{"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}
{"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}
{"title":"Theoretical Analysis of Learned Database Operations under Distribution Shift through Distribution Learnability.","authors":"Sepanta Zeighami, Cyrus Shahabi","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Use of machine learning to perform database operations, such as indexing, cardinality estimation, and sorting, is shown to provide substantial performance benefits. However, when datasets change and data distribution shifts, empirical results also show performance degradation for learned models, possibly to worse than non-learned alternatives. This, together with a lack of theoretical understanding of learned methods undermines their practical applicability, since there are no guarantees on how well the models will perform after deployment. In this paper, we present the first known theoretical characterization of the performance of learned models in dynamic datasets, for the aforementioned operations. Our results show novel theoretical characteristics achievable by learned models and provide bounds on the performance of the models that characterize their advantages over non-learned methods, showing why and when learned models can outperform the alternatives. Our analysis develops the <i>distribution learnability</i> framework and novel theoretical tools which build the foundation for the analysis of learned database operations in the future.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"235 ","pages":"58283-58305"},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11534081/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142577095","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}
Yinjun Wu, Mayank Keoliya, Kan Chen, Neelay Velingker, Ziyang Li, Emily J Getzen, Qi Long, Mayur Naik, Ravi B Parikh, Eric Wong
{"title":"DISCRET: Synthesizing Faithful Explanations For Treatment Effect Estimation.","authors":"Yinjun Wu, Mayank Keoliya, Kan Chen, Neelay Velingker, Ziyang Li, Emily J Getzen, Qi Long, Mayur Naik, Ravi B Parikh, Eric Wong","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Designing faithful yet accurate AI models is challenging, particularly in the field of individual treatment effect estimation (ITE). ITE prediction models deployed in critical settings such as healthcare should ideally be (i) accurate, and (ii) provide faithful explanations. However, current solutions are inadequate: state-of-the-art black-box models do not supply explanations, post-hoc explainers for black-box models lack faithfulness guarantees, and self-interpretable models greatly compromise accuracy. To address these issues, we propose DISCRET, a self-interpretable ITE framework that synthesizes faithful, rule-based explanations for each sample. A key insight behind DISCRET is that explanations can serve dually as <i>database queries</i> to identify similar subgroups of samples. We provide a novel RL algorithm to efficiently synthesize these explanations from a large search space. We evaluate DISCRET on diverse tasks involving tabular, image, and text data. DISCRET outperforms the best self-interpretable models and has accuracy comparable to the best black-box models while providing faithful explanations. DISCRET is available at https://github.com/wuyinjun-1993/DISCRET-ICML2024.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"235 ","pages":"53597-53618"},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11350397/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142115743","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}
Brian Cho, Yaroslav Mukhin, Kyra Gan, Ivana Malenica
{"title":"Kernel Debiased Plug-in Estimation: Simultaneous, Automated Debiasing without Influence Functions for Many Target Parameters.","authors":"Brian Cho, Yaroslav Mukhin, Kyra Gan, Ivana Malenica","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>When estimating target parameters in nonparametric models with nuisance parameters, substituting the unknown nuisances with nonparametric estimators can introduce \"plug-in bias.\" Traditional methods addressing this suboptimal bias-variance trade-off rely on the <i>influence function</i> (IF) of the target parameter. When estimating multiple target parameters, these methods require debiasing the nuisance parameter multiple times using the corresponding IFs, which poses analytical and computational challenges. In this work, we leverage the <i>targeted maximum likelihood estimation</i> (TMLE) framework to propose a novel method named <i>kernel debiased plug-in estimation</i> (KDPE). KDPE refines an initial estimate through regularized likelihood maximization steps, employing a nonparametric model based on <i>reproducing kernel Hilbert spaces</i>. We show that KDPE: (i) simultaneously debiases <i>all</i> pathwise differentiable target parameters that satisfy our regularity conditions, (ii) does not require the IF for implementation, and (iii) remains computationally tractable. We numerically illustrate the use of KDPE and validate our theoretical results.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"235 ","pages":"8534-8555"},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11359899/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142115744","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}
Theodore Papamarkou, Tolga Birdal, Michael Bronstein, Gunnar Carlsson, Justin Curry, Yue Gao, Mustafa Hajij, Roland Kwitt, Pietro Liò, Paolo Di Lorenzo, Vasileios Maroulas, Nina Miolane, Farzana Nasrin, Karthikeyan Natesan Ramamurthy, Bastian Rieck, Simone Scardapane, Michael T Schaub, Petar Veličković, Bei Wang, Yusu Wang, Guo-Wei Wei, Ghada Zamzmi
{"title":"Position: Topological Deep Learning is the New Frontier for Relational Learning.","authors":"Theodore Papamarkou, Tolga Birdal, Michael Bronstein, Gunnar Carlsson, Justin Curry, Yue Gao, Mustafa Hajij, Roland Kwitt, Pietro Liò, Paolo Di Lorenzo, Vasileios Maroulas, Nina Miolane, Farzana Nasrin, Karthikeyan Natesan Ramamurthy, Bastian Rieck, Simone Scardapane, Michael T Schaub, Petar Veličković, Bei Wang, Yusu Wang, Guo-Wei Wei, Ghada Zamzmi","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Topological deep learning (TDL) is a rapidly evolving field that uses topological features to understand and design deep learning models. This paper posits that TDL is the new frontier for relational learning. TDL may complement graph representation learning and geometric deep learning by incorporating topological concepts, and can thus provide a natural choice for various machine learning settings. To this end, this paper discusses open problems in TDL, ranging from practical benefits to theoretical foundations. For each problem, it outlines potential solutions and future research opportunities. At the same time, this paper serves as an invitation to the scientific community to actively participate in TDL research to unlock the potential of this emerging field.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"235 ","pages":"39529-39555"},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11973457/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143804858","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}
Ran Xu, Yiwen Lu, Chang Liu, Yong Chen, Yan Sun, Xiao Hu, Joyce C Ho, Carl Yang
{"title":"From Basic to Extra Features: Hypergraph Transformer Pretrain-then-Finetuning for Balanced Clinical Predictions on EHR.","authors":"Ran Xu, Yiwen Lu, Chang Liu, Yong Chen, Yan Sun, Xiao Hu, Joyce C Ho, Carl Yang","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Electronic Health Records (EHRs) contain rich patient information and are crucial for clinical research and practice. In recent years, deep learning models have been applied to EHRs, but they often rely on massive features, which may not be readily available for all patients. We propose HTP-Star, which leverages hypergraph structures with a pretrain-then-finetune framework for modeling EHR data, enabling seamless integration of additional features. Additionally, we design two techniques, namely (1) <i>Smoothness-inducing Regularization</i> and (2) <i>Group-balanced Reweighting</i>, to enhance the model's robustness during finetuning. Through experiments conducted on two real EHR datasets, we demonstrate that HTP-Star consistently outperforms various baselines while striking a balance between patients with basic and extra features.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"248 ","pages":"182-197"},"PeriodicalIF":0.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11876795/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143560252","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}
Hiba Ahsan, Denis Jered McInerney, Jisoo Kim, Christopher Potter, Geoffrey Young, Silvio Amir, Byron C Wallace
{"title":"Retrieving Evidence from EHRs with LLMs: Possibilities and Challenges.","authors":"Hiba Ahsan, Denis Jered McInerney, Jisoo Kim, Christopher Potter, Geoffrey Young, Silvio Amir, Byron C Wallace","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Unstructured data in Electronic Health Records (EHRs) often contains critical information-complementary to imaging-that could inform radiologists' diagnoses. But the large volume of notes often associated with patients together with time constraints renders manually identifying relevant evidence practically infeasible. In this work we propose and evaluate a zero-shot strategy for using LLMs as a mechanism to efficiently retrieve and summarize unstructured evidence in patient EHR relevant to a given query. Our method entails tasking an LLM to infer whether a patient has, or is at risk of, a particular condition on the basis of associated notes; if so, we ask the model to summarize the supporting evidence. Under expert evaluation, we find that this LLM-based approach provides outputs consistently preferred to a pre-LLM information retrieval baseline. Manual evaluation is expensive, so we also propose and validate a method using an LLM to evaluate (other) LLM outputs for this task, allowing us to scale up evaluation. Our findings indicate the promise of LLMs as interfaces to EHR, but also highlight the outstanding challenge posed by \"hallucinations\". In this setting, however, we show that model confidence in outputs strongly correlates with faithful summaries, offering a practical means to limit confabulations.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"248 ","pages":"489-505"},"PeriodicalIF":0.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11368037/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142121291","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}
Hui Wei, Maxwell A Xu, Colin Samplawski, James M Rehg, Santosh Kumar, Benjamin M Marlin
{"title":"Temporally Multi-Scale Sparse Self-Attention for Physical Activity Data Imputation.","authors":"Hui Wei, Maxwell A Xu, Colin Samplawski, James M Rehg, Santosh Kumar, Benjamin M Marlin","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Wearable sensors enable health researchers to continuously collect data pertaining to the physiological state of individuals in real-world settings. However, such data can be subject to extensive missingness due to a complex combination of factors. In this work, we study the problem of imputation of missing step count data, one of the most ubiquitous forms of wearable sensor data. We construct a novel and large scale data set consisting of a training set with over 3 million hourly step count observations and a test set with over 2.5 million hourly step count observations. We propose a domain knowledge-informed sparse self-attention model for this task that captures the temporal multi-scale nature of step-count data. We assess the performance of the model relative to baselines and conduct ablation studies to verify our specific model designs.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"248 ","pages":"137-154"},"PeriodicalIF":0.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11421853/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142334005","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}
{"title":"s-SuStaIn: Scaling subtype and stage inference via simultaneous clustering of subjects and biomarkers.","authors":"Raghav Tandon, James J Lah, Cassie S Mitchell","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Event-based models (EBM) provide an important platform for modeling disease progression. This work successfully extends previous EBM approaches to work with larger sets of biomarkers while simultaneously modeling heterogeneity in disease progression trajectories. We develop and validate the s-SuStain method for scalable event-based modeling of disease progression subtypes using large numbers of features. s-SuStaIn is typically an order of magnitude faster than its predecessor (SuStaIn). Moreover, we perform a case study with s-SuStaIn using open access cross-sectional Alzheimer's Disease Neuroimaging (ADNI) data to stage AD patients into four subtypes based on dynamic disease progression. s-SuStaIn shows that the inferred subtypes and stages predict progression to AD among MCI subjects. The subtypes show difference in AD incidence-rates and reveal clinically meaningful progression trajectories when mapped to a brain atlas.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"248 ","pages":"461-476"},"PeriodicalIF":0.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11881980/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143568330","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}