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Multimodal electronic health record (EHR) data can offer a holistic assessment of a patient's health status, supporting various predictive healthcare tasks. Recently, several studies have embraced the multitask learning approach in the healthcare domain, exploiting the inherent correlations among clinical tasks to predict multiple outcomes simultaneously. However, existing methods necessitate samples to possess complete labels for all tasks, which places heavy demands on the data and restricts the flexibility of the model. Meanwhile, within a multitask framework with multimodal inputs, how to comprehensively consider the information disparity among modalities and among tasks still remains a challenging problem. To tackle these issues, a unified healthcare prediction model, also named by \textbf{FlexCare}, is proposed to flexibly accommodate incomplete multimodal inputs, promoting the adaption to multiple healthcare tasks. The proposed model breaks the conventional paradigm of parallel multitask prediction by decomposing it into a series of asynchronous single-task prediction. Specifically, a task-agnostic multimodal information extraction module is presented to capture decorrelated representations of diverse intra- and inter-modality patterns. Taking full account of the information disparities between different modalities and different tasks, we present a task-guided hierarchical multimodal fusion module that integrates the refined modality-level representations into an individual patient-level representation. Experimental results on multiple tasks from MIMIC-IV/MIMIC-CXR/MIMIC-NOTE datasets demonstrate the effectiveness of the proposed method. Additionally, further analysis underscores the feasibility and potential of employing such a multitask strategy in the healthcare domain. The source code is available at https://github.com/mhxu1998/FlexCare., Comment: Accepted by KDD 2024 (Research Track)

The Mixture-of-Expert (MoE) technique plays a crucial role in expanding the size of DNN model parameters. However, it faces the challenge of extended all-to-all communication latency during the training process. Existing methods attempt to mitigate this issue by overlapping all-to-all with expert computation. Yet, these methods frequently fall short of achieving sufficient overlap, consequently restricting the potential for performance enhancements. In our study, we extend the scope of this challenge by considering overlap at the broader training graph level. During the forward pass, we enable non-MoE computations to overlap with all-to-all through careful partitioning and pipelining. In the backward pass, we achieve overlap with all-to-all by scheduling gradient weight computations. We implement these techniques in Lancet, a system using compiler-based optimization to automatically enhance MoE model training. Our extensive evaluation reveals that Lancet significantly reduces the time devoted to non-overlapping communication, by as much as 77%. Moreover, it achieves a notable end-to-end speedup of up to 1.3 times when compared to the state-of-the-art solutions., Comment: 11 pages, 16 figures. Published in MLSys'24

In the domain of dynamic graph representation learning (DGRL), the efficient and comprehensive capture of temporal evolution within real-world networks is crucial. Spiking Neural Networks (SNNs), known as their temporal dynamics and low-power characteristic, offer an efficient solution for temporal processing in DGRL task. However, owing to the spike-based information encoding mechanism of SNNs, existing DGRL methods employed SNNs face limitations in their representational capacity. Given this issue, we propose a novel framework named Spike-induced Graph Neural Network (SiGNN) for learning enhanced spatialtemporal representations on dynamic graphs. In detail, a harmonious integration of SNNs and GNNs is achieved through an innovative Temporal Activation (TA) mechanism. Benefiting from the TA mechanism, SiGNN not only effectively exploits the temporal dynamics of SNNs but also adeptly circumvents the representational constraints imposed by the binary nature of spikes. Furthermore, leveraging the inherent adaptability of SNNs, we explore an in-depth analysis of the evolutionary patterns within dynamic graphs across multiple time granularities. This approach facilitates the acquisition of a multiscale temporal node representation.Extensive experiments on various real-world dynamic graph datasets demonstrate the superior performance of SiGNN in the node classification task.

Fluid motion can be considered as a point cloud transformation when using the SPH method. Compared to traditional numerical analysis methods, using machine learning techniques to learn physics simulations can achieve near-accurate results, while significantly increasing efficiency. In this paper, we propose an innovative approach for 3D fluid simulations utilizing an Attention-based Dual-pipeline Network, which employs a dual-pipeline architecture, seamlessly integrated with an Attention-based Feature Fusion Module. Unlike previous methods, which often make difficult trade-offs between global fluid control and physical law constraints, we find a way to achieve a better balance between these two crucial aspects with a well-designed dual-pipeline approach. Additionally, we design a Type-aware Input Module to adaptively recognize particles of different types and perform feature fusion afterward, such that fluid-solid coupling issues can be better dealt with. Furthermore, we propose a new dataset, Tank3D, to further explore the network's ability to handle more complicated scenes. The experiments demonstrate that our approach not only attains a quantitative enhancement in various metrics, surpassing the state-of-the-art methods but also signifies a qualitative leap in neural network-based simulation by faithfully adhering to the physical laws. Code and video demonstrations are available at https://github.com/chenyu-xjtu/DualFluidNet., Comment: 14 pages

On-device memory concerns in distributed deep learning have become severe due to (i) the growth of model size in multi-GPU training, and (ii) the wide adoption of deep neural networks for federated learning on IoT devices which have limited storage. In such settings, communication efficient optimization methods are attractive alternatives, however they still struggle with memory issues. To tackle these challenges, we propose an communication efficient method called contractive error feedback (ConEF). As opposed to SGD with error-feedback (EFSGD) that inefficiently manages memory, ConEF obtains the sweet spot of convergence and memory usage, and achieves communication efficiency by leveraging biased and all-reducable gradient compression. We empirically validate ConEF on various learning tasks that include image classification, language modeling, and machine translation and observe that ConEF saves 80\% - 90\% of the extra memory in EFSGD with almost no loss on test performance, while also achieving 1.3x - 5x speedup of SGD. Through our work, we also demonstrate the feasibility and convergence of ConEF to clear up the theoretical barrier of integrating ConEF to popular memory efficient frameworks such as ZeRO-3.

Multi-task model training has been adopted to enable a single deep neural network model (often a large language model) to handle multiple tasks (e.g., question answering and text summarization). Multi-task training commonly receives input sequences of highly different lengths due to the diverse contexts of different tasks. Padding (to the same sequence length) or packing (short examples into long sequences of the same length) is usually adopted to prepare input samples for model training, which is nonetheless not space or computation efficient. This paper proposes a dynamic micro-batching approach to tackle sequence length variation and enable efficient multi-task model training. We advocate pipeline-parallel training of the large model with variable-length micro-batches, each of which potentially comprises a different number of samples. We optimize micro-batch construction using a dynamic programming-based approach, and handle micro-batch execution time variation through dynamic pipeline and communication scheduling, enabling highly efficient pipeline training. Extensive evaluation on the FLANv2 dataset demonstrates up to 4.39x higher training throughput when training T5, and 3.25x when training GPT, as compared with packing-based baselines. DynaPipe's source code is publicly available at https://github.com/awslabs/optimizing-multitask-training-through-dynamic-pipelines., Comment: 18 pages, 18 figures

Based on the message-passing paradigm, there has been an amount of research proposing diverse and impressive feature propagation mechanisms to improve the performance of GNNs. However, less focus has been put on feature transformation, another major operation of the message-passing framework. In this paper, we first empirically investigate the performance of the feature transformation operation in several typical GNNs. Unexpectedly, we notice that GNNs do not completely free up the power of the inherent feature transformation operation. By this observation, we propose the Bi-directional Knowledge Transfer (BiKT), a plug-and-play approach to unleash the potential of the feature transformation operations without modifying the original architecture. Taking the feature transformation operation as a derived representation learning model that shares parameters with the original GNN, the direct prediction by this model provides a topological-agnostic knowledge feedback that can further instruct the learning of GNN and the feature transformations therein. On this basis, BiKT not only allows us to acquire knowledge from both the GNN and its derived model but promotes each other by injecting the knowledge into the other. In addition, a theoretical analysis is further provided to demonstrate that BiKT improves the generalization bound of the GNNs from the perspective of domain adaption. An extensive group of experiments on up to 7 datasets with 5 typical GNNs demonstrates that BiKT brings up to 0.5% - 4% performance gain over the original GNN, which means a boosted GNN is obtained. Meanwhile, the derived model also shows a powerful performance to compete with or even surpass the original GNN, enabling us to flexibly apply it independently to some other specific downstream tasks., Comment: 13 pages, 9 figures

Point cloud analytics has become a critical workload for embedded and mobile platforms across various applications. Farthest point sampling (FPS) is a fundamental and widely used kernel in point cloud processing. However, the heavy external memory access makes FPS a performance bottleneck for real-time point cloud processing. Although bucket-based farthest point sampling can significantly reduce unnecessary memory accesses during the point sampling stage, the KD-tree construction stage becomes the predominant contributor to execution time. In this paper, we present FuseFPS, an architecture and algorithm co-design for bucket-based farthest point sampling. We first propose a hardware-friendly sampling-driven KD-tree construction algorithm. The algorithm fuses the KD-tree construction stage into the point sampling stage, further reducing memory accesses. Then, we design an efficient accelerator for bucket-based point sampling. The accelerator can offload the entire bucket-based FPS kernel at a low hardware cost. Finally, we evaluate our approach on various point cloud datasets. The detailed experiments show that compared to the state-of-the-art accelerator QuickFPS, FuseFPS achieves about 4.3$\times$ and about 6.1$\times$ improvements on speed and power efficiency, respectively., Comment: conference for ASP-DAC 2024

Transformers are central in modern natural language processing and computer vision applications. Despite recent works devoted to reducing the quadratic cost of such models (as a function of the sequence length), dealing with ultra long sequences (e.g., with more than 16K tokens) remains challenging. Applications such as answering questions based on a book or summarizing a scientific article are inefficient or infeasible. Here, we propose to significantly improve the efficiency of Transformers for ultra long sequences, by compressing the sequence into a much smaller representation at each layer. Specifically, by exploiting the fact that in many tasks, only a small subset of special tokens (we call VIP-tokens) are most relevant to the final prediction, we propose a VIP-token centric compression (VCC) scheme which selectively compresses the sequence based on their impact on approximating the representation of the VIP-tokens. Compared with competitive baselines, our algorithm is not only efficient (achieving more than $3\times$ efficiency gain compared to baselines on 4K and 16K lengths), but also offers competitive/better performance on a large number of tasks. Further, we show that our algorithm scales to 128K tokens (or more) while consistently offering accuracy improvement., Comment: 10 pages main text, 12 pages appendix, preprint

This work proposes POMP, a prompt pre-training method for vision-language models. Being memory and computation efficient, POMP enables the learned prompt to condense semantic information for a rich set of visual concepts with over twenty-thousand classes. Once pre-trained, the prompt with a strong transferable ability can be directly plugged into a variety of visual recognition tasks including image classification, semantic segmentation, and object detection, to boost recognition performances in a zero-shot manner. Empirical evaluation shows that POMP achieves state-of-the-art performances on 21 datasets, e.g., 67.0% average accuracy on 10 classification datasets (+3.1% compared to CoOp) and 84.4 hIoU on open-vocabulary Pascal VOC segmentation (+6.9 compared to ZSSeg). Our code is available at https://github.com/amazon-science/prompt-pretraining., Comment: Code is available at https://github.com/amazon-science/prompt-pretraining

Based on the Manhattan World assumption, most existing indoor layout estimation schemes focus on recovering layouts from vertically compressed 1D sequences. However, the compression procedure confuses the semantics of different planes, yielding inferior performance with ambiguous interpretability. To address this issue, we propose to disentangle this 1D representation by pre-segmenting orthogonal (vertical and horizontal) planes from a complex scene, explicitly capturing the geometric cues for indoor layout estimation. Considering the symmetry between the floor boundary and ceiling boundary, we also design a soft-flipping fusion strategy to assist the pre-segmentation. Besides, we present a feature assembling mechanism to effectively integrate shallow and deep features with distortion distribution awareness. To compensate for the potential errors in pre-segmentation, we further leverage triple attention to reconstruct the disentangled sequences for better performance. Experiments on four popular benchmarks demonstrate our superiority over existing SoTA solutions, especially on the 3DIoU metric. The code is available at \url{https://github.com/zhijieshen-bjtu/DOPNet}., Comment: Accepted to CVPR2023

Recent years have seen an increase in the development of large deep learning (DL) models, which makes training efficiency crucial. Common practice is struggling with the trade-off between usability and performance. On one hand, DL frameworks such as PyTorch use dynamic graphs to facilitate model developers at a price of sub-optimal model training performance. On the other hand, practitioners propose various approaches to improving the training efficiency by sacrificing some of the flexibility, ranging from making the graph static for more thorough optimization (e.g., XLA) to customizing optimization towards large-scale distributed training (e.g., DeepSpeed and Megatron-LM). In this paper, we aim to address the tension between usability and training efficiency through separation of concerns. Inspired by DL compilers that decouple the platform-specific optimizations of a tensor-level operator from its arithmetic definition, this paper proposes a schedule language, Slapo, to decouple model execution from definition. Specifically, Slapo works on a PyTorch model and uses a set of schedule primitives to convert the model for common model training optimizations such as high-performance kernels, effective 3D parallelism, and efficient activation checkpointing. Compared to existing optimization solutions, Slapo progressively optimizes the model "as-needed" through high-level primitives, and thus preserving programmability and debuggability for users to a large extent. Our evaluation results show that by scheduling the existing hand-crafted optimizations in a systematic way using Slapo, we are able to improve training throughput by up to 2.92x on a single machine with 8 NVIDIA V100 GPUs, and by up to 1.41x on multiple machines with up to 64 GPUs, when compared to the out-of-the-box performance of DeepSpeed and Megatron-LM., Comment: Accepted to ASPLOS'24

Pre-trained large language models can efficiently interpolate human-written prompts in a natural way. Multitask prompted learning can help generalization through a diverse set of tasks at once, thus enhancing the potential for more effective downstream fine-tuning. To perform efficient multitask-inference in the same batch, parameter-efficient fine-tuning methods such as prompt tuning have been proposed. However, the existing prompt tuning methods may lack generalization. We propose SPT, a semi-parametric prompt tuning method for multitask prompted learning. The novel component of SPT is a memory bank from where memory prompts are retrieved based on discrete prompts. Extensive experiments, such as (i) fine-tuning a full language model with SPT on 31 different tasks from 8 different domains and evaluating zero-shot generalization on 9 heldout datasets under 5 NLP task categories and (ii) pretraining SPT on the GLUE datasets and evaluating fine-tuning on the SuperGLUE datasets, demonstrate effectiveness of SPT.

The mixture of Expert (MoE) parallelism is a recent advancement that scales up the model size with constant computational cost. MoE selects different sets of parameters (i.e., experts) for each incoming token, resulting in a sparsely-activated model. Despite several successful applications of MoE, its training efficiency degrades significantly as the number of experts increases. The routing stage in MoE relies on the efficiency of the All2All communication collective, which suffers from network congestion and has poor scalability. To mitigate these issues, we introduce SMILE, which exploits heterogeneous network bandwidth and splits a single-step routing into bi-level routing. Our experimental results show that the proposed method obtains a 2.5x speedup over Switch Transformer in terms of pretraining throughput on the Colossal Clean Crawled Corpus without losing any convergence speed.

Graph neural networks (GNNs) have shown remarkable performance on homophilic graph data while being far less impressive when handling non-homophilic graph data due to the inherent low-pass filtering property of GNNs. In general, since real-world graphs are often complex mixtures of diverse subgraph patterns, learning a universal spectral filter on the graph from the global perspective as in most current works may still suffer from great difficulty in adapting to the variation of local patterns. On the basis of the theoretical analysis of local patterns, we rethink the existing spectral filtering methods and propose the node-oriented spectral filtering for graph neural network (namely NFGNN). By estimating the node-oriented spectral filter for each node, NFGNN is provided with the capability of precise local node positioning via the generalized translated operator, thus discriminating the variations of local homophily patterns adaptively. Meanwhile, the utilization of re-parameterization brings a good trade-off between global consistency and local sensibility for learning the node-oriented spectral filters. Furthermore, we theoretically analyze the localization property of NFGNN, demonstrating that the signal after adaptive filtering is still positioned around the corresponding node. Extensive experimental results demonstrate that the proposed NFGNN achieves more favorable performance., Comment: 15 pages, 10 figures, accepted by TPAMI

Existing out-of-distribution (OOD) detection methods are typically benchmarked on training sets with balanced class distributions. However, in real-world applications, it is common for the training sets to have long-tailed distributions. In this work, we first demonstrate that existing OOD detection methods commonly suffer from significant performance degradation when the training set is long-tail distributed. Through analysis, we posit that this is because the models struggle to distinguish the minority tail-class in-distribution samples, from the true OOD samples, making the tail classes more prone to be falsely detected as OOD. To solve this problem, we propose Partial and Asymmetric Supervised Contrastive Learning (PASCL), which explicitly encourages the model to distinguish between tail-class in-distribution samples and OOD samples. To further boost in-distribution classification accuracy, we propose Auxiliary Branch Finetuning, which uses two separate branches of BN and classification layers for anomaly detection and in-distribution classification, respectively. The intuition is that in-distribution and OOD anomaly data have different underlying distributions. Our method outperforms previous state-of-the-art method by $1.29\%$, $1.45\%$, $0.69\%$ anomaly detection false positive rate (FPR) and $3.24\%$, $4.06\%$, $7.89\%$ in-distribution classification accuracy on CIFAR10-LT, CIFAR100-LT, and ImageNet-LT, respectively. Code and pre-trained models are available at https://github.com/amazon-research/long-tailed-ood-detection., Comment: ICML 2022

Adversarial training (AT) defends deep neural networks against adversarial attacks. One challenge that limits its practical application is the performance degradation on clean samples. A major bottleneck identified by previous works is the widely used batch normalization (BN), which struggles to model the different statistics of clean and adversarial training samples in AT. Although the dominant approach is to extend BN to capture this mixture of distribution, we propose to completely eliminate this bottleneck by removing all BN layers in AT. Our normalizer-free robust training (NoFrost) method extends recent advances in normalizer-free networks to AT for its unexplored advantage on handling the mixture distribution challenge. We show that NoFrost achieves adversarial robustness with only a minor sacrifice on clean sample accuracy. On ImageNet with ResNet50, NoFrost achieves $74.06\%$ clean accuracy, which drops merely $2.00\%$ from standard training. In contrast, BN-based AT obtains $59.28\%$ clean accuracy, suffering a significant $16.78\%$ drop from standard training. In addition, NoFrost achieves a $23.56\%$ adversarial robustness against PGD attack, which improves the $13.57\%$ robustness in BN-based AT. We observe better model smoothness and larger decision margins from NoFrost, which make the models less sensitive to input perturbations and thus more robust. Moreover, when incorporating more data augmentations into NoFrost, it achieves comprehensive robustness against multiple distribution shifts. Code and pre-trained models are public at https://github.com/amazon-research/normalizer-free-robust-training., Comment: ICML 2022

We present results from a large-scale experiment on pretraining encoders with non-embedding parameter counts ranging from 700M to 9.3B, their subsequent distillation into smaller models ranging from 17M-170M parameters, and their application to the Natural Language Understanding (NLU) component of a virtual assistant system. Though we train using 70% spoken-form data, our teacher models perform comparably to XLM-R and mT5 when evaluated on the written-form Cross-lingual Natural Language Inference (XNLI) corpus. We perform a second stage of pretraining on our teacher models using in-domain data from our system, improving error rates by 3.86% relative for intent classification and 7.01% relative for slot filling. We find that even a 170M-parameter model distilled from our Stage 2 teacher model has 2.88% better intent classification and 7.69% better slot filling error rates when compared to the 2.3B-parameter teacher trained only on public data (Stage 1), emphasizing the importance of in-domain data for pretraining. When evaluated offline using labeled NLU data, our 17M-parameter Stage 2 distilled model outperforms both XLM-R Base (85M params) and DistillBERT (42M params) by 4.23% to 6.14%, respectively. Finally, we present results from a full virtual assistant experimentation platform, where we find that models trained using our pretraining and distillation pipeline outperform models distilled from 85M-parameter teachers by 3.74%-4.91% on an automatic measurement of full-system user dissatisfaction., Comment: KDD 2022

Existing general purpose frameworks for gigantic model training, i.e., dense models with billions of parameters, cannot scale efficiently on cloud environment with various networking conditions due to large communication overheads. In this paper, we propose MiCS, which Minimizes the Communication Scale to bring down communication overhead. Specifically, by decreasing the number of participants in a communication collective, MiCS can utilize heterogeneous network bandwidth, reduce network traffic over slower links, reduce the latency of communications for maintaining high network bandwidth utilization, and amortize expensive global gradient synchronization overhead. Our evaluation on AWS shows that the system throughput of MiCS is up to 2.89$\times$ that of the state-of-the-art large model training systems. MiCS achieves near-linear scaling efficiency, which is up to 1.27$\times$ that of DeepSpeed. MiCS allows us to train a proprietary model with 100 billion parameters on 512 GPUs with 99.4% weak-scaling efficiency, and it is able to saturate over 54.5% theoretical computation power of each GPU on a public cloud with less GPU memory and more restricted networks than DGX-A100 clusters.

Benefiting from the powerful expressive capability of graphs, graph-based approaches have been popularly applied to handle multi-modal medical data and achieved impressive performance in various biomedical applications. For disease prediction tasks, most existing graph-based methods tend to define the graph manually based on specified modality (e.g., demographic information), and then integrated other modalities to obtain the patient representation by Graph Representation Learning (GRL). However, constructing an appropriate graph in advance is not a simple matter for these methods. Meanwhile, the complex correlation between modalities is ignored. These factors inevitably yield the inadequacy of providing sufficient information about the patient's condition for a reliable diagnosis. To this end, we propose an end-to-end Multi-modal Graph Learning framework (MMGL) for disease prediction with multi-modality. To effectively exploit the rich information across multi-modality associated with the disease, modality-aware representation learning is proposed to aggregate the features of each modality by leveraging the correlation and complementarity between the modalities. Furthermore, instead of defining the graph manually, the latent graph structure is captured through an effective way of adaptive graph learning. It could be jointly optimized with the prediction model, thus revealing the intrinsic connections among samples. Our model is also applicable to the scenario of inductive learning for those unseen data. An extensive group of experiments on two disease prediction tasks demonstrates that the proposed MMGL achieves more favorable performance. The code of MMGL is available at \url{https://github.com/SsGood/MMGL}., Comment: Published by IEEE TMI

Recent approaches have shown that training deep neural networks directly on large-scale image-text pair collections enables zero-shot transfer on various recognition tasks. One central issue is how this can be generalized to object detection, which involves the non-semantic task of localization as well as semantic task of classification. To solve this problem, we introduce a vision-language embedding alignment method that transfers the generalization capabilities of a pretrained model such as CLIP to an object detector like YOLOv5. We formulate a loss function that allows us to align the image and text embeddings from the pretrained model CLIP with the modified semantic prediction head from the detector. With this method, we are able to train an object detector that achieves state-of-the-art performance on the COCO, ILSVRC, and Visual Genome zero-shot detection benchmarks. During inference, our model can be adapted to detect any number of object classes without additional training. We also find that standard object detection scaling can transfer well to our method and find consistent improvements across various scales of YOLOv5 models and the YOLOv3 model. Lastly, we develop a self-labeling method that provides a significant score improvement without needing extra images nor labels., Comment: Code: https://github.com/Johnathan-Xie/ZSD-YOLO