Albert Tseng, Jerry Chee, Qingyao Sun, Volodymyr Kuleshov, Christopher De Sa
Post-training quantization (PTQ) reduces the memory footprint of LLMs by quantizing their weights to low-precision. In this work, we introduce QuIP#, a weight-only PTQ method that achieves state-of-the-art results in extreme compression regimes (≤ 4 bits per weight) using three novel techniques. First, QuIP# improves QuIP's (Chee et al., 2023) incoherence processing by using the randomized Hadamard transform, which is faster and has better theoretical properties. Second, QuIP# uses vector quantization to take advantage of the ball-shaped sub-Gaussian distribution that incoherent weights possess: specifically, we introduce a set of hardware-efficient codebooks based on the highly symmetric lattice, which achieves the optimal 8-dimension unit ball packing. Third, QuIP# uses fine-tuning to improve fidelity to the original model. Our experiments show that QuIP# outperforms existing PTQ methods, enables new behaviors in PTQ scaling, and supports fast inference. Our code can be found at https://github.com/Cornell-RelaxML/quip-sharp.
训练后量化(PTQ)通过将llm的权重量化到低精度,减少了llm的内存占用。在这项工作中,我们介绍了QuIP#,这是一种仅限权重的PTQ方法,使用三种新技术在极端压缩状态(每重量≤4比特)下实现了最先进的结果。首先,quip#通过使用随机Hadamard变换改进了QuIP (Chee et al., 2023)的非相干处理,该变换速度更快,具有更好的理论性质。其次,quip#使用矢量量化来利用非相干权值所具有的球状亚高斯分布:具体来说,我们引入了一组基于高度对称的e8晶格的硬件高效码本,实现了最优的8维单位球填充。第三,quip#使用微调来提高原始模型的保真度。我们的实验表明,quip#优于现有的PTQ方法,在PTQ扩展中实现了新的行为,并支持快速推理。我们的代码可以在https://github.com/Cornell-RelaxML/quip-sharp上找到。
{"title":"QuIP#: Even Better LLM Quantization with Hadamard Incoherence and Lattice Codebooks.","authors":"Albert Tseng, Jerry Chee, Qingyao Sun, Volodymyr Kuleshov, Christopher De Sa","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Post-training quantization (PTQ) reduces the memory footprint of LLMs by quantizing their weights to low-precision. In this work, we introduce QuIP#, a weight-only PTQ method that achieves state-of-the-art results in extreme compression regimes (≤ 4 bits per weight) using three novel techniques. First, QuIP# improves QuIP's (Chee et al., 2023) incoherence processing by using the randomized Hadamard transform, which is faster and has better theoretical properties. Second, QuIP# uses vector quantization to take advantage of the ball-shaped sub-Gaussian distribution that incoherent weights possess: specifically, we introduce a set of hardware-efficient codebooks based on the highly symmetric <math> <msub><mrow><mi>E</mi></mrow> <mrow><mn>8</mn></mrow> </msub> </math> lattice, which achieves the optimal 8-dimension unit ball packing. Third, QuIP# uses fine-tuning to improve fidelity to the original model. Our experiments show that QuIP# outperforms existing PTQ methods, enables new behaviors in PTQ scaling, and supports fast inference. Our code can be found at https://github.com/Cornell-RelaxML/quip-sharp.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"235 ","pages":"48630-48656"},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12395268/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144981748","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yi Liu, Alexander W Levis, Sharon-Lise Normand, Larry Han
Recent years have experienced increasing utilization of complex machine learning models across multiple sources of data to inform more generalizable decision-making. However, distribution shifts across data sources and privacy concerns related to sharing individual-level data, coupled with a lack of uncertainty quantification from machine learning predictions, make it challenging to achieve valid inferences in multi-source environments. In this paper, we consider the problem of obtaining distribution-free prediction intervals for a target population, leveraging multiple potentially biased data sources. We derive the efficient influence functions for the quantiles of unobserved outcomes in the target and source populations, and show that one can incorporate machine learning prediction algorithms in the estimation of nuisance functions while still achieving parametric rates of convergence to nominal coverage probabilities. Moreover, when conditional outcome invariance is violated, we propose a data-adaptive strategy to upweight informative data sources for efficiency gain and downweight non-informative data sources for bias reduction. We highlight the robustness and efficiency of our proposals for a variety of conformal scores and data-generating mechanisms via extensive synthetic experiments. Hospital length of stay prediction intervals for pediatric patients undergoing a high-risk cardiac surgical procedure between 2016-2022 in the U.S. illustrate the utility of our methodology.
{"title":"Multi-Source Conformal Inference Under Distribution Shift.","authors":"Yi Liu, Alexander W Levis, Sharon-Lise Normand, Larry Han","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Recent years have experienced increasing utilization of complex machine learning models across multiple sources of data to inform more generalizable decision-making. However, distribution shifts across data sources and privacy concerns related to sharing individual-level data, coupled with a lack of uncertainty quantification from machine learning predictions, make it challenging to achieve valid inferences in multi-source environments. In this paper, we consider the problem of obtaining distribution-free prediction intervals for a target population, leveraging multiple potentially biased data sources. We derive the efficient influence functions for the quantiles of unobserved outcomes in the target and source populations, and show that one can incorporate machine learning prediction algorithms in the estimation of nuisance functions while still achieving parametric rates of convergence to nominal coverage probabilities. Moreover, when conditional outcome invariance is violated, we propose a data-adaptive strategy to upweight informative data sources for efficiency gain and downweight non-informative data sources for bias reduction. We highlight the robustness and efficiency of our proposals for a variety of conformal scores and data-generating mechanisms via extensive synthetic experiments. Hospital length of stay prediction intervals for pediatric patients undergoing a high-risk cardiac surgical procedure between 2016-2022 in the U.S. illustrate the utility of our methodology.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"235 ","pages":"31344-31382"},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11345809/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142082878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Toru Shirakawa, Yi Li, Yulun Wu, Sky Qiu, Yuxuan Li, Mingduo Zhao, Hiroyasu Iso, Mark van der Laan
We propose Deep Longitudinal Targeted Minimum Loss-based Estimation (Deep LTMLE), a novel approach to estimate the mean of counterfactual outcome under dynamic treatment policies in longitudinal problem settings. Our approach utilizes a transformer architecture with heterogeneous type embedding trained using temporal-difference learning. After obtaining an initial estimate using the transformer, following the targeted minimum loss-based likelihood estimation (TMLE) framework, we statistically corrected for the bias commonly associated with machine learning algorithms. Furthermore, our method also facilitates statistical inference by enabling the provision of 95% confidence intervals grounded in asymptotic statistical theory. Simulation results demonstrate our method's superior performance over existing approaches, particularly in complex, long time-horizon scenarios. It remains effective in small-sample, short-duration contexts, matching the performance of asymptotically efficient estimators. To demonstrate our method in practice, we applied our method to estimate counterfactual mean outcomes for standard versus intensive blood pressure management strategies in a real-world cardiovascular epidemiology cohort study.
{"title":"Longitudinal Targeted Minimum Loss-based Estimation with Temporal-Difference Heterogeneous Transformer.","authors":"Toru Shirakawa, Yi Li, Yulun Wu, Sky Qiu, Yuxuan Li, Mingduo Zhao, Hiroyasu Iso, Mark van der Laan","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>We propose Deep Longitudinal Targeted Minimum Loss-based Estimation (Deep LTMLE), a novel approach to estimate the mean of counterfactual outcome under dynamic treatment policies in longitudinal problem settings. Our approach utilizes a transformer architecture with heterogeneous type embedding trained using temporal-difference learning. After obtaining an initial estimate using the transformer, following the targeted minimum loss-based likelihood estimation (TMLE) framework, we statistically corrected for the bias commonly associated with machine learning algorithms. Furthermore, our method also facilitates statistical inference by enabling the provision of 95% confidence intervals grounded in asymptotic statistical theory. Simulation results demonstrate our method's superior performance over existing approaches, particularly in complex, long time-horizon scenarios. It remains effective in small-sample, short-duration contexts, matching the performance of asymptotically efficient estimators. To demonstrate our method in practice, we applied our method to estimate counterfactual mean outcomes for standard versus intensive blood pressure management strategies in a real-world cardiovascular epidemiology cohort study.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"235 ","pages":"45097-45113"},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12681028/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145703172","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
This paper presents FedType, a simple yet pioneering framework designed to fill research gaps in heterogeneous model aggregation within federated learning (FL). FedType introduces small identical proxy models for clients, serving as agents for information exchange, ensuring model security, and achieving efficient communication simultaneously. To transfer knowledge between large private and small proxy models on clients, we propose a novel uncertainty-based asymmetrical reciprocity learning method, eliminating the need for any public data. Comprehensive experiments conducted on benchmark datasets demonstrate the efficacy and generalization ability of FedType across diverse settings. Our approach redefines federated learning paradigms by bridging model heterogeneity, eliminating reliance on public data, prioritizing client privacy, and reducing communication costs.
{"title":"Bridging Model Heterogeneity in Federated Learning via Uncertainty-based Asymmetrical Reciprocity Learning.","authors":"Jiaqi Wang, Chenxu Zhao, Lingjuan Lyu, Quanzeng You, Mengdi Huai, Fenglong Ma","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>This paper presents FedType, a simple yet pioneering framework designed to fill research gaps in heterogeneous model aggregation within federated learning (FL). FedType introduces small identical proxy models for clients, serving as agents for information exchange, ensuring model security, and achieving efficient communication simultaneously. To transfer knowledge between large private and small proxy models on clients, we propose a novel uncertainty-based asymmetrical reciprocity learning method, eliminating the need for any public data. Comprehensive experiments conducted on benchmark datasets demonstrate the efficacy and generalization ability of FedType across diverse settings. Our approach redefines federated learning paradigms by bridging model heterogeneity, eliminating reliance on public data, prioritizing client privacy, and reducing communication costs.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"235 ","pages":"52290-52308"},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12038961/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144054941","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Inverse problems arise in a multitude of applications, where the goal is to recover a clean signal from noisy and possibly (non)linear observations. The difficulty of a reconstruction problem depends on multiple factors, such as the structure of the ground truth signal, the severity of the degradation and the complex interactions between the above. This results in natural sample-by-sample variation in the difficulty of a reconstruction task, which is often overlooked by contemporary techniques. Our key observation is that most existing inverse problem solvers lack the ability to adapt their compute power to the difficulty of the reconstruction task, resulting in subpar performance and wasteful resource allocation. We propose a novel method that we call severity encoding, to estimate the degradation severity of noisy, degraded signals in the latent space of an autoencoder. We show that the estimated severity has strong correlation with the true corruption level and can give useful hints at the difficulty of reconstruction problems on a sample-by-sample basis. Furthermore, we propose a reconstruction method based on latent diffusion models that leverages the predicted degradation severities to fine-tune the reverse diffusion sampling trajectory and thus achieve sample-adaptive inference times. Our framework acts as a wrapper that can be combined with any latent diffusion-based baseline solver, imbuing it with sample-adaptivity and acceleration. We perform numerical experiments on both linear and nonlinear inverse problems and demonstrate that our technique greatly improves the performance of the baseline solver and achieves up to 10× acceleration in mean sampling speed.
{"title":"Adapt and Diffuse: Sample-Adaptive Reconstruction Via Latent Diffusion Models.","authors":"Zalan Fabian, Berk Tinaz, Mahdi Soltanolkotabi","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Inverse problems arise in a multitude of applications, where the goal is to recover a clean signal from noisy and possibly (non)linear observations. The difficulty of a reconstruction problem depends on multiple factors, such as the structure of the ground truth signal, the severity of the degradation and the complex interactions between the above. This results in natural sample-by-sample variation in the difficulty of a reconstruction task, which is often overlooked by contemporary techniques. Our key observation is that most existing inverse problem solvers lack the ability to adapt their compute power to the difficulty of the reconstruction task, resulting in subpar performance and wasteful resource allocation. We propose a novel method that we call severity encoding, to estimate the degradation severity of noisy, degraded signals in the latent space of an autoencoder. We show that the estimated severity has strong correlation with the true corruption level and can give useful hints at the difficulty of reconstruction problems on a sample-by-sample basis. Furthermore, we propose a reconstruction method based on latent diffusion models that leverages the predicted degradation severities to fine-tune the reverse diffusion sampling trajectory and thus achieve sample-adaptive inference times. Our framework acts as a wrapper that can be combined with any latent diffusion-based baseline solver, imbuing it with sample-adaptivity and acceleration. We perform numerical experiments on both linear and nonlinear inverse problems and demonstrate that our technique greatly improves the performance of the baseline solver and achieves up to 10× acceleration in mean sampling speed.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"235 ","pages":"12723-12753"},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11421836/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142334004","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Meng Xia, Jonathan Wilson, Benjamin Goldstein, Ricardo Henao
The use of machine learning models to predict clinical outcomes from (longitudinal) electronic health record (EHR) data is becoming increasingly popular due to advances in deep architectures, representation learning, and the growing availability of large EHR datasets. Existing models generally assume access to the same data sources during both training and inference stages. However, this assumption is often challenged by the fact that real-world clinical datasets originate from various data sources (with distinct sets of covariates), which though can be available for training (in a research or retrospective setting), are more realistically only partially available (a subset of such sets) for inference when deployed. So motivated, we introduce Contrastive Learning for clinical Outcome Prediction with Partial data Sources (CLOPPS), that trains encoders to capture information across different data sources and then leverages them to build classifiers restricting access to a single data source. This approach can be used with existing cross-sectional or longitudinal outcome classification models. We present experiments on two real-world datasets demonstrating that CLOPPS consistently outperforms strong baselines in several practical scenarios.
{"title":"Contrastive Learning for Clinical Outcome Prediction with Partial Data Sources.","authors":"Meng Xia, Jonathan Wilson, Benjamin Goldstein, Ricardo Henao","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The use of machine learning models to predict clinical outcomes from (longitudinal) electronic health record (EHR) data is becoming increasingly popular due to advances in deep architectures, representation learning, and the growing availability of large EHR datasets. Existing models generally assume access to the same data sources during both training and inference stages. However, this assumption is often challenged by the fact that real-world clinical datasets originate from various data sources (with distinct sets of covariates), which though can be available for training (in a research or retrospective setting), are more realistically only partially available (a subset of such sets) for inference when deployed. So motivated, we introduce Contrastive Learning for clinical Outcome Prediction with Partial data Sources (CLOPPS), that trains encoders to capture information across different data sources and then leverages them to build classifiers restricting access to a single data source. This approach can be used with existing cross-sectional or longitudinal outcome classification models. We present experiments on two real-world datasets demonstrating that CLOPPS consistently outperforms strong baselines in several practical scenarios.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"235 ","pages":"54156-54177"},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11326519/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141989752","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Diffusion models have established new state of the art in a multitude of computer vision tasks, including image restoration. Diffusion-based inverse problem solvers generate reconstructions of exceptional visual quality from heavily corrupted measurements. However, in what is widely known as the perception-distortion trade-off, the price of perceptually appealing reconstructions is often paid in declined distortion metrics, such as PSNR. Distortion metrics measure faithfulness to the observation, a crucial requirement in inverse problems. In this work, we propose a novel framework for inverse problem solving, namely we assume that the observation comes from a stochastic degradation process that gradually degrades and noises the original clean image. We learn to reverse the degradation process in order to recover the clean image. Our technique maintains consistency with the original measurement throughout the reverse process, and allows for great flexibility in trading off perceptual quality for improved distortion metrics and sampling speedup via early-stopping. We demonstrate the efficiency of our method on different high-resolution datasets and inverse problems, achieving great improvements over other state-of-the-art diffusion-based methods with respect to both perceptual and distortion metrics.
{"title":"DiracDiffusion: Denoising and Incremental Reconstruction with Assured Data-Consistency.","authors":"Zalan Fabian, Berk Tinaz, Mahdi Soltanolkotabi","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Diffusion models have established new state of the art in a multitude of computer vision tasks, including image restoration. Diffusion-based inverse problem solvers generate reconstructions of exceptional visual quality from heavily corrupted measurements. However, in what is widely known as the perception-distortion trade-off, the price of perceptually appealing reconstructions is often paid in declined distortion metrics, such as PSNR. Distortion metrics measure faithfulness to the observation, a crucial requirement in inverse problems. In this work, we propose a novel framework for inverse problem solving, namely we assume that the observation comes from a stochastic degradation process that gradually degrades and noises the original clean image. We learn to reverse the degradation process in order to recover the clean image. Our technique maintains consistency with the original measurement throughout the reverse process, and allows for great flexibility in trading off perceptual quality for improved distortion metrics and sampling speedup via early-stopping. We demonstrate the efficiency of our method on different high-resolution datasets and inverse problems, achieving great improvements over other state-of-the-art diffusion-based methods with respect to both perceptual and distortion metrics.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"235 ","pages":"12754-12783"},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11483186/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142482675","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Selective labels occur when label observations are subject to a decision-making process; e.g., diagnoses that depend on the administration of laboratory tests. We study a clinically-inspired selective label problem called disparate censorship, where labeling biases vary across subgroups and unlabeled individuals are imputed as "negative" (i.e., no diagnostic test = no illness). Machine learning models naïvely trained on such labels could amplify labeling bias. Inspired by causal models of selective labels, we propose Disparate Censorship Expectation-Maximization (DCEM), an algorithm for learning in the presence of disparate censorship. We theoretically analyze how DCEM mitigates the effects of disparate censorship on model performance. We validate DCEM on synthetic data, showing that it improves bias mitigation (area between ROC curves) without sacrificing discriminative performance (AUC) compared to baselines. We achieve similar results in a sepsis classification task using clinical data.
{"title":"From Biased Selective Labels to Pseudo-Labels: An Expectation-Maximization Framework for Learning from Biased Decisions.","authors":"Trenton Chang, Jenna Wiens","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Selective labels occur when label observations are subject to a decision-making process; <i>e.g</i>., diagnoses that depend on the administration of laboratory tests. We study a clinically-inspired selective label problem called disparate censorship, where labeling biases vary across subgroups and unlabeled individuals are imputed as \"negative\" (<i>i.e</i>., no diagnostic test = no illness). Machine learning models naïvely trained on such labels could amplify labeling bias. Inspired by causal models of selective labels, we propose Disparate Censorship Expectation-Maximization (DCEM), an algorithm for learning in the presence of disparate censorship. We theoretically analyze how DCEM mitigates the effects of disparate censorship on model performance. We validate DCEM on synthetic data, showing that it improves bias mitigation (area between ROC curves) without sacrificing discriminative performance (AUC) compared to baselines. We achieve similar results in a sepsis classification task using clinical data.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"235 ","pages":"6286-6324"},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12199211/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144509908","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Benjamin Billot, Neel Dey, Esra Abaci Turk, P Ellen Grant, Polina Golland
The robustness and accuracy of multi-organ segmentation networks is limited by the scarcity of labels. A common strategy to alleviate the annotation burden is to use partially labelled datasets, where each image can be annotated for a subset of all organs of interest. Unfortunately, this approach causes inconsistencies in the background class since it can now include target organs. Moreover, we consider the even more relaxed setting of region-based segmentation, where voxels can be labelled for super-regions, thus causing further inconsistencies across annotations. Here we propose CoNeMOS (Conditional Network for Multi-Organ Segmentation), a framework that leverages a label-conditioned network for synergistic learning on partially labelled region-based segmentations. Conditioning is achieved by combining convolutions with expressive Feature-wise Linear Modulation (FiLM) layers, whose parameters are controlled by an auxiliary network. In contrast to other conditioning methods, FiLM layers are stable to train and add negligible computation overhead, which enables us to condition the entire network. As a result, the network can learn where it needs to extract shared or label-specific features, instead of imposing it with the architecture (e.g., with different segmentation heads). By encouraging flexible synergies across labels, our method obtains state-of-the-art results for the segmentation of challenging low-resolution fetal MRI data. Our code is available at https://github.com/BBillot/CoNeMOS.
{"title":"Network conditioning for synergistic learning on partial annotations.","authors":"Benjamin Billot, Neel Dey, Esra Abaci Turk, P Ellen Grant, Polina Golland","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The robustness and accuracy of multi-organ segmentation networks is limited by the scarcity of labels. A common strategy to alleviate the annotation burden is to use partially labelled datasets, where each image can be annotated for a subset of all organs of interest. Unfortunately, this approach causes inconsistencies in the background class since it can now include target organs. Moreover, we consider the even more relaxed setting of region-based segmentation, where voxels can be labelled for super-regions, thus causing further inconsistencies across annotations. Here we propose CoNeMOS (Conditional Network for Multi-Organ Segmentation), a framework that leverages a label-conditioned network for synergistic learning on partially labelled region-based segmentations. Conditioning is achieved by combining convolutions with expressive Feature-wise Linear Modulation (FiLM) layers, whose parameters are controlled by an auxiliary network. In contrast to other conditioning methods, FiLM layers are stable to train and add negligible computation overhead, which enables us to condition the entire network. As a result, the network can <i>learn</i> where it needs to extract shared or label-specific features, instead of imposing it with the architecture (e.g., with different segmentation heads). By encouraging flexible synergies across labels, our method obtains state-of-the-art results for the segmentation of challenging low-resolution fetal MRI data. Our code is available at https://github.com/BBillot/CoNeMOS.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"250 ","pages":"119-130"},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12393823/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144981797","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Self-supervised learning (SSL) is an approach to pretrain models with unlabeled datasets and extract useful feature representations such that these models can be easily fine-tuned for various downstream tasks. Self-pretraining applies SSL on curated task-specific datasets without using task-specific labels. Increasing availability of public data repositories has now made it possible to utilize diverse and large, task unrelated datasets to pretrain models in the "wild" using SSL. However, the benefit of such wild-pretraining over self-pretraining has not been studied in the context of medical image analysis. Hence, we analyzed transformers (Swin and ViT) and a convolutional neural network created using wild- and self-pretraining trained to segment lung tumors from 3D-computed tomography (CT) scans in terms of: (a) accuracy, (b) fine-tuning epoch efficiency, and (c) robustness to image acquisition differences (contrast versus non-contrast, slice thickness, and image reconstruction kernels). We also studied feature reuse using centered kernel alignment (CKA) with the Swin networks. Our analysis with two independent testing (public N = 139; internal N = 196) datasets showed that wild-pretrained Swin models significantly outperformed self-pretrained Swin for the various imaging acquisitions. Fine-tuning epoch efficiency was higher for both wild-pretrained Swin and ViT models compared to their self-pretrained counterparts. Feature reuse close to the final encoder layers was lower than in the early layers for wild-pretrained models irrespective of the pretext tasks used in SSL. Models and code will be made available through GitHub upon manuscript acceptance.
{"title":"Self-supervised pretraining in the wild imparts image acquisition robustness to medical image transformers: an application to lung cancer segmentation.","authors":"Jue Jiang, Harini Veeraraghavan","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Self-supervised learning (SSL) is an approach to pretrain models with unlabeled datasets and extract useful feature representations such that these models can be easily fine-tuned for various downstream tasks. Self-pretraining applies SSL on curated task-specific datasets without using task-specific labels. Increasing availability of public data repositories has now made it possible to utilize diverse and large, task unrelated datasets to pretrain models in the \"wild\" using SSL. However, the benefit of such wild-pretraining over self-pretraining has not been studied in the context of medical image analysis. Hence, we analyzed transformers (Swin and ViT) and a convolutional neural network created using wild- and self-pretraining trained to segment lung tumors from 3D-computed tomography (CT) scans in terms of: (a) accuracy, (b) fine-tuning epoch efficiency, and (c) robustness to image acquisition differences (contrast versus non-contrast, slice thickness, and image reconstruction kernels). We also studied feature reuse using centered kernel alignment (CKA) with the Swin networks. Our analysis with two independent testing (public N = 139; internal N = 196) datasets showed that wild-pretrained Swin models significantly outperformed self-pretrained Swin for the various imaging acquisitions. Fine-tuning epoch efficiency was higher for both wild-pretrained Swin and ViT models compared to their self-pretrained counterparts. Feature reuse close to the final encoder layers was lower than in the early layers for wild-pretrained models irrespective of the pretext tasks used in SSL. Models and code will be made available through GitHub upon manuscript acceptance.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"250 ","pages":"708-721"},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11741178/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143017993","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}