new

Get trending papers in your email inbox!

Subscribe

Daily Papers

byAK and the research community

Nov 24

SliceGPT: Compress Large Language Models by Deleting Rows and Columns

Large language models have become the cornerstone of natural language processing, but their use comes with substantial costs in terms of compute and memory resources. Sparsification provides a solution to alleviate these resource constraints, and recent works have shown that trained models can be sparsified post-hoc. Existing sparsification techniques face challenges as they need additional data structures and offer constrained speedup with current hardware. In this paper we present SliceGPT, a new post-training sparsification scheme which replaces each weight matrix with a smaller (dense) matrix, reducing the embedding dimension of the network. Through extensive experimentation, we show that SliceGPT can remove up to 25% of the model parameters (including embeddings) for LLAMA2-70B, OPT 66B and Phi-2 models while maintaining 99%, 99% and 90% zero-shot task performance of the dense model respectively. Our sliced models run on fewer GPUs and run faster without any additional code optimization: on 24GB consumer GPUs we reduce the total compute for inference on LLAMA2-70B to 64% of that of the dense model; on 40GB A100 GPUs we reduce it to 66%. We offer a new insight, computational invariance in transformer networks, which enables SliceGPT and we hope it will inspire and enable future avenues to reduce memory and computation demands for pre-trained models. Code is available at: https://github.com/microsoft/TransformerCompression

  • 5 authors
Jan 26, 2024 6

SlimMoE: Structured Compression of Large MoE Models via Expert Slimming and Distillation

The Mixture of Experts (MoE) architecture has emerged as a powerful paradigm for scaling large language models (LLMs) while maintaining inference efficiency. However, their enormous memory requirements make them prohibitively expensive to fine-tune or deploy in resource-constrained environments. To address this challenge, we introduce SlimMoE, a multi-stage compression framework for transforming large MoE models into much smaller, efficient variants without incurring the prohibitive costs of training from scratch. Our method systematically reduces parameter counts by slimming experts and transferring knowledge through intermediate stages, effectively mitigating the performance degradation common in one-shot pruning approaches. Using this framework, we compress Phi 3.5-MoE (41.9B total/6.6B activated parameters) to create Phi-mini-MoE (7.6B total/2.4B activated parameters) and Phi-tiny-MoE (3.8B total/1.1B activated parameters) using only 400B tokens--less than 10% of the original model's training data. These compressed models can be fine-tuned on a single GPU (A100 for Phi-mini-MoE, A6000 for Phi-tiny-MoE), making them highly suitable for academic and resource-limited settings. Our experiments demonstrate that these compressed models outperform others of similar size and remain competitive with larger models. For instance, Phi-mini-MoE achieves similar or better performance to Phi-3-mini using only 2/3 of the activated parameters and yields comparable MMLU scores to Llama 3.1 8B despite having significantly lower latency. Our findings demonstrate that structured pruning combined with staged distillation offers an effective path to creating high-quality, compact MoE models, paving the way for broader adoption of MoE architectures. We make our models publicly available at https://huggingface.co/microsoft/Phi-mini-MoE-instruct and https://huggingface.co/microsoft/Phi-tiny-MoE-instruct .

  • 7 authors
Jun 23 2

SlimPajama-DC: Understanding Data Combinations for LLM Training

This paper aims to understand the impacts of various data combinations (e.g., web text, wikipedia, github, books) on the training of large language models using SlimPajama. SlimPajama is a rigorously deduplicated, multi-source dataset, which has been refined and further deduplicated to 627B tokens from the extensive 1.2T tokens RedPajama dataset contributed by Together. We've termed our research as SlimPajama-DC, an empirical analysis designed to uncover fundamental characteristics and best practices associated with employing SlimPajama in the training of large language models. During our research with SlimPajama, two pivotal observations emerged: (1) Global deduplication vs. local deduplication. We analyze and discuss how global (across different sources of datasets) and local (within the single source of dataset) deduplications affect the performance of trained models. (2) Proportions of high-quality/highly-deduplicated multi-source datasets in the combination. To study this, we construct six configurations of SlimPajama dataset and train individual ones using 1.3B Cerebras-GPT model with Alibi and SwiGLU. Our best configuration outperforms the 1.3B model trained on RedPajama using the same number of training tokens by a significant margin. All our 1.3B models are trained on Cerebras 16times CS-2 cluster with a total of 80 PFLOP/s in bf16 mixed precision. We further extend our discoveries (such as increasing data diversity is crucial after global deduplication) on a 7B model with large batch-size training. Our models and the separate SlimPajama-DC datasets are available at: https://huggingface.co/MBZUAI-LLM and https://huggingface.co/datasets/cerebras/SlimPajama-627B.

  • 8 authors
Sep 19, 2023 1

SliderEdit: Continuous Image Editing with Fine-Grained Instruction Control

Instruction-based image editing models have recently achieved impressive performance, enabling complex edits to an input image from a multi-instruction prompt. However, these models apply each instruction in the prompt with a fixed strength, limiting the user's ability to precisely and continuously control the intensity of individual edits. We introduce SliderEdit, a framework for continuous image editing with fine-grained, interpretable instruction control. Given a multi-part edit instruction, SliderEdit disentangles the individual instructions and exposes each as a globally trained slider, allowing smooth adjustment of its strength. Unlike prior works that introduced slider-based attribute controls in text-to-image generation, typically requiring separate training or fine-tuning for each attribute or concept, our method learns a single set of low-rank adaptation matrices that generalize across diverse edits, attributes, and compositional instructions. This enables continuous interpolation along individual edit dimensions while preserving both spatial locality and global semantic consistency. We apply SliderEdit to state-of-the-art image editing models, including FLUX-Kontext and Qwen-Image-Edit, and observe substantial improvements in edit controllability, visual consistency, and user steerability. To the best of our knowledge, we are the first to explore and propose a framework for continuous, fine-grained instruction control in instruction-based image editing models. Our results pave the way for interactive, instruction-driven image manipulation with continuous and compositional control.

  • 6 authors
Nov 12 2

Sliding Windows Are Not the End: Exploring Full Ranking with Long-Context Large Language Models

Large Language Models (LLMs) have shown exciting performance in listwise passage ranking. Due to the limited input length, existing methods often adopt the sliding window strategy. Such a strategy, though effective, is inefficient as it involves repetitive and serialized processing, which usually re-evaluates relevant passages multiple times. As a result, it incurs redundant API costs, which are proportional to the number of inference tokens. The development of long-context LLMs enables the full ranking of all passages within a single inference, avoiding redundant API costs. In this paper, we conduct a comprehensive study of long-context LLMs for ranking tasks in terms of efficiency and effectiveness. Surprisingly, our experiments reveal that full ranking with long-context LLMs can deliver superior performance in the supervised fine-tuning setting with a huge efficiency improvement. Furthermore, we identify two limitations of fine-tuning the full ranking model based on existing methods: (1) sliding window strategy fails to produce a full ranking list as a training label, and (2) the language modeling loss cannot emphasize top-ranked passage IDs in the label. To alleviate these issues, we propose a new complete listwise label construction approach and a novel importance-aware learning objective for full ranking. Experiments show the superior performance of our method over baselines. Our codes are available at https://github.com/8421BCD/fullrank.

  • 7 authors
Dec 19, 2024

SlideChat: A Large Vision-Language Assistant for Whole-Slide Pathology Image Understanding

Despite the progress made by multimodal large language models (MLLMs) in computational pathology, they remain limited by a predominant focus on patch-level analysis, missing essential contextual information at the whole-slide level. The lack of large-scale instruction datasets and the gigapixel scale of whole slide images (WSIs) pose significant developmental challenges. In this paper, we present SlideChat, the first vision-language assistant capable of understanding gigapixel whole-slide images, exhibiting excellent multimodal conversational capability and response complex instruction across diverse pathology scenarios. To support its development, we created SlideInstruction, the largest instruction-following dataset for WSIs consisting of 4.2K WSI captions and 176K VQA pairs with multiple categories. Furthermore, we propose SlideBench, a multimodal benchmark that incorporates captioning and VQA tasks to assess SlideChat's capabilities in varied clinical settings such as microscopy, diagnosis. Compared to both general and specialized MLLMs, SlideChat exhibits exceptional capabilities achieving state-of-the-art performance on 18 of 22 tasks. For example, it achieved an overall accuracy of 81.17% on SlideBench-VQA (TCGA), and 54.15% on SlideBench-VQA (BCNB). We will fully release SlideChat, SlideInstruction and SlideBench as open-source resources to facilitate research and development in computational pathology.

  • 11 authors
Oct 15, 2024

0.1% Data Makes Segment Anything Slim

The formidable model size and demanding computational requirements of Segment Anything Model (SAM) have rendered it cumbersome for deployment on resource-constrained devices. Existing approaches for SAM compression typically involve training a new network from scratch, posing a challenging trade-off between compression costs and model performance. To address this issue, this paper introduces SlimSAM, a novel SAM compression method that achieves superior performance with remarkably low training costs. This is achieved by the efficient reuse of pre-trained SAMs through a unified pruning-distillation framework. To enhance knowledge inheritance from the original SAM, we employ an innovative alternate slimming strategy that partitions the compression process into a progressive procedure. Diverging from prior pruning techniques, we meticulously prune and distill decoupled model structures in an alternating fashion. Furthermore, a novel label-free pruning criterion is also proposed to align the pruning objective with the optimization target, thereby boosting the post-distillation after pruning. SlimSAM yields significant performance improvements while demanding over 10 times less training costs than any other existing methods. Even when compared to the original SAM-H, SlimSAM achieves approaching performance while reducing parameter counts to merely 0.9% (5.7M), MACs to 0.8% (21G), and requiring only 0.1% (10k) of the SAM training data. Code is available at url{http://github.com/czg1225/SlimSAM}.

  • 4 authors
Dec 8, 2023

Slimmable Encoders for Flexible Split DNNs in Bandwidth and Resource Constrained IoT Systems

The execution of large deep neural networks (DNN) at mobile edge devices requires considerable consumption of critical resources, such as energy, while imposing demands on hardware capabilities. In approaches based on edge computing the execution of the models is offloaded to a compute-capable device positioned at the edge of 5G infrastructures. The main issue of the latter class of approaches is the need to transport information-rich signals over wireless links with limited and time-varying capacity. The recent split computing paradigm attempts to resolve this impasse by distributing the execution of DNN models across the layers of the systems to reduce the amount of data to be transmitted while imposing minimal computing load on mobile devices. In this context, we propose a novel split computing approach based on slimmable ensemble encoders. The key advantage of our design is the ability to adapt computational load and transmitted data size in real-time with minimal overhead and time. This is in contrast with existing approaches, where the same adaptation requires costly context switching and model loading. Moreover, our model outperforms existing solutions in terms of compression efficacy and execution time, especially in the context of weak mobile devices. We present a comprehensive comparison with the most advanced split computing solutions, as well as an experimental evaluation on GPU-less devices.

  • 4 authors
Jun 22, 2023

SlimFit: Memory-Efficient Fine-Tuning of Transformer-based Models Using Training Dynamics

Transformer-based models, such as BERT and ViT, have achieved state-of-the-art results across different natural language processing (NLP) and computer vision (CV) tasks. However, these models are extremely memory intensive during their fine-tuning process, making them difficult to deploy on GPUs with limited memory resources. To address this issue, we introduce a new tool called SlimFit that reduces the memory requirements of these models by dynamically analyzing their training dynamics and freezing less-contributory layers during fine-tuning. The layers to freeze are chosen using a runtime inter-layer scheduling algorithm. SlimFit adopts quantization and pruning for particular layers to balance the load of dynamic activations and to minimize the memory footprint of static activations, where static activations refer to those that cannot be discarded regardless of freezing. This allows SlimFit to freeze up to 95% of layers and reduce the overall on-device GPU memory usage of transformer-based models such as ViT and BERT by an average of 2.2x, across different NLP and CV benchmarks/datasets such as GLUE, SQuAD 2.0, CIFAR-10, CIFAR-100 and ImageNet with an average degradation of 0.2% in accuracy. For such NLP and CV tasks, SlimFit can reduce up to 3.1x the total on-device memory usage with an accuracy degradation of only up to 0.4%. As a result, while fine-tuning of ViT on ImageNet and BERT on SQuAD 2.0 with a batch size of 128 requires 3 and 2 32GB GPUs respectively, SlimFit enables their fine-tuning on a single 32GB GPU without any significant accuracy degradation.

  • 7 authors
May 29, 2023

SliM-LLM: Salience-Driven Mixed-Precision Quantization for Large Language Models

Large language models (LLMs) achieve remarkable performance in natural language understanding but require substantial computation and memory resources. Post-training quantization (PTQ) is a powerful compression technique extensively investigated in LLMs. However, existing PTQ methods are still not ideal in terms of accuracy and efficiency, especially with below 4 bit-widths. Standard PTQ methods using group-wise quantization suffer difficulties in quantizing LLMs accurately to such low-bit, but advanced methods remaining high-precision weights element-wisely are hard to realize their theoretical hardware efficiency. This paper presents a Salience-Driven Mixed-Precision Quantization scheme for LLMs, namely SliM-LLM. The scheme exploits the salience distribution of weights to determine optimal bit-width and quantizers for accurate LLM quantization, while aligning bit-width partition to groups for compact memory usage and fast integer inference. Specifically, the proposed SliM-LLM mainly relies on two novel techniques: (1) Salience-Determined Bit Allocation utilizes the clustering characteristics of salience distribution to allocate the bit-widths of each group, increasing the accuracy of quantized LLMs and maintaining the inference efficiency; (2) Salience-Weighted Quantizer Calibration optimizes the parameters of the quantizer by considering the element-wise salience within the group, balancing the maintenance of salient information and minimization of errors. Comprehensive experiments show that SliM-LLM significantly improves the accuracy of LLMs at ultra-low bits, e.g., 2-bit LLaMA-7B achieves a 5.5-times memory-saving than original model on NVIDIA A800 GPUs, and 48% decrease of perplexity compared to the state-of-the-art gradient-free PTQ method. Moreover, SliM-LLM+, which is integrated from the extension of SliM-LLM with gradient-based quantizers, further reduces perplexity by 35.1%.

  • 8 authors
May 23, 2024

Sliced Recursive Transformer

We present a neat yet effective recursive operation on vision transformers that can improve parameter utilization without involving additional parameters. This is achieved by sharing weights across the depth of transformer networks. The proposed method can obtain a substantial gain (~2%) simply using naive recursive operation, requires no special or sophisticated knowledge for designing principles of networks, and introduces minimal computational overhead to the training procedure. To reduce the additional computation caused by recursive operation while maintaining the superior accuracy, we propose an approximating method through multiple sliced group self-attentions across recursive layers which can reduce the cost consumption by 10~30% with minimal performance loss. We call our model Sliced Recursive Transformer (SReT), a novel and parameter-efficient vision transformer design that is compatible with a broad range of other designs for efficient ViT architectures. Our best model establishes significant improvement on ImageNet-1K over state-of-the-art methods while containing fewer parameters. The proposed weight sharing mechanism by sliced recursion structure allows us to build a transformer with more than 100 or even 1000 shared layers with ease while keeping a compact size (13~15M), to avoid optimization difficulties when the model is too large. The flexible scalability has shown great potential for scaling up models and constructing extremely deep vision transformers. Code is available at https://github.com/szq0214/SReT.

  • 3 authors
Nov 9, 2021

SlimFlow: Training Smaller One-Step Diffusion Models with Rectified Flow

Diffusion models excel in high-quality generation but suffer from slow inference due to iterative sampling. While recent methods have successfully transformed diffusion models into one-step generators, they neglect model size reduction, limiting their applicability in compute-constrained scenarios. This paper aims to develop small, efficient one-step diffusion models based on the powerful rectified flow framework, by exploring joint compression of inference steps and model size. The rectified flow framework trains one-step generative models using two operations, reflow and distillation. Compared with the original framework, squeezing the model size brings two new challenges: (1) the initialization mismatch between large teachers and small students during reflow; (2) the underperformance of naive distillation on small student models. To overcome these issues, we propose Annealing Reflow and Flow-Guided Distillation, which together comprise our SlimFlow framework. With our novel framework, we train a one-step diffusion model with an FID of 5.02 and 15.7M parameters, outperforming the previous state-of-the-art one-step diffusion model (FID=6.47, 19.4M parameters) on CIFAR10. On ImageNet 64times64 and FFHQ 64times64, our method yields small one-step diffusion models that are comparable to larger models, showcasing the effectiveness of our method in creating compact, efficient one-step diffusion models.

  • 3 authors
Jul 17, 2024

Slight Corruption in Pre-training Data Makes Better Diffusion Models

Diffusion models (DMs) have shown remarkable capabilities in generating realistic high-quality images, audios, and videos. They benefit significantly from extensive pre-training on large-scale datasets, including web-crawled data with paired data and conditions, such as image-text and image-class pairs. Despite rigorous filtering, these pre-training datasets often inevitably contain corrupted pairs where conditions do not accurately describe the data. This paper presents the first comprehensive study on the impact of such corruption in pre-training data of DMs. We synthetically corrupt ImageNet-1K and CC3M to pre-train and evaluate over 50 conditional DMs. Our empirical findings reveal that various types of slight corruption in pre-training can significantly enhance the quality, diversity, and fidelity of the generated images across different DMs, both during pre-training and downstream adaptation stages. Theoretically, we consider a Gaussian mixture model and prove that slight corruption in the condition leads to higher entropy and a reduced 2-Wasserstein distance to the ground truth of the data distribution generated by the corruptly trained DMs. Inspired by our analysis, we propose a simple method to improve the training of DMs on practical datasets by adding condition embedding perturbations (CEP). CEP significantly improves the performance of various DMs in both pre-training and downstream tasks. We hope that our study provides new insights into understanding the data and pre-training processes of DMs.

  • 9 authors
May 30, 2024

SLIM: Skill Learning with Multiple Critics

Self-supervised skill learning aims to acquire useful behaviors that leverage the underlying dynamics of the environment. Latent variable models, based on mutual information maximization, have been successful in this task but still struggle in the context of robotic manipulation. As it requires impacting a possibly large set of degrees of freedom composing the environment, mutual information maximization fails alone in producing useful and safe manipulation behaviors. Furthermore, tackling this by augmenting skill discovery rewards with additional rewards through a naive combination might fail to produce desired behaviors. To address this limitation, we introduce SLIM, a multi-critic learning approach for skill discovery with a particular focus on robotic manipulation. Our main insight is that utilizing multiple critics in an actor-critic framework to gracefully combine multiple reward functions leads to a significant improvement in latent-variable skill discovery for robotic manipulation while overcoming possible interference occurring among rewards which hinders convergence to useful skills. Furthermore, in the context of tabletop manipulation, we demonstrate the applicability of our novel skill discovery approach to acquire safe and efficient motor primitives in a hierarchical reinforcement learning fashion and leverage them through planning, significantly surpassing baseline approaches for skill discovery.

  • 4 authors
Feb 1, 2024

Sliced Wasserstein Estimation with Control Variates

The sliced Wasserstein (SW) distances between two probability measures are defined as the expectation of the Wasserstein distance between two one-dimensional projections of the two measures. The randomness comes from a projecting direction that is used to project the two input measures to one dimension. Due to the intractability of the expectation, Monte Carlo integration is performed to estimate the value of the SW distance. Despite having various variants, there has been no prior work that improves the Monte Carlo estimation scheme for the SW distance in terms of controlling its variance. To bridge the literature on variance reduction and the literature on the SW distance, we propose computationally efficient control variates to reduce the variance of the empirical estimation of the SW distance. The key idea is to first find Gaussian approximations of projected one-dimensional measures, then we utilize the closed-form of the Wasserstein-2 distance between two Gaussian distributions to design the control variates. In particular, we propose using a lower bound and an upper bound of the Wasserstein-2 distance between two fitted Gaussians as two computationally efficient control variates. We empirically show that the proposed control variate estimators can help to reduce the variance considerably when comparing measures over images and point-clouds. Finally, we demonstrate the favorable performance of the proposed control variate estimators in gradient flows to interpolate between two point-clouds and in deep generative modeling on standard image datasets, such as CIFAR10 and CelebA.

  • 2 authors
Apr 30, 2023

SLING: Sino Linguistic Evaluation of Large Language Models

To understand what kinds of linguistic knowledge are encoded by pretrained Chinese language models (LMs), we introduce the benchmark of Sino LINGuistics (SLING), which consists of 38K minimal sentence pairs in Mandarin Chinese grouped into 9 high-level linguistic phenomena. Each pair demonstrates the acceptability contrast of a specific syntactic or semantic phenomenon (e.g., The keys are lost vs. The keys is lost), and an LM should assign lower perplexity to the acceptable sentence. In contrast to the CLiMP dataset (Xiang et al., 2021), which also contains Chinese minimal pairs and was created by translating the vocabulary of the English BLiMP dataset, the minimal pairs in SLING are derived primarily by applying syntactic and lexical transformations to naturally-occurring, linguist-annotated sentences from the Chinese Treebank 9.0, thus addressing severe issues in CLiMP's data generation process. We test 18 publicly available pretrained monolingual (e.g., BERT-base-zh, CPM) and multi-lingual (e.g., mT5, XLM) language models on SLING. Our experiments show that the average accuracy for LMs is far below human performance (69.7% vs. 97.1%), while BERT-base-zh achieves the highest accuracy (84.8%) of all tested LMs, even much larger ones. Additionally, we find that most LMs have a strong gender and number (singular/plural) bias, and they perform better on local phenomena than hierarchical ones.

  • 4 authors
Oct 20, 2022

LADDER: Language Driven Slice Discovery and Error Rectification

Error slice discovery is crucial to diagnose and mitigate model errors. Current clustering or discrete attribute-based slice discovery methods face key limitations: 1) clustering results in incoherent slices, while assigning discrete attributes to slices leads to incomplete coverage of error patterns due to missing or insufficient attributes; 2) these methods lack complex reasoning, preventing them from fully explaining model biases; 3) they fail to integrate domain knowledge, limiting their usage in specialized fields \eg radiology. We propose\ladder (Language-Driven Discovery and Error Rectification), to address the limitations by: (1) leveraging the flexibility of natural language to address incompleteness, (2) employing LLM's latent domain knowledge and advanced reasoning to analyze sentences and derive testable hypotheses directly, identifying biased attributes, and form coherent error slices without clustering. Existing mitigation methods typically address only the worst-performing group, often amplifying errors in other subgroups. In contrast,\ladder generates pseudo attributes from the discovered hypotheses to mitigate errors across all biases without explicit attribute annotations or prior knowledge of bias. Rigorous evaluations on 6 datasets spanning natural and medical images -- comparing 200+ classifiers with diverse architectures, pretraining strategies, and LLMs -- show that\ladder consistently outperforms existing baselines in discovering and mitigating biases.

BostonU Boston University
Jul 31, 2024

GNN-ViTCap: GNN-Enhanced Multiple Instance Learning with Vision Transformers for Whole Slide Image Classification and Captioning

Microscopic assessment of histopathology images is vital for accurate cancer diagnosis and treatment. Whole Slide Image (WSI) classification and captioning have become crucial tasks in computer-aided pathology. However, microscopic WSI face challenges such as redundant patches and unknown patch positions due to subjective pathologist captures. Moreover, generating automatic pathology captions remains a significant challenge. To address these issues, we introduce a novel GNN-ViTCap framework for classification and caption generation from histopathological microscopic images. First, a visual feature extractor generates patch embeddings. Redundant patches are then removed by dynamically clustering these embeddings using deep embedded clustering and selecting representative patches via a scalar dot attention mechanism. We build a graph by connecting each node to its nearest neighbors in the similarity matrix and apply a graph neural network to capture both local and global context. The aggregated image embeddings are projected into the language model's input space through a linear layer and combined with caption tokens to fine-tune a large language model. We validate our method on the BreakHis and PatchGastric datasets. GNN-ViTCap achieves an F1 score of 0.934 and an AUC of 0.963 for classification, along with a BLEU-4 score of 0.811 and a METEOR score of 0.569 for captioning. Experimental results demonstrate that GNN-ViTCap outperforms state of the art approaches, offering a reliable and efficient solution for microscopy based patient diagnosis.

  • 5 authors
Jul 9

Revisiting End-to-End Learning with Slide-level Supervision in Computational Pathology

Pre-trained encoders for offline feature extraction followed by multiple instance learning (MIL) aggregators have become the dominant paradigm in computational pathology (CPath), benefiting cancer diagnosis and prognosis. However, performance limitations arise from the absence of encoder fine-tuning for downstream tasks and disjoint optimization with MIL. While slide-level supervised end-to-end (E2E) learning is an intuitive solution to this issue, it faces challenges such as high computational demands and suboptimal results. These limitations motivate us to revisit E2E learning. We argue that prior work neglects inherent E2E optimization challenges, leading to performance disparities compared to traditional two-stage methods. In this paper, we pioneer the elucidation of optimization challenge caused by sparse-attention MIL and propose a novel MIL called ABMILX. It mitigates this problem through global correlation-based attention refinement and multi-head mechanisms. With the efficient multi-scale random patch sampling strategy, an E2E trained ResNet with ABMILX surpasses SOTA foundation models under the two-stage paradigm across multiple challenging benchmarks, while remaining computationally efficient (<10 RTX3090 hours). We show the potential of E2E learning in CPath and calls for greater research focus in this area. The code is https://github.com/DearCaat/E2E-WSI-ABMILX.

  • 7 authors
Jun 2 1

Self-slimmed Vision Transformer

Vision transformers (ViTs) have become the popular structures and outperformed convolutional neural networks (CNNs) on various vision tasks. However, such powerful transformers bring a huge computation burden, because of the exhausting token-to-token comparison. The previous works focus on dropping insignificant tokens to reduce the computational cost of ViTs. But when the dropping ratio increases, this hard manner will inevitably discard the vital tokens, which limits its efficiency. To solve the issue, we propose a generic self-slimmed learning approach for vanilla ViTs, namely SiT. Specifically, we first design a novel Token Slimming Module (TSM), which can boost the inference efficiency of ViTs by dynamic token aggregation. As a general method of token hard dropping, our TSM softly integrates redundant tokens into fewer informative ones. It can dynamically zoom visual attention without cutting off discriminative token relations in the images, even with a high slimming ratio. Furthermore, we introduce a concise Feature Recalibration Distillation (FRD) framework, wherein we design a reverse version of TSM (RTSM) to recalibrate the unstructured token in a flexible auto-encoder manner. Due to the similar structure between teacher and student, our FRD can effectively leverage structure knowledge for better convergence. Finally, we conduct extensive experiments to evaluate our SiT. It demonstrates that our method can speed up ViTs by 1.7x with negligible accuracy drop, and even speed up ViTs by 3.6x while maintaining 97% of their performance. Surprisingly, by simply arming LV-ViT with our SiT, we achieve new state-of-the-art performance on ImageNet. Code is available at https://github.com/Sense-X/SiT.

  • 7 authors
Nov 24, 2021

PRISM: A Multi-Modal Generative Foundation Model for Slide-Level Histopathology

Foundation models in computational pathology promise to unlock the development of new clinical decision support systems and models for precision medicine. However, there is a mismatch between most clinical analysis, which is defined at the level of one or more whole slide images, and foundation models to date, which process the thousands of image tiles contained in a whole slide image separately. The requirement to train a network to aggregate information across a large number of tiles in multiple whole slide images limits these models' impact. In this work, we present a slide-level foundation model for H&E-stained histopathology, PRISM, that builds on Virchow tile embeddings and leverages clinical report text for pre-training. Using the tile embeddings, PRISM produces slide-level embeddings with the ability to generate clinical reports, resulting in several modes of use. Using text prompts, PRISM achieves zero-shot cancer detection and sub-typing performance approaching and surpassing that of a supervised aggregator model. Using the slide embeddings with linear classifiers, PRISM surpasses supervised aggregator models. Furthermore, we demonstrate that fine-tuning of the PRISM slide encoder yields label-efficient training for biomarker prediction, a task that typically suffers from low availability of training data; an aggregator initialized with PRISM and trained on as little as 10% of the training data can outperform a supervised baseline that uses all of the data.

  • 22 authors
May 16, 2024

A slice classification neural network for automated classification of axial PET/CT slices from a multi-centric lymphoma dataset

Automated slice classification is clinically relevant since it can be incorporated into medical image segmentation workflows as a preprocessing step that would flag slices with a higher probability of containing tumors, thereby directing physicians attention to the important slices. In this work, we train a ResNet-18 network to classify axial slices of lymphoma PET/CT images (collected from two institutions) depending on whether the slice intercepted a tumor (positive slice) in the 3D image or if the slice did not (negative slice). Various instances of the network were trained on 2D axial datasets created in different ways: (i) slice-level split and (ii) patient-level split; inputs of different types were used: (i) only PET slices and (ii) concatenated PET and CT slices; and different training strategies were employed: (i) center-aware (CAW) and (ii) center-agnostic (CAG). Model performances were compared using the area under the receiver operating characteristic curve (AUROC) and the area under the precision-recall curve (AUPRC), and various binary classification metrics. We observe and describe a performance overestimation in the case of slice-level split as compared to the patient-level split training. The model trained using patient-level split data with the network input containing only PET slices in the CAG training regime was the best performing/generalizing model on a majority of metrics. Our models were additionally more closely compared using the sensitivity metric on the positive slices from their respective test sets.

  • 8 authors
Mar 11, 2024

ConSlide: Asynchronous Hierarchical Interaction Transformer with Breakup-Reorganize Rehearsal for Continual Whole Slide Image Analysis

Whole slide image (WSI) analysis has become increasingly important in the medical imaging community, enabling automated and objective diagnosis, prognosis, and therapeutic-response prediction. However, in clinical practice, the ever-evolving environment hamper the utility of WSI analysis models. In this paper, we propose the FIRST continual learning framework for WSI analysis, named ConSlide, to tackle the challenges of enormous image size, utilization of hierarchical structure, and catastrophic forgetting by progressive model updating on multiple sequential datasets. Our framework contains three key components. The Hierarchical Interaction Transformer (HIT) is proposed to model and utilize the hierarchical structural knowledge of WSI. The Breakup-Reorganize (BuRo) rehearsal method is developed for WSI data replay with efficient region storing buffer and WSI reorganizing operation. The asynchronous updating mechanism is devised to encourage the network to learn generic and specific knowledge respectively during the replay stage, based on a nested cross-scale similarity learning (CSSL) module. We evaluated the proposed ConSlide on four public WSI datasets from TCGA projects. It performs best over other state-of-the-art methods with a fair WSI-based continual learning setting and achieves a better trade-off of the overall performance and forgetting on previous task

  • 6 authors
Aug 25, 2023

Self-Attention Amortized Distributional Projection Optimization for Sliced Wasserstein Point-Cloud Reconstruction

Max sliced Wasserstein (Max-SW) distance has been widely known as a solution for less discriminative projections of sliced Wasserstein (SW) distance. In applications that have various independent pairs of probability measures, amortized projection optimization is utilized to predict the ``max" projecting directions given two input measures instead of using projected gradient ascent multiple times. Despite being efficient, Max-SW and its amortized version cannot guarantee metricity property due to the sub-optimality of the projected gradient ascent and the amortization gap. Therefore, we propose to replace Max-SW with distributional sliced Wasserstein distance with von Mises-Fisher (vMF) projecting distribution (v-DSW). Since v-DSW is a metric with any non-degenerate vMF distribution, its amortized version can guarantee the metricity when performing amortization. Furthermore, current amortized models are not permutation invariant and symmetric. To address the issue, we design amortized models based on self-attention architecture. In particular, we adopt efficient self-attention architectures to make the computation linear in the number of supports. With the two improvements, we derive self-attention amortized distributional projection optimization and show its appealing performance in point-cloud reconstruction and its downstream applications.

  • 3 authors
Jan 11, 2023

Multimodal Lecture Presentations Dataset: Understanding Multimodality in Educational Slides

Lecture slide presentations, a sequence of pages that contain text and figures accompanied by speech, are constructed and presented carefully in order to optimally transfer knowledge to students. Previous studies in multimedia and psychology attribute the effectiveness of lecture presentations to their multimodal nature. As a step toward developing AI to aid in student learning as intelligent teacher assistants, we introduce the Multimodal Lecture Presentations dataset as a large-scale benchmark testing the capabilities of machine learning models in multimodal understanding of educational content. Our dataset contains aligned slides and spoken language, for 180+ hours of video and 9000+ slides, with 10 lecturers from various subjects (e.g., computer science, dentistry, biology). We introduce two research tasks which are designed as stepping stones towards AI agents that can explain (automatically captioning a lecture presentation) and illustrate (synthesizing visual figures to accompany spoken explanations) educational content. We provide manual annotations to help implement these two research tasks and evaluate state-of-the-art models on them. Comparing baselines and human student performances, we find that current models struggle in (1) weak crossmodal alignment between slides and spoken text, (2) learning novel visual mediums, (3) technical language, and (4) long-range sequences. Towards addressing this issue, we also introduce PolyViLT, a multimodal transformer trained with a multi-instance learning loss that is more effective than current approaches. We conclude by shedding light on the challenges and opportunities in multimodal understanding of educational presentations.

  • 5 authors
Aug 17, 2022

Enhancing Whole Slide Pathology Foundation Models through Stain Normalization

Recent advancements in digital pathology have led to the development of numerous foundational models that utilize self-supervised learning on patches extracted from gigapixel whole slide images (WSIs). While this approach leverages vast amounts of unlabeled data, we have discovered a significant issue: features extracted from these self-supervised models tend to cluster by individual WSIs, a phenomenon we term WSI-specific feature collapse. This problem can potentially limit the model's generalization ability and performance on various downstream tasks. To address this issue, we introduce Stain Normalized Pathology Foundational Model, a novel foundational model trained on patches that have undergone stain normalization. Stain normalization helps reduce color variability arising from different laboratories and scanners, enabling the model to learn more consistent features. Stain Normalized Pathology Foundational Model is trained using 285,153,903 patches extracted from a total of 34,795 WSIs, combining data from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) project. Our experiments demonstrate that Stain Normalized Pathology Foundational Model significantly mitigates the feature collapse problem, indicating that the model has learned more generalized features rather than overfitting to individual WSI characteristics. We compared Stain Normalized Pathology Foundational Model with state-of-the-art models across six downstream task datasets, and our results show that Stain Normalized Pathology Foundational Model achieves excellent performance relative to the number of WSIs used and the model's parameter count. This suggests that the application of stain normalization has substantially improved the model's efficiency and generalization capabilities.

  • 5 authors
Aug 1, 2024

Multiple Instance Learning Framework with Masked Hard Instance Mining for Whole Slide Image Classification

The whole slide image (WSI) classification is often formulated as a multiple instance learning (MIL) problem. Since the positive tissue is only a small fraction of the gigapixel WSI, existing MIL methods intuitively focus on identifying salient instances via attention mechanisms. However, this leads to a bias towards easy-to-classify instances while neglecting hard-to-classify instances. Some literature has revealed that hard examples are beneficial for modeling a discriminative boundary accurately. By applying such an idea at the instance level, we elaborate a novel MIL framework with masked hard instance mining (MHIM-MIL), which uses a Siamese structure (Teacher-Student) with a consistency constraint to explore the potential hard instances. With several instance masking strategies based on attention scores, MHIM-MIL employs a momentum teacher to implicitly mine hard instances for training the student model, which can be any attention-based MIL model. This counter-intuitive strategy essentially enables the student to learn a better discriminating boundary. Moreover, the student is used to update the teacher with an exponential moving average (EMA), which in turn identifies new hard instances for subsequent training iterations and stabilizes the optimization. Experimental results on the CAMELYON-16 and TCGA Lung Cancer datasets demonstrate that MHIM-MIL outperforms other latest methods in terms of performance and training cost. The code is available at: https://github.com/DearCaat/MHIM-MIL.

  • 6 authors
Jul 27, 2023

Rethinking Multiple Instance Learning for Whole Slide Image Classification: A Good Instance Classifier is All You Need

Weakly supervised whole slide image classification is usually formulated as a multiple instance learning (MIL) problem, where each slide is treated as a bag, and the patches cut out of it are treated as instances. Existing methods either train an instance classifier through pseudo-labeling or aggregate instance features into a bag feature through attention mechanisms and then train a bag classifier, where the attention scores can be used for instance-level classification. However, the pseudo instance labels constructed by the former usually contain a lot of noise, and the attention scores constructed by the latter are not accurate enough, both of which affect their performance. In this paper, we propose an instance-level MIL framework based on contrastive learning and prototype learning to effectively accomplish both instance classification and bag classification tasks. To this end, we propose an instance-level weakly supervised contrastive learning algorithm for the first time under the MIL setting to effectively learn instance feature representation. We also propose an accurate pseudo label generation method through prototype learning. We then develop a joint training strategy for weakly supervised contrastive learning, prototype learning, and instance classifier training. Extensive experiments and visualizations on four datasets demonstrate the powerful performance of our method. Codes will be available.

  • 5 authors
Jul 5, 2023

Diffusion Probabilistic Model Made Slim

Despite the recent visually-pleasing results achieved, the massive computational cost has been a long-standing flaw for diffusion probabilistic models (DPMs), which, in turn, greatly limits their applications on resource-limited platforms. Prior methods towards efficient DPM, however, have largely focused on accelerating the testing yet overlooked their huge complexity and sizes. In this paper, we make a dedicated attempt to lighten DPM while striving to preserve its favourable performance. We start by training a small-sized latent diffusion model (LDM) from scratch, but observe a significant fidelity drop in the synthetic images. Through a thorough assessment, we find that DPM is intrinsically biased against high-frequency generation, and learns to recover different frequency components at different time-steps. These properties make compact networks unable to represent frequency dynamics with accurate high-frequency estimation. Towards this end, we introduce a customized design for slim DPM, which we term as Spectral Diffusion (SD), for light-weight image synthesis. SD incorporates wavelet gating in its architecture to enable frequency dynamic feature extraction at every reverse steps, and conducts spectrum-aware distillation to promote high-frequency recovery by inverse weighting the objective based on spectrum magni tudes. Experimental results demonstrate that, SD achieves 8-18x computational complexity reduction as compared to the latent diffusion models on a series of conditional and unconditional image generation tasks while retaining competitive image fidelity.

  • 4 authors
Nov 27, 2022

ALMA observations of massive clouds in the central molecular zone: slim filaments tracing parsec-scale shocks

The central molecular zone (CMZ) of our Galaxy exhibits widespread emission from SiO and various complex organic molecules (COMs), yet the exact origin of such emission is uncertain. Here we report the discovery of a unique class of long (>0.5 pc) and narrow (<0.03 pc) filaments in the emission of SiO 5-4 and eight additional molecular lines, including several COMs, in our ALMA 1.3 mm spectral line observations toward two massive molecular clouds in the CMZ, which we name as slim filaments. However, these filaments are not detected in the 1.3 mm continuum at the 5sigma level. Their line-of-sight velocities are coherent and inconsistent with being outflows. The column densities and relative abundances of the detected molecules are statistically similar to those in protostellar outflows but different from those in dense cores within the same clouds. Turbulent pressure in these filaments dominates over self gravity and leads to hydrostatic inequilibrium, indicating that they are a different class of objects than the dense gas filaments in dynamical equilibrium ubiquitously found in nearby molecular clouds. We argue that these newly detected slim filaments are associated with parsec-scale shocks, likely arising from dynamic interactions between shock waves and molecular clouds. The dissipation of the slim filaments may replenish SiO and COMs in the interstellar medium and lead to their widespread emission in the CMZ.

  • 25 authors
Feb 6

From a Tiny Slip to a Giant Leap: An LLM-Based Simulation for Fake News Evolution

With the growing spread of misinformation online, research has increasingly focused on detecting and tracking fake news. However, an overlooked issue is that fake news does not naturally exist in social networks -- it often originates from distorted facts or deliberate fabrication by malicious actors. Understanding how true news gradually evolves into fake news is critical for early detection and prevention, reducing its spread and impact. Hence, in this paper, we take the first step toward simulating and revealing this evolution, proposing a Fake News evolUtion Simulation framEwork (FUSE) based on large language models (LLMs). Specifically, we employ LLM as agents to represent individuals in a simulated social network. We define four types of agents commonly observed in daily interactions: spreaders, who propagate information; commentators, who provide opinions and interpretations; verifiers, who check the accuracy of information; and bystanders, who passively observe without engaging. For simulated environments, we model various social network structures, such as high-clustering networks and scale-free networks, to mirror real-world network dynamics. Each day, the agents engage in belief exchanges, reflect on their thought processes, and reintroduce the news accordingly. Given the lack of prior work in this area, we developed a FUSE-EVAL evaluation framework to measure the deviation from true news during the fake news evolution process. The results show that FUSE successfully captures the underlying patterns of how true news transforms into fake news and accurately reproduces previously discovered instances of fake news, aligning closely with human evaluations. Moreover, our work provides insights into the fact that combating fake news should not be delayed until it has fully evolved; instead, prevention in advance is key to achieving better outcomes.

  • 5 authors
Oct 24, 2024

Multistain Pretraining for Slide Representation Learning in Pathology

Developing self-supervised learning (SSL) models that can learn universal and transferable representations of H&E gigapixel whole-slide images (WSIs) is becoming increasingly valuable in computational pathology. These models hold the potential to advance critical tasks such as few-shot classification, slide retrieval, and patient stratification. Existing approaches for slide representation learning extend the principles of SSL from small images (e.g., 224 x 224 patches) to entire slides, usually by aligning two different augmentations (or views) of the slide. Yet the resulting representation remains constrained by the limited clinical and biological diversity of the views. Instead, we postulate that slides stained with multiple markers, such as immunohistochemistry, can be used as different views to form a rich task-agnostic training signal. To this end, we introduce Madeleine, a multimodal pretraining strategy for slide representation learning. Madeleine is trained with a dual global-local cross-stain alignment objective on large cohorts of breast cancer samples (N=4,211 WSIs across five stains) and kidney transplant samples (N=12,070 WSIs across four stains). We demonstrate the quality of slide representations learned by Madeleine on various downstream evaluations, ranging from morphological and molecular classification to prognostic prediction, comprising 21 tasks using 7,299 WSIs from multiple medical centers. Code is available at https://github.com/mahmoodlab/MADELEINE.

  • 10 authors
Aug 5, 2024

WeakSTIL: Weak whole-slide image level stromal tumor infiltrating lymphocyte scores are all you need

We present WeakSTIL, an interpretable two-stage weak label deep learning pipeline for scoring the percentage of stromal tumor infiltrating lymphocytes (sTIL%) in H&E-stained whole-slide images (WSIs) of breast cancer tissue. The sTIL% score is a prognostic and predictive biomarker for many solid tumor types. However, due to the high labeling efforts and high intra- and interobserver variability within and between expert annotators, this biomarker is currently not used in routine clinical decision making. WeakSTIL compresses tiles of a WSI using a feature extractor pre-trained with self-supervised learning on unlabeled histopathology data and learns to predict precise sTIL% scores for each tile in the tumor bed by using a multiple instance learning regressor that only requires a weak WSI-level label. By requiring only a weak label, we overcome the large annotation efforts required to train currently existing TIL detection methods. We show that WeakSTIL is at least as good as other TIL detection methods when predicting the WSI-level sTIL% score, reaching a coefficient of determination of 0.45pm0.15 when compared to scores generated by an expert pathologist, and an AUC of 0.89pm0.05 when treating it as the clinically interesting sTIL-high vs sTIL-low classification task. Additionally, we show that the intermediate tile-level predictions of WeakSTIL are highly interpretable, which suggests that WeakSTIL pays attention to latent features related to the number of TILs and the tissue type. In the future, WeakSTIL may be used to provide consistent and interpretable sTIL% predictions to stratify breast cancer patients into targeted therapy arms.

  • 6 authors
Sep 13, 2021