-one capabilities of our model, we can easily build a multi-modal chat system that responds to any interactive request for image creation using a single model to serve as the backend, avoiding the cumbersome pipeline typically employed in visual agents. Code and models will be available on the project page: https://ali-vilab.github.io/ace-page/.

  • 8 authors
·
Sep 30, 2024 2

GenCompositor: Generative Video Compositing with Diffusion Transformer

Video compositing combines live-action footage to create video production, serving as a crucial technique in video creation and film production. Traditional pipelines require intensive labor efforts and expert collaboration, resulting in lengthy production cycles and high manpower costs. To address this issue, we automate this process with generative models, called generative video compositing. This new task strives to adaptively inject identity and motion information of foreground video to the target video in an interactive manner, allowing users to customize the size, motion trajectory, and other attributes of the dynamic elements added in final video. Specifically, we designed a novel Diffusion Transformer (DiT) pipeline based on its intrinsic properties. To maintain consistency of the target video before and after editing, we revised a light-weight DiT-based background preservation branch with masked token injection. As to inherit dynamic elements from other sources, a DiT fusion block is proposed using full self-attention, along with a simple yet effective foreground augmentation for training. Besides, for fusing background and foreground videos with different layouts based on user control, we developed a novel position embedding, named Extended Rotary Position Embedding (ERoPE). Finally, we curated a dataset comprising 61K sets of videos for our new task, called VideoComp. This data includes complete dynamic elements and high-quality target videos. Experiments demonstrate that our method effectively realizes generative video compositing, outperforming existing possible solutions in fidelity and consistency.

  • 7 authors
·
Sep 2 4

Calorie Aware Automatic Meal Kit Generation from an Image

Calorie and nutrition research has attained increased interest in recent years. But, due to the complexity of the problem, literature in this area focuses on a limited subset of ingredients or dish types and simple convolutional neural networks or traditional machine learning. Simultaneously, estimation of ingredient portions can help improve calorie estimation and meal re-production from a given image. In this paper, given a single cooking image, a pipeline for calorie estimation and meal re-production for different servings of the meal is proposed. The pipeline contains two stages. In the first stage, a set of ingredients associated with the meal in the given image are predicted. In the second stage, given image features and ingredients, portions of the ingredients and finally the total meal calorie are simultaneously estimated using a deep transformer-based model. Portion estimation introduced in the model helps improve calorie estimation and is also beneficial for meal re-production in different serving sizes. To demonstrate the benefits of the pipeline, the model can be used for meal kits generation. To evaluate the pipeline, the large scale dataset Recipe1M is used. Prior to experiments, the Recipe1M dataset is parsed and explicitly annotated with portions of ingredients. Experiments show that using ingredients and their portions significantly improves calorie estimation. Also, a visual interface is created in which a user can interact with the pipeline to reach accurate calorie estimations and generate a meal kit for cooking purposes.

  • 2 authors
·
Dec 17, 2021

DeepASA: An Object-Oriented One-for-All Network for Auditory Scene Analysis

We propose DeepASA, a one-for-all model for auditory scene analysis that performs multi-input multi-output (MIMO) source separation, dereverberation, sound event detection (SED), audio classification, and direction-of-arrival estimation (DoAE) within a unified framework. DeepASA is designed for complex auditory scenes where multiple, often similar, sound sources overlap in time and move dynamically in space. To achieve robust and consistent inference across tasks, we introduce an object-oriented processing (OOP) strategy. This approach encapsulates diverse auditory features into object-centric representations and refines them through a chain-of-inference (CoI) mechanism. The pipeline comprises a dynamic temporal kernel-based feature extractor, a transformer-based aggregator, and an object separator that yields per-object features. These features feed into multiple task-specific decoders. Our object-centric representations naturally resolve the parameter association ambiguity inherent in traditional track-wise processing. However, early-stage object separation can lead to failure in downstream ASA tasks. To address this, we implement temporal coherence matching (TCM) within the chain-of-inference, enabling multi-task fusion and iterative refinement of object features using estimated auditory parameters. We evaluate DeepASA on representative spatial audio benchmark datasets, including ASA2, MC-FUSS, and STARSS23. Experimental results show that our model achieves state-of-the-art performance across all evaluated tasks, demonstrating its effectiveness in both source separation and auditory parameter estimation under diverse spatial auditory scenes.

  • 3 authors
·
Sep 21

MotionRAG: Motion Retrieval-Augmented Image-to-Video Generation

Image-to-video generation has made remarkable progress with the advancements in diffusion models, yet generating videos with realistic motion remains highly challenging. This difficulty arises from the complexity of accurately modeling motion, which involves capturing physical constraints, object interactions, and domain-specific dynamics that are not easily generalized across diverse scenarios. To address this, we propose MotionRAG, a retrieval-augmented framework that enhances motion realism by adapting motion priors from relevant reference videos through Context-Aware Motion Adaptation (CAMA). The key technical innovations include: (i) a retrieval-based pipeline extracting high-level motion features using video encoder and specialized resamplers to distill semantic motion representations; (ii) an in-context learning approach for motion adaptation implemented through a causal transformer architecture; (iii) an attention-based motion injection adapter that seamlessly integrates transferred motion features into pretrained video diffusion models. Extensive experiments demonstrate that our method achieves significant improvements across multiple domains and various base models, all with negligible computational overhead during inference. Furthermore, our modular design enables zero-shot generalization to new domains by simply updating the retrieval database without retraining any components. This research enhances the core capability of video generation systems by enabling the effective retrieval and transfer of motion priors, facilitating the synthesis of realistic motion dynamics.

  • 5 authors
·
Sep 30 2

GeoMAE: Masked Geometric Target Prediction for Self-supervised Point Cloud Pre-Training

This paper tries to address a fundamental question in point cloud self-supervised learning: what is a good signal we should leverage to learn features from point clouds without annotations? To answer that, we introduce a point cloud representation learning framework, based on geometric feature reconstruction. In contrast to recent papers that directly adopt masked autoencoder (MAE) and only predict original coordinates or occupancy from masked point clouds, our method revisits differences between images and point clouds and identifies three self-supervised learning objectives peculiar to point clouds, namely centroid prediction, normal estimation, and curvature prediction. Combined with occupancy prediction, these four objectives yield an nontrivial self-supervised learning task and mutually facilitate models to better reason fine-grained geometry of point clouds. Our pipeline is conceptually simple and it consists of two major steps: first, it randomly masks out groups of points, followed by a Transformer-based point cloud encoder; second, a lightweight Transformer decoder predicts centroid, normal, and curvature for points in each voxel. We transfer the pre-trained Transformer encoder to a downstream peception model. On the nuScene Datset, our model achieves 3.38 mAP improvment for object detection, 2.1 mIoU gain for segmentation, and 1.7 AMOTA gain for multi-object tracking. We also conduct experiments on the Waymo Open Dataset and achieve significant performance improvements over baselines as well.

  • 4 authors
·
May 15, 2023

UAlign: Pushing the Limit of Template-free Retrosynthesis Prediction with Unsupervised SMILES Alignment

Retrosynthesis planning poses a formidable challenge in the organic chemical industry, particularly in pharmaceuticals. Single-step retrosynthesis prediction, a crucial step in the planning process, has witnessed a surge in interest in recent years due to advancements in AI for science. Various deep learning-based methods have been proposed for this task in recent years, incorporating diverse levels of additional chemical knowledge dependency. This paper introduces UAlign, a template-free graph-to-sequence pipeline for retrosynthesis prediction. By combining graph neural networks and Transformers, our method can more effectively leverage the inherent graph structure of molecules. Based on the fact that the majority of molecule structures remain unchanged during a chemical reaction, we propose a simple yet effective SMILES alignment technique to facilitate the reuse of unchanged structures for reactant generation. Extensive experiments show that our method substantially outperforms state-of-the-art template-free and semi-template-based approaches. Importantly, Our template-free method achieves effectiveness comparable to, or even surpasses, established powerful template-based methods. Scientific contribution: We present a novel graph-to-sequence template-free retrosynthesis prediction pipeline that overcomes the limitations of Transformer-based methods in molecular representation learning and insufficient utilization of chemical information. We propose an unsupervised learning mechanism for establishing product-atom correspondence with reactant SMILES tokens, achieving even better results than supervised SMILES alignment methods. Extensive experiments demonstrate that UAlign significantly outperforms state-of-the-art template-free methods and rivals or surpasses template-based approaches, with up to 5\% (top-5) and 5.4\% (top-10) increased accuracy over the strongest baseline.

  • 7 authors
·
Mar 24, 2024

Annotating the Tweebank Corpus on Named Entity Recognition and Building NLP Models for Social Media Analysis

Social media data such as Twitter messages ("tweets") pose a particular challenge to NLP systems because of their short, noisy, and colloquial nature. Tasks such as Named Entity Recognition (NER) and syntactic parsing require highly domain-matched training data for good performance. To date, there is no complete training corpus for both NER and syntactic analysis (e.g., part of speech tagging, dependency parsing) of tweets. While there are some publicly available annotated NLP datasets of tweets, they are only designed for individual tasks. In this study, we aim to create Tweebank-NER, an English NER corpus based on Tweebank V2 (TB2), train state-of-the-art (SOTA) Tweet NLP models on TB2, and release an NLP pipeline called Twitter-Stanza. We annotate named entities in TB2 using Amazon Mechanical Turk and measure the quality of our annotations. We train the Stanza pipeline on TB2 and compare with alternative NLP frameworks (e.g., FLAIR, spaCy) and transformer-based models. The Stanza tokenizer and lemmatizer achieve SOTA performance on TB2, while the Stanza NER tagger, part-of-speech (POS) tagger, and dependency parser achieve competitive performance against non-transformer models. The transformer-based models establish a strong baseline in Tweebank-NER and achieve the new SOTA performance in POS tagging and dependency parsing on TB2. We release the dataset and make both the Stanza pipeline and BERTweet-based models available "off-the-shelf" for use in future Tweet NLP research. Our source code, data, and pre-trained models are available at: https://github.com/social-machines/TweebankNLP.

  • 4 authors
·
Jan 18, 2022

Learn to Rank Risky Investors: A Case Study of Predicting Retail Traders' Behaviour and Profitability

Identifying risky traders with high profits in financial markets is crucial for market makers, such as trading exchanges, to ensure effective risk management through real-time decisions on regulation compliance and hedging. However, capturing the complex and dynamic behaviours of individual traders poses significant challenges. Traditional classification and anomaly detection methods often establish a fixed risk boundary, failing to account for this complexity and dynamism. To tackle this issue, we propose a profit-aware risk ranker (PA-RiskRanker) that reframes the problem of identifying risky traders as a ranking task using Learning-to-Rank (LETOR) algorithms. Our approach features a Profit-Aware binary cross entropy (PA-BCE) loss function and a transformer-based ranker enhanced with a self-cross-trader attention pipeline. These components effectively integrate profit and loss (P&L) considerations into the training process while capturing intra- and inter-trader relationships. Our research critically examines the limitations of existing deep learning-based LETOR algorithms in trading risk management, which often overlook the importance of P&L in financial scenarios. By prioritising P&L, our method improves risky trader identification, achieving an 8.4% increase in F1 score compared to state-of-the-art (SOTA) ranking models like Rankformer. Additionally, it demonstrates a 10%-17% increase in average profit compared to all benchmark models.

  • 2 authors
·
Sep 20

Taming Feed-forward Reconstruction Models as Latent Encoders for 3D Generative Models

Recent AI-based 3D content creation has largely evolved along two paths: feed-forward image-to-3D reconstruction approaches and 3D generative models trained with 2D or 3D supervision. In this work, we show that existing feed-forward reconstruction methods can serve as effective latent encoders for training 3D generative models, thereby bridging these two paradigms. By reusing powerful pre-trained reconstruction models, we avoid computationally expensive encoder network training and obtain rich 3D latent features for generative modeling for free. However, the latent spaces of reconstruction models are not well-suited for generative modeling due to their unstructured nature. To enable flow-based model training on these latent features, we develop post-processing pipelines, including protocols to standardize the features and spatial weighting to concentrate on important regions. We further incorporate a 2D image space perceptual rendering loss to handle the high-dimensional latent spaces. Finally, we propose a multi-stream transformer-based rectified flow architecture to achieve linear scaling and high-quality text-conditioned 3D generation. Our framework leverages the advancements of feed-forward reconstruction models to enhance the scalability of 3D generative modeling, achieving both high computational efficiency and state-of-the-art performance in text-to-3D generation.

  • 4 authors
·
Dec 31, 2024

Improving the Performance of Radiology Report De-identification with Large-Scale Training and Benchmarking Against Cloud Vendor Methods

Objective: To enhance automated de-identification of radiology reports by scaling transformer-based models through extensive training datasets and benchmarking performance against commercial cloud vendor systems for protected health information (PHI) detection. Materials and Methods: In this retrospective study, we built upon a state-of-the-art, transformer-based, PHI de-identification pipeline by fine-tuning on two large annotated radiology corpora from Stanford University, encompassing chest X-ray, chest CT, abdomen/pelvis CT, and brain MR reports and introducing an additional PHI category (AGE) into the architecture. Model performance was evaluated on test sets from Stanford and the University of Pennsylvania (Penn) for token-level PHI detection. We further assessed (1) the stability of synthetic PHI generation using a "hide-in-plain-sight" method and (2) performance against commercial systems. Precision, recall, and F1 scores were computed across all PHI categories. Results: Our model achieved overall F1 scores of 0.973 on the Penn dataset and 0.996 on the Stanford dataset, outperforming or maintaining the previous state-of-the-art model performance. Synthetic PHI evaluation showed consistent detectability (overall F1: 0.959 [0.958-0.960]) across 50 independently de-identified Penn datasets. Our model outperformed all vendor systems on synthetic Penn reports (overall F1: 0.960 vs. 0.632-0.754). Discussion: Large-scale, multimodal training improved cross-institutional generalization and robustness. Synthetic PHI generation preserved data utility while ensuring privacy. Conclusion: A transformer-based de-identification model trained on diverse radiology datasets outperforms prior academic and commercial systems in PHI detection and establishes a new benchmark for secure clinical text processing.

  • 8 authors
·
Nov 6

Brain Captioning: Decoding human brain activity into images and text

Every day, the human brain processes an immense volume of visual information, relying on intricate neural mechanisms to perceive and interpret these stimuli. Recent breakthroughs in functional magnetic resonance imaging (fMRI) have enabled scientists to extract visual information from human brain activity patterns. In this study, we present an innovative method for decoding brain activity into meaningful images and captions, with a specific focus on brain captioning due to its enhanced flexibility as compared to brain decoding into images. Our approach takes advantage of cutting-edge image captioning models and incorporates a unique image reconstruction pipeline that utilizes latent diffusion models and depth estimation. We utilized the Natural Scenes Dataset, a comprehensive fMRI dataset from eight subjects who viewed images from the COCO dataset. We employed the Generative Image-to-text Transformer (GIT) as our backbone for captioning and propose a new image reconstruction pipeline based on latent diffusion models. The method involves training regularized linear regression models between brain activity and extracted features. Additionally, we incorporated depth maps from the ControlNet model to further guide the reconstruction process. We evaluate our methods using quantitative metrics for both generated captions and images. Our brain captioning approach outperforms existing methods, while our image reconstruction pipeline generates plausible images with improved spatial relationships. In conclusion, we demonstrate significant progress in brain decoding, showcasing the enormous potential of integrating vision and language to better understand human cognition. Our approach provides a flexible platform for future research, with potential applications in various fields, including neural art, style transfer, and portable devices.

  • 5 authors
·
May 19, 2023

MonoDINO-DETR: Depth-Enhanced Monocular 3D Object Detection Using a Vision Foundation Model

This paper proposes novel methods to enhance the performance of monocular 3D object detection models by leveraging the generalized feature extraction capabilities of a vision foundation model. Unlike traditional CNN-based approaches, which often suffer from inaccurate depth estimation and rely on multi-stage object detection pipelines, this study employs a Vision Transformer (ViT)-based foundation model as the backbone, which excels at capturing global features for depth estimation. It integrates a detection transformer (DETR) architecture to improve both depth estimation and object detection performance in a one-stage manner. Specifically, a hierarchical feature fusion block is introduced to extract richer visual features from the foundation model, further enhancing feature extraction capabilities. Depth estimation accuracy is further improved by incorporating a relative depth estimation model trained on large-scale data and fine-tuning it through transfer learning. Additionally, the use of queries in the transformer's decoder, which consider reference points and the dimensions of 2D bounding boxes, enhances recognition performance. The proposed model outperforms recent state-of-the-art methods, as demonstrated through quantitative and qualitative evaluations on the KITTI 3D benchmark and a custom dataset collected from high-elevation racing environments. Code is available at https://github.com/JihyeokKim/MonoDINO-DETR.

  • 4 authors
·
Jan 31

DreamClear: High-Capacity Real-World Image Restoration with Privacy-Safe Dataset Curation

Image restoration (IR) in real-world scenarios presents significant challenges due to the lack of high-capacity models and comprehensive datasets. To tackle these issues, we present a dual strategy: GenIR, an innovative data curation pipeline, and DreamClear, a cutting-edge Diffusion Transformer (DiT)-based image restoration model. GenIR, our pioneering contribution, is a dual-prompt learning pipeline that overcomes the limitations of existing datasets, which typically comprise only a few thousand images and thus offer limited generalizability for larger models. GenIR streamlines the process into three stages: image-text pair construction, dual-prompt based fine-tuning, and data generation & filtering. This approach circumvents the laborious data crawling process, ensuring copyright compliance and providing a cost-effective, privacy-safe solution for IR dataset construction. The result is a large-scale dataset of one million high-quality images. Our second contribution, DreamClear, is a DiT-based image restoration model. It utilizes the generative priors of text-to-image (T2I) diffusion models and the robust perceptual capabilities of multi-modal large language models (MLLMs) to achieve photorealistic restoration. To boost the model's adaptability to diverse real-world degradations, we introduce the Mixture of Adaptive Modulator (MoAM). It employs token-wise degradation priors to dynamically integrate various restoration experts, thereby expanding the range of degradations the model can address. Our exhaustive experiments confirm DreamClear's superior performance, underlining the efficacy of our dual strategy for real-world image restoration. Code and pre-trained models will be available at: https://github.com/shallowdream204/DreamClear.

  • 7 authors
·
Oct 24, 2024 3

AeroReformer: Aerial Referring Transformer for UAV-based Referring Image Segmentation

As a novel and challenging task, referring segmentation combines computer vision and natural language processing to localize and segment objects based on textual descriptions. While referring image segmentation (RIS) has been extensively studied in natural images, little attention has been given to aerial imagery, particularly from unmanned aerial vehicles (UAVs). The unique challenges of UAV imagery, including complex spatial scales, occlusions, and varying object orientations, render existing RIS approaches ineffective. A key limitation has been the lack of UAV-specific datasets, as manually annotating pixel-level masks and generating textual descriptions is labour-intensive and time-consuming. To address this gap, we design an automatic labelling pipeline that leverages pre-existing UAV segmentation datasets and Multimodal Large Language Models (MLLM) for generating textual descriptions. Furthermore, we propose Aerial Referring Transformer (AeroReformer), a novel framework for UAV referring image segmentation (UAV-RIS), featuring a Vision-Language Cross-Attention Module (VLCAM) for effective cross-modal understanding and a Rotation-Aware Multi-Scale Fusion (RAMSF) decoder to enhance segmentation accuracy in aerial scenes. Extensive experiments on two newly developed datasets demonstrate the superiority of AeroReformer over existing methods, establishing a new benchmark for UAV-RIS. The datasets and code will be publicly available at: https://github.com/lironui/AeroReformer.

  • 2 authors
·
Feb 23

Student Answer Forecasting: Transformer-Driven Answer Choice Prediction for Language Learning

Intelligent Tutoring Systems (ITS) enhance personalized learning by predicting student answers to provide immediate and customized instruction. However, recent research has primarily focused on the correctness of the answer rather than the student's performance on specific answer choices, limiting insights into students' thought processes and potential misconceptions. To address this gap, we present MCQStudentBert, an answer forecasting model that leverages the capabilities of Large Language Models (LLMs) to integrate contextual understanding of students' answering history along with the text of the questions and answers. By predicting the specific answer choices students are likely to make, practitioners can easily extend the model to new answer choices or remove answer choices for the same multiple-choice question (MCQ) without retraining the model. In particular, we compare MLP, LSTM, BERT, and Mistral 7B architectures to generate embeddings from students' past interactions, which are then incorporated into a finetuned BERT's answer-forecasting mechanism. We apply our pipeline to a dataset of language learning MCQ, gathered from an ITS with over 10,000 students to explore the predictive accuracy of MCQStudentBert, which incorporates student interaction patterns, in comparison to correct answer prediction and traditional mastery-learning feature-based approaches. This work opens the door to more personalized content, modularization, and granular support.

  • 7 authors
·
May 30, 2024

Dense2MoE: Restructuring Diffusion Transformer to MoE for Efficient Text-to-Image Generation

Diffusion Transformer (DiT) has demonstrated remarkable performance in text-to-image generation; however, its large parameter size results in substantial inference overhead. Existing parameter compression methods primarily focus on pruning, but aggressive pruning often leads to severe performance degradation due to reduced model capacity. To address this limitation, we pioneer the transformation of a dense DiT into a Mixture of Experts (MoE) for structured sparsification, reducing the number of activated parameters while preserving model capacity. Specifically, we replace the Feed-Forward Networks (FFNs) in DiT Blocks with MoE layers, reducing the number of activated parameters in the FFNs by 62.5\%. Furthermore, we propose the Mixture of Blocks (MoB) to selectively activate DiT blocks, thereby further enhancing sparsity. To ensure an effective dense-to-MoE conversion, we design a multi-step distillation pipeline, incorporating Taylor metric-based expert initialization, knowledge distillation with load balancing, and group feature loss for MoB optimization. We transform large diffusion transformers (e.g., FLUX.1 [dev]) into an MoE structure, reducing activated parameters by 60\% while maintaining original performance and surpassing pruning-based approaches in extensive experiments. Overall, Dense2MoE establishes a new paradigm for efficient text-to-image generation.

  • 5 authors
·
Oct 10

Efficient Feature Extraction Using Light-Weight CNN Attention-Based Deep Learning Architectures for Ultrasound Fetal Plane Classification

Ultrasound fetal imaging is beneficial to support prenatal development because it is affordable and non-intrusive. Nevertheless, fetal plane classification (FPC) remains challenging and time-consuming for obstetricians since it depends on nuanced clinical aspects, which increases the difficulty in identifying relevant features of the fetal anatomy. Thus, to assist with its accurate feature extraction, a lightweight artificial intelligence architecture leveraging convolutional neural networks and attention mechanisms is proposed to classify the largest benchmark ultrasound dataset. The approach fine-tunes from lightweight EfficientNet feature extraction backbones pre-trained on the ImageNet1k. to classify key fetal planes such as the brain, femur, thorax, cervix, and abdomen. Our methodology incorporates the attention mechanism to refine features and 3-layer perceptrons for classification, achieving superior performance with the highest Top-1 accuracy of 96.25%, Top-2 accuracy of 99.80% and F1-Score of 0.9576. Importantly, the model has 40x fewer trainable parameters than existing benchmark ensemble or transformer pipelines, facilitating easy deployment on edge devices to help clinical practitioners with real-time FPC. The findings are also interpreted using GradCAM to carry out clinical correlation to aid doctors with diagnostics and improve treatment plans for expectant mothers.

  • 4 authors
·
Oct 22, 2024

I-Segmenter: Integer-Only Vision Transformer for Efficient Semantic Segmentation

Vision Transformers (ViTs) have recently achieved strong results in semantic segmentation, yet their deployment on resource-constrained devices remains limited due to their high memory footprint and computational cost. Quantization offers an effective strategy to improve efficiency, but ViT-based segmentation models are notoriously fragile under low precision, as quantization errors accumulate across deep encoder-decoder pipelines. We introduce I-Segmenter, the first fully integer-only ViT segmentation framework. Building on the Segmenter architecture, I-Segmenter systematically replaces floating-point operations with integer-only counterparts. To further stabilize both training and inference, we propose lambda-ShiftGELU, a novel activation function that mitigates the limitations of uniform quantization in handling long-tailed activation distributions. In addition, we remove the L2 normalization layer and replace bilinear interpolation in the decoder with nearest neighbor upsampling, ensuring integer-only execution throughout the computational graph. Extensive experiments show that I-Segmenter achieves accuracy within a reasonable margin of its FP32 baseline (5.1 % on average), while reducing model size by up to 3.8x and enabling up to 1.2x faster inference with optimized runtimes. Notably, even in one-shot PTQ with a single calibration image, I-Segmenter delivers competitive accuracy, underscoring its practicality for real-world deployment.

  • 3 authors
·
Sep 12

AniMer: Animal Pose and Shape Estimation Using Family Aware Transformer

Quantitative analysis of animal behavior and biomechanics requires accurate animal pose and shape estimation across species, and is important for animal welfare and biological research. However, the small network capacity of previous methods and limited multi-species dataset leave this problem underexplored. To this end, this paper presents AniMer to estimate animal pose and shape using family aware Transformer, enhancing the reconstruction accuracy of diverse quadrupedal families. A key insight of AniMer is its integration of a high-capacity Transformer-based backbone and an animal family supervised contrastive learning scheme, unifying the discriminative understanding of various quadrupedal shapes within a single framework. For effective training, we aggregate most available open-sourced quadrupedal datasets, either with 3D or 2D labels. To improve the diversity of 3D labeled data, we introduce CtrlAni3D, a novel large-scale synthetic dataset created through a new diffusion-based conditional image generation pipeline. CtrlAni3D consists of about 10k images with pixel-aligned SMAL labels. In total, we obtain 41.3k annotated images for training and validation. Consequently, the combination of a family aware Transformer network and an expansive dataset enables AniMer to outperform existing methods not only on 3D datasets like Animal3D and CtrlAni3D, but also on out-of-distribution Animal Kingdom dataset. Ablation studies further demonstrate the effectiveness of our network design and CtrlAni3D in enhancing the performance of AniMer for in-the-wild applications. The project page of AniMer is https://luoxue-star.github.io/AniMer_project_page/.

  • 8 authors
·
Dec 1, 2024

AniMer+: Unified Pose and Shape Estimation Across Mammalia and Aves via Family-Aware Transformer

In the era of foundation models, achieving a unified understanding of different dynamic objects through a single network has the potential to empower stronger spatial intelligence. Moreover, accurate estimation of animal pose and shape across diverse species is essential for quantitative analysis in biological research. However, this topic remains underexplored due to the limited network capacity of previous methods and the scarcity of comprehensive multi-species datasets. To address these limitations, we introduce AniMer+, an extended version of our scalable AniMer framework. In this paper, we focus on a unified approach for reconstructing mammals (mammalia) and birds (aves). A key innovation of AniMer+ is its high-capacity, family-aware Vision Transformer (ViT) incorporating a Mixture-of-Experts (MoE) design. Its architecture partitions network layers into taxa-specific components (for mammalia and aves) and taxa-shared components, enabling efficient learning of both distinct and common anatomical features within a single model. To overcome the critical shortage of 3D training data, especially for birds, we introduce a diffusion-based conditional image generation pipeline. This pipeline produces two large-scale synthetic datasets: CtrlAni3D for quadrupeds and CtrlAVES3D for birds. To note, CtrlAVES3D is the first large-scale, 3D-annotated dataset for birds, which is crucial for resolving single-view depth ambiguities. Trained on an aggregated collection of 41.3k mammalian and 12.4k avian images (combining real and synthetic data), our method demonstrates superior performance over existing approaches across a wide range of benchmarks, including the challenging out-of-domain Animal Kingdom dataset. Ablation studies confirm the effectiveness of both our novel network architecture and the generated synthetic datasets in enhancing real-world application performance.

  • 6 authors
·
Jul 31

A Practical Survey on Faster and Lighter Transformers

Recurrent neural networks are effective models to process sequences. However, they are unable to learn long-term dependencies because of their inherent sequential nature. As a solution, Vaswani et al. introduced the Transformer, a model solely based on the attention mechanism that is able to relate any two positions of the input sequence, hence modelling arbitrary long dependencies. The Transformer has improved the state-of-the-art across numerous sequence modelling tasks. However, its effectiveness comes at the expense of a quadratic computational and memory complexity with respect to the sequence length, hindering its adoption. Fortunately, the deep learning community has always been interested in improving the models' efficiency, leading to a plethora of solutions such as parameter sharing, pruning, mixed-precision, and knowledge distillation. Recently, researchers have directly addressed the Transformer's limitation by designing lower-complexity alternatives such as the Longformer, Reformer, Linformer, and Performer. However, due to the wide range of solutions, it has become challenging for researchers and practitioners to determine which methods to apply in practice in order to meet the desired trade-off between capacity, computation, and memory. This survey addresses this issue by investigating popular approaches to make Transformers faster and lighter and by providing a comprehensive explanation of the methods' strengths, limitations, and underlying assumptions.

  • 3 authors
·
Mar 26, 2021

A Survey of Techniques for Optimizing Transformer Inference

Recent years have seen a phenomenal rise in performance and applications of transformer neural networks. The family of transformer networks, including Bidirectional Encoder Representations from Transformer (BERT), Generative Pretrained Transformer (GPT) and Vision Transformer (ViT), have shown their effectiveness across Natural Language Processing (NLP) and Computer Vision (CV) domains. Transformer-based networks such as ChatGPT have impacted the lives of common men. However, the quest for high predictive performance has led to an exponential increase in transformers' memory and compute footprint. Researchers have proposed techniques to optimize transformer inference at all levels of abstraction. This paper presents a comprehensive survey of techniques for optimizing the inference phase of transformer networks. We survey techniques such as knowledge distillation, pruning, quantization, neural architecture search and lightweight network design at the algorithmic level. We further review hardware-level optimization techniques and the design of novel hardware accelerators for transformers. We summarize the quantitative results on the number of parameters/FLOPs and accuracy of several models/techniques to showcase the tradeoff exercised by them. We also outline future directions in this rapidly evolving field of research. We believe that this survey will educate both novice and seasoned researchers and also spark a plethora of research efforts in this field.

  • 5 authors
·
Jul 16, 2023

A Comprehensive Survey on Applications of Transformers for Deep Learning Tasks

Transformer is a deep neural network that employs a self-attention mechanism to comprehend the contextual relationships within sequential data. Unlike conventional neural networks or updated versions of Recurrent Neural Networks (RNNs) such as Long Short-Term Memory (LSTM), transformer models excel in handling long dependencies between input sequence elements and enable parallel processing. As a result, transformer-based models have attracted substantial interest among researchers in the field of artificial intelligence. This can be attributed to their immense potential and remarkable achievements, not only in Natural Language Processing (NLP) tasks but also in a wide range of domains, including computer vision, audio and speech processing, healthcare, and the Internet of Things (IoT). Although several survey papers have been published highlighting the transformer's contributions in specific fields, architectural differences, or performance evaluations, there is still a significant absence of a comprehensive survey paper encompassing its major applications across various domains. Therefore, we undertook the task of filling this gap by conducting an extensive survey of proposed transformer models from 2017 to 2022. Our survey encompasses the identification of the top five application domains for transformer-based models, namely: NLP, Computer Vision, Multi-Modality, Audio and Speech Processing, and Signal Processing. We analyze the impact of highly influential transformer-based models in these domains and subsequently classify them based on their respective tasks using a proposed taxonomy. Our aim is to shed light on the existing potential and future possibilities of transformers for enthusiastic researchers, thus contributing to the broader understanding of this groundbreaking technology.

  • 7 authors
·
Jun 11, 2023

ByteTransformer: A High-Performance Transformer Boosted for Variable-Length Inputs

Transformers have become keystone models in natural language processing over the past decade. They have achieved great popularity in deep learning applications, but the increasing sizes of the parameter spaces required by transformer models generate a commensurate need to accelerate performance. Natural language processing problems are also routinely faced with variable-length sequences, as word counts commonly vary among sentences. Existing deep learning frameworks pad variable-length sequences to a maximal length, which adds significant memory and computational overhead. In this paper, we present ByteTransformer, a high-performance transformer boosted for variable-length inputs. We propose a padding-free algorithm that liberates the entire transformer from redundant computations on zero padded tokens. In addition to algorithmic-level optimization, we provide architecture-aware optimizations for transformer functional modules, especially the performance-critical algorithm Multi-Head Attention (MHA). Experimental results on an NVIDIA A100 GPU with variable-length sequence inputs validate that our fused MHA outperforms PyTorch by 6.13x. The end-to-end performance of ByteTransformer for a forward BERT transformer surpasses state-of-the-art transformer frameworks, such as PyTorch JIT, TensorFlow XLA, Tencent TurboTransformer, Microsoft DeepSpeed-Inference and NVIDIA FasterTransformer, by 87\%, 131\%, 138\%, 74\% and 55\%, respectively. We also demonstrate the general applicability of our optimization methods to other BERT-like models, including ALBERT, DistilBERT, and DeBERTa.

  • 8 authors
·
Oct 6, 2022

Dynamic Chunking for End-to-End Hierarchical Sequence Modeling

Despite incredible progress in language models (LMs) in recent years, largely resulting from moving away from specialized models designed for specific tasks to general models based on powerful architectures (e.g. the Transformer) that learn everything from raw data, pre-processing steps such as tokenization remain a barrier to true end-to-end foundation models. We introduce a collection of new techniques that enable a dynamic chunking mechanism which automatically learns content -- and context -- dependent segmentation strategies learned jointly with the rest of the model. Incorporating this into an explicit hierarchical network (H-Net) allows replacing the (implicitly hierarchical) tokenization-LM-detokenization pipeline with a single model learned fully end-to-end. When compute- and data- matched, an H-Net with one stage of hierarchy operating at the byte level outperforms a strong Transformer language model operating over BPE tokens. Iterating the hierarchy to multiple stages further increases its performance by modeling multiple levels of abstraction, demonstrating significantly better scaling with data and matching a token-based Transformer of twice its size. H-Nets pretrained on English show significantly increased character-level robustness, and qualitatively learn meaningful data-dependent chunking strategies without any heuristics or explicit supervision. Finally, the H-Net's improvement over tokenized pipelines is further increased in languages and modalities with weaker tokenization heuristics, such as Chinese and code, or DNA sequences (nearly 4x improvement in data efficiency over baselines), showing the potential of true end-to-end models that learn and scale better from unprocessed data.

  • 3 authors
·
Jul 10 4

LMUFormer: Low Complexity Yet Powerful Spiking Model With Legendre Memory Units

Transformer models have demonstrated high accuracy in numerous applications but have high complexity and lack sequential processing capability making them ill-suited for many streaming applications at the edge where devices are heavily resource-constrained. Thus motivated, many researchers have proposed reformulating the transformer models as RNN modules which modify the self-attention computation with explicit states. However, these approaches often incur significant performance degradation. The ultimate goal is to develop a model that has the following properties: parallel training, streaming and low-cost inference, and SOTA performance. In this paper, we propose a new direction to achieve this goal. We show how architectural modifications to a recurrent model can help push its performance toward Transformer models while retaining its sequential processing capability. Specifically, inspired by the recent success of Legendre Memory Units (LMU) in sequence learning tasks, we propose LMUFormer, which augments the LMU with convolutional patch embedding and convolutional channel mixer. Moreover, we present a spiking version of this architecture, which introduces the benefit of states within the patch embedding and channel mixer modules while simultaneously reducing the computing complexity. We evaluated our architectures on multiple sequence datasets. In comparison to SOTA transformer-based models within the ANN domain on the SCv2 dataset, our LMUFormer demonstrates comparable performance while necessitating a remarkable 53 times reduction in parameters and a substantial 65 times decrement in FLOPs. Additionally, owing to our model's proficiency in real-time data processing, we can achieve a 32.03% reduction in sequence length, all while incurring an inconsequential decline in performance. Our code is publicly available at https://github.com/zeyuliu1037/LMUFormer.git.

  • 4 authors
·
Jan 19, 2024

On the Expressive Power of a Variant of the Looped Transformer

Besides natural language processing, transformers exhibit extraordinary performance in solving broader applications, including scientific computing and computer vision. Previous works try to explain this from the expressive power and capability perspectives that standard transformers are capable of performing some algorithms. To empower transformers with algorithmic capabilities and motivated by the recently proposed looped transformer (Yang et al., 2024; Giannou et al., 2023), we design a novel transformer block, dubbed Algorithm Transformer (abbreviated as AlgoFormer). Compared with the standard transformer and vanilla looped transformer, the proposed AlgoFormer can achieve significantly higher expressiveness in algorithm representation when using the same number of parameters. In particular, inspired by the structure of human-designed learning algorithms, our transformer block consists of a pre-transformer that is responsible for task pre-processing, a looped transformer for iterative optimization algorithms, and a post-transformer for producing the desired results after post-processing. We provide theoretical evidence of the expressive power of the AlgoFormer in solving some challenging problems, mirroring human-designed algorithms. Furthermore, some theoretical and empirical results are presented to show that the designed transformer has the potential to be smarter than human-designed algorithms. Experimental results demonstrate the empirical superiority of the proposed transformer in that it outperforms the standard transformer and vanilla looped transformer in some challenging tasks.

  • 9 authors
·
Feb 21, 2024

AxFormer: Accuracy-driven Approximation of Transformers for Faster, Smaller and more Accurate NLP Models

Transformers have greatly advanced the state-of-the-art in Natural Language Processing (NLP) in recent years, but present very large computation and storage requirements. We observe that the design process of Transformers (pre-train a foundation model on a large dataset in a self-supervised manner, and subsequently fine-tune it for different downstream tasks) leads to task-specific models that are highly over-parameterized, adversely impacting both accuracy and inference efficiency. We propose AxFormer, a systematic framework that applies accuracy-driven approximations to create optimized transformer models for a given downstream task. AxFormer combines two key optimizations -- accuracy-driven pruning and selective hard attention. Accuracy-driven pruning identifies and removes parts of the fine-tuned transformer that hinder performance on the given downstream task. Sparse hard-attention optimizes attention blocks in selected layers by eliminating irrelevant word aggregations, thereby helping the model focus only on the relevant parts of the input. In effect, AxFormer leads to models that are more accurate, while also being faster and smaller. Our experiments on GLUE and SQUAD tasks show that AxFormer models are up to 4.5% more accurate, while also being up to 2.5X faster and up to 3.2X smaller than conventional fine-tuned models. In addition, we demonstrate that AxFormer can be combined with previous efforts such as distillation or quantization to achieve further efficiency gains.

  • 4 authors
·
Oct 7, 2020

EcoFormer: Energy-Saving Attention with Linear Complexity

Transformer is a transformative framework that models sequential data and has achieved remarkable performance on a wide range of tasks, but with high computational and energy cost. To improve its efficiency, a popular choice is to compress the models via binarization which constrains the floating-point values into binary ones to save resource consumption owing to cheap bitwise operations significantly. However, existing binarization methods only aim at minimizing the information loss for the input distribution statistically, while ignoring the pairwise similarity modeling at the core of the attention. To this end, we propose a new binarization paradigm customized to high-dimensional softmax attention via kernelized hashing, called EcoFormer, to map the original queries and keys into low-dimensional binary codes in Hamming space. The kernelized hash functions are learned to match the ground-truth similarity relations extracted from the attention map in a self-supervised way. Based on the equivalence between the inner product of binary codes and the Hamming distance as well as the associative property of matrix multiplication, we can approximate the attention in linear complexity by expressing it as a dot-product of binary codes. Moreover, the compact binary representations of queries and keys enable us to replace most of the expensive multiply-accumulate operations in attention with simple accumulations to save considerable on-chip energy footprint on edge devices. Extensive experiments on both vision and language tasks show that EcoFormer consistently achieves comparable performance with standard attentions while consuming much fewer resources. For example, based on PVTv2-B0 and ImageNet-1K, Ecoformer achieves a 73% on-chip energy footprint reduction with only a 0.33% performance drop compared to the standard attention. Code is available at https://github.com/ziplab/EcoFormer.

  • 5 authors
·
Sep 19, 2022

Activator: GLU Activations as The Core Functions of a Vision Transformer

Transformer architecture currently represents the main driver behind many successes in a variety of tasks addressed by deep learning, especially the recent advances in natural language processing (NLP) culminating with large language models (LLM). In addition, transformer architecture has found a wide spread of interest from computer vision (CV) researchers and practitioners, allowing for many advancements in vision-related tasks and opening the door for multi-task and multi-modal deep learning architectures that share the same principle of operation. One drawback to these architectures is their reliance on the scaled dot product attention mechanism with the softmax activation function, which is computationally expensive and requires large compute capabilities both for training and inference. This paper investigates substituting the attention mechanism usually adopted for transformer architecture with an architecture incorporating gated linear unit (GLU) activation within a multi-layer perceptron (MLP) structure in conjunction with the default MLP incorporated in the traditional transformer design. Another step forward taken by this paper is to eliminate the second non-gated MLP to further reduce the computational cost. Experimental assessments conducted by this research show that both proposed modifications and reductions offer competitive performance in relation to baseline architectures, in support of the aims of this work in establishing a more efficient yet capable alternative to the traditional attention mechanism as the core component in designing transformer architectures.

  • 2 authors
·
May 24, 2024

Wide Attention Is The Way Forward For Transformers?

The Transformer is an extremely powerful and prominent deep learning architecture. In this work, we challenge the commonly held belief in deep learning that going deeper is better, and show an alternative design approach that is building wider attention Transformers. We demonstrate that wide single layer Transformer models can compete with or outperform deeper ones in a variety of Natural Language Processing (NLP) tasks when both are trained from scratch. The impact of changing the model aspect ratio on Transformers is then studied systematically. This ratio balances the number of layers and the number of attention heads per layer while keeping the total number of attention heads and all other hyperparameters constant. On average, across 4 NLP tasks and 10 attention types, single layer wide models perform 0.3% better than their deep counterparts. We show an in-depth evaluation and demonstrate how wide models require a far smaller memory footprint and can run faster on commodity hardware, in addition, these wider models are also more interpretable. For example, a single layer Transformer on the IMDb byte level text classification has 3.1x faster inference latency on a CPU than its equally accurate deeper counterpart, and is half the size. We therefore put forward wider and shallower models as a viable and desirable alternative for small models on NLP tasks, and as an important area of research for domains beyond this.

  • 4 authors
·
Oct 2, 2022

Blockwise Compression of Transformer-based Models without Retraining

Transformer-based models, exemplified by GPT-3, ChatGPT, and GPT-4, have recently garnered considerable attention in both academia and industry due to their promising performance in general language tasks. Nevertheless, these models typically involve computationally encoding processes, and in some cases, decoding processes as well, both of which are fundamentally large-scale matrix multiplication. These operations bring the inevitable challenges of massive computation resources and huge memory footprint, usually requiring at least 10^23 FLOPs and hundreds of gigabytes, respectively. A common method to address this issue is to reduce the computational and memory requirements by applying layerwise quantization to the transformer, replacing the usual fp32 data type with a low-bit equivalent. Unfortunately, this method often leads to decreased model accuracy and necessitates time-consuming retraining. Such retraining not only requires fine-tuning skills but also substantial computational resources, posing challenges for users. To specifically tackle these issues, we propose BCT, a framework of blockwise compression for transformers without retraining, aiming to facilitate model deployment. Unlike layerwise compression methods, BCT achieves finer compression of the entire transformer by operating blockwise. This method mitigates data distribution deviation caused by quantization, eliminating the requirement for retraining. BCT effectively compresses all components of the model, including but not limited to the embedding, matrix multiplication, GELU, Softmax, layer normalization, and intermediate results. In a case study, an efficient model is compressed by BCT achieving up to 7.988x compression. Subsequently, we also evaluate it on several General Language Understanding Evaluation (GLUE) datasets.

  • 2 authors
·
Apr 3, 2023

Lean Attention: Hardware-Aware Scalable Attention Mechanism for the Decode-Phase of Transformers

Transformer-based models have emerged as one of the most widely used architectures for natural language processing, natural language generation, and image generation. The size of the state-of-the-art models has increased steadily reaching billions of parameters. These huge models are memory hungry and incur significant inference latency even on cutting edge AI-accelerators, such as GPUs. Specifically, the time and memory complexity of the attention operation is quadratic in terms of the total context length, i.e., prompt and output tokens. Thus, several optimizations such as key-value tensor caching and FlashAttention computation have been proposed to deliver the low latency demands of applications relying on such large models. However, these techniques do not cater to the computationally distinct nature of different phases during inference. To that end, we propose LeanAttention, a scalable technique of computing self-attention for the token-generation phase (decode-phase) of decoder-only transformer models. LeanAttention enables scaling the attention mechanism implementation for the challenging case of long context lengths by re-designing the execution flow for the decode-phase. We identify that the associative property of online softmax can be treated as a reduction operation thus allowing us to parallelize the attention computation over these large context lengths. We extend the "stream-K" style reduction of tiled calculation to self-attention to enable parallel computation resulting in an average of 2.6x attention execution speedup over FlashAttention-2 and up to 8.33x speedup for 512k context lengths.

  • 5 authors
·
May 16, 2024

Deep Optimizer States: Towards Scalable Training of Transformer Models Using Interleaved Offloading

Transformers and large language models~(LLMs) have seen rapid adoption in all domains. Their sizes have exploded to hundreds of billions of parameters and keep increasing. Under these circumstances, the training of transformers is very expensive and often hits a ``memory wall'', i.e., even when using 3D parallelism (pipeline, tensor, data) and aggregating the memory of many GPUs, it is still not enough to hold the necessary data structures (model parameters, optimizer state, gradients, activations) in GPU memory. To compensate, state-of-the-art approaches offload the optimizer state, at least partially, to the host memory and perform hybrid CPU-GPU computations. However, the management of the combined host-GPU memory is often suboptimal and results in poor overlapping between data movements and computations. This leads to missed opportunities to simultaneously leverage the interconnect bandwidth and computational capabilities of CPUs and GPUs. In this paper, we leverage a key observation that the interleaving of the forward, backward and update phases generate fluctuations in the GPU memory utilization, which can be exploited to dynamically move a part of the optimizer state between the host and the GPU memory at each iteration. To this end, we design and implement \proj, a novel technique to split the LLM into subgroups, whose update phase is scheduled on either the CPU or the GPU based on our proposed performance model that addresses the trade-off between data movement cost, acceleration on the GPUs vs the CPUs, and competition for shared resources. We integrate our approach with DeepSpeed and demonstrate 2.5times faster iterations over state-of-the-art approaches using extensive experiments.

  • 5 authors
·
Oct 25, 2024

Ladder-residual: parallelism-aware architecture for accelerating large model inference with communication overlapping

Large language model inference is both memory-intensive and time-consuming, often requiring distributed algorithms to efficiently scale. Various model parallelism strategies are used in multi-gpu training and inference to partition computation across multiple devices, reducing memory load and computation time. However, using model parallelism necessitates communication of information between GPUs, which has been a major bottleneck and limits the gains obtained by scaling up the number of devices. We introduce Ladder Residual, a simple architectural modification applicable to all residual-based models that enables straightforward overlapping that effectively hides the latency of communication. Our insight is that in addition to systems optimization, one can also redesign the model architecture to decouple communication from computation. While Ladder Residual can allow communication-computation decoupling in conventional parallelism patterns, we focus on Tensor Parallelism in this paper, which is particularly bottlenecked by its heavy communication. For a Transformer model with 70B parameters, applying Ladder Residual to all its layers can achieve 30% end-to-end wall clock speed up at inference time with TP sharding over 8 devices. We refer the resulting Transformer model as the Ladder Transformer. We train a 1B and 3B Ladder Transformer from scratch and observe comparable performance to a standard dense transformer baseline. We also show that it is possible to convert parts of the Llama-3.1 8B model to our Ladder Residual architecture with minimal accuracy degradation by only retraining for 3B tokens.

  • 10 authors
·
Jan 11

FMViT: A multiple-frequency mixing Vision Transformer

The transformer model has gained widespread adoption in computer vision tasks in recent times. However, due to the quadratic time and memory complexity of self-attention, which is proportional to the number of input tokens, most existing Vision Transformers (ViTs) encounter challenges in achieving efficient performance in practical industrial deployment scenarios, such as TensorRT and CoreML, where traditional CNNs excel. Although some recent attempts have been made to design CNN-Transformer hybrid architectures to tackle this problem, their overall performance has not met expectations. To tackle these challenges, we propose an efficient hybrid ViT architecture named FMViT. This approach enhances the model's expressive power by blending high-frequency features and low-frequency features with varying frequencies, enabling it to capture both local and global information effectively. Additionally, we introduce deploy-friendly mechanisms such as Convolutional Multigroup Reparameterization (gMLP), Lightweight Multi-head Self-Attention (RLMHSA), and Convolutional Fusion Block (CFB) to further improve the model's performance and reduce computational overhead. Our experiments demonstrate that FMViT surpasses existing CNNs, ViTs, and CNNTransformer hybrid architectures in terms of latency/accuracy trade-offs for various vision tasks. On the TensorRT platform, FMViT outperforms Resnet101 by 2.5% (83.3% vs. 80.8%) in top-1 accuracy on the ImageNet dataset while maintaining similar inference latency. Moreover, FMViT achieves comparable performance with EfficientNet-B5, but with a 43% improvement in inference speed. On CoreML, FMViT outperforms MobileOne by 2.6% in top-1 accuracy on the ImageNet dataset, with inference latency comparable to MobileOne (78.5% vs. 75.9%). Our code can be found at https://github.com/tany0699/FMViT.

  • 3 authors
·
Nov 9, 2023 1

FIT: Far-reaching Interleaved Transformers

We present FIT: a transformer-based architecture with efficient self-attention and adaptive computation. Unlike original transformers, which operate on a single sequence of data tokens, we divide the data tokens into groups, with each group being a shorter sequence of tokens. We employ two types of transformer layers: local layers operate on data tokens within each group, while global layers operate on a smaller set of introduced latent tokens. These layers, comprising the same set of self-attention and feed-forward layers as standard transformers, are interleaved, and cross-attention is used to facilitate information exchange between data and latent tokens within the same group. The attention complexity is O(n^2) locally within each group of size n, but can reach O(L^{{4}/{3}}) globally for sequence length of L. The efficiency can be further enhanced by relying more on global layers that perform adaptive computation using a smaller set of latent tokens. FIT is a versatile architecture and can function as an encoder, diffusion decoder, or autoregressive decoder. We provide initial evidence demonstrating its effectiveness in high-resolution image understanding and generation tasks. Notably, FIT exhibits potential in performing end-to-end training on gigabit-scale data, such as 6400times6400 images, or 160K tokens (after patch tokenization), within a memory capacity of 16GB, without requiring specific optimizations or model parallelism.

  • 2 authors
·
May 21, 2023 2

Universal Approximation Theorem for a Single-Layer Transformer

Deep learning employs multi-layer neural networks trained via the backpropagation algorithm. This approach has achieved success across many domains and relies on adaptive gradient methods such as the Adam optimizer. Sequence modeling evolved from recurrent neural networks to attention-based models, culminating in the Transformer architecture. Transformers have achieved state-of-the-art performance in natural language processing (for example, BERT and GPT-3) and have been applied in computer vision and computational biology. However, theoretical understanding of these models remains limited. In this paper, we examine the mathematical foundations of deep learning and Transformers and present a novel theoretical result. We review key concepts from linear algebra, probability, and optimization that underpin deep learning, and we analyze the multi-head self-attention mechanism and the backpropagation algorithm in detail. Our main contribution is a universal approximation theorem for Transformers: we prove that a single-layer Transformer, comprising one self-attention layer followed by a position-wise feed-forward network with ReLU activation, can approximate any continuous sequence-to-sequence mapping on a compact domain to arbitrary precision. We provide a formal statement and a complete proof. Finally, we present case studies that demonstrate the practical implications of this result. Our findings advance the theoretical understanding of Transformer models and help bridge the gap between theory and practice.

  • 1 authors
·
Jul 11

Transformer in Transformer

Transformer is a new kind of neural architecture which encodes the input data as powerful features via the attention mechanism. Basically, the visual transformers first divide the input images into several local patches and then calculate both representations and their relationship. Since natural images are of high complexity with abundant detail and color information, the granularity of the patch dividing is not fine enough for excavating features of objects in different scales and locations. In this paper, we point out that the attention inside these local patches are also essential for building visual transformers with high performance and we explore a new architecture, namely, Transformer iN Transformer (TNT). Specifically, we regard the local patches (e.g., 16times16) as "visual sentences" and present to further divide them into smaller patches (e.g., 4times4) as "visual words". The attention of each word will be calculated with other words in the given visual sentence with negligible computational costs. Features of both words and sentences will be aggregated to enhance the representation ability. Experiments on several benchmarks demonstrate the effectiveness of the proposed TNT architecture, e.g., we achieve an 81.5% top-1 accuracy on the ImageNet, which is about 1.7% higher than that of the state-of-the-art visual transformer with similar computational cost. The PyTorch code is available at https://github.com/huawei-noah/CV-Backbones, and the MindSpore code is available at https://gitee.com/mindspore/models/tree/master/research/cv/TNT.

  • 6 authors
·
Feb 26, 2021 1

Understanding In-Context Learning in Transformers and LLMs by Learning to Learn Discrete Functions

In order to understand the in-context learning phenomenon, recent works have adopted a stylized experimental framework and demonstrated that Transformers can learn gradient-based learning algorithms for various classes of real-valued functions. However, the limitations of Transformers in implementing learning algorithms, and their ability to learn other forms of algorithms are not well understood. Additionally, the degree to which these capabilities are confined to attention-based models is unclear. Furthermore, it remains to be seen whether the insights derived from these stylized settings can be extrapolated to pretrained Large Language Models (LLMs). In this work, we take a step towards answering these questions by demonstrating the following: (a) On a test-bed with a variety of Boolean function classes, we find that Transformers can nearly match the optimal learning algorithm for 'simpler' tasks, while their performance deteriorates on more 'complex' tasks. Additionally, we find that certain attention-free models perform (almost) identically to Transformers on a range of tasks. (b) When provided a teaching sequence, i.e. a set of examples that uniquely identifies a function in a class, we show that Transformers learn more sample-efficiently. Interestingly, our results show that Transformers can learn to implement two distinct algorithms to solve a single task, and can adaptively select the more sample-efficient algorithm depending on the sequence of in-context examples. (c) Lastly, we show that extant LLMs, e.g. LLaMA-2, GPT-4, can compete with nearest-neighbor baselines on prediction tasks that are guaranteed to not be in their training set.

  • 4 authors
·
Oct 4, 2023