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Publications
MixEHR-Nest: Identifying Subphenotypes within Electronic Health Records through Hierarchical Guided-Topic Modeling
Automatic subphenotyping from electronic health records (EHRs)provides numerous opportunities to understand diseases with unique subgroups a… (voir plus)nd enhance personalized medicine for patients. However, existing machine learning algorithms either focus on specific diseases for better interpretability or produce coarse-grained phenotype topics without considering nuanced disease patterns. In this study, we propose a guided topic model, MixEHR-Nest, to infer sub-phenotype topics from thousands of disease using multi-modal EHR data. Specifically, MixEHR-Nest detects multiple subtopics from each phenotype topic, whose prior is guided by the expert-curated phenotype concepts such as Phenotype Codes (PheCodes) or Clinical Classification Software (CCS) codes. We evaluated MixEHR-Nest on two EHR datasets: (1) the MIMIC-III dataset consisting of over 38 thousand patients from intensive care unit (ICU) from Beth Israel Deaconess Medical Center (BIDMC) in Boston, USA; (2) the healthcare administrative database PopHR, comprising 1.3 million patients from Montreal, Canada. Experimental results demonstrate that MixEHR-Nest can identify subphenotypes with distinct patterns within each phenotype, which are predictive for disease progression and severity. Consequently, MixEHR-Nest distinguishes between type 1 and type 2 diabetes by inferring subphenotypes using CCS codes, which do not differentiate these two subtype concepts. Additionally, MixEHR-Nest not only improved the prediction accuracy of short-term mortality of ICU patients and initial insulin treatment in diabetic patients but also revealed the contributions of subphenotypes. For longitudinal analysis, MixEHR-Nest identified subphenotypes of distinct age prevalence under the same phenotypes, such as asthma, leukemia, epilepsy, and depression. The MixEHR-Nest software is available at GitHub: https://github.com/li-lab-mcgill/MixEHR-Nest.
The rise of AI-driven manipulation poses significant risks to societal trust and democratic processes. Yet, studying these effects in real-w… (voir plus)orld settings at scale is ethically and logistically impractical, highlighting a need for simulation tools that can model these dynamics in controlled settings to enable experimentation with possible defenses. We present a simulation environment designed to address this. We elaborate upon the Concordia framework that simulates offline, `real life' activity by adding online interactions to the simulation through social media with the integration of a Mastodon server. We improve simulation efficiency and information flow, and add a set of measurement tools, particularly longitudinal surveys. We demonstrate the simulator with a tailored example in which we track agents' political positions and show how partisan manipulation of agents can affect election results.
The rise of AI-driven manipulation poses significant risks to societal trust and democratic processes. Yet, studying these effects in real-w… (voir plus)orld settings at scale is ethically and logistically impractical, highlighting a need for simulation tools that can model these dynamics in controlled settings to enable experimentation with possible defenses. We present a simulation environment designed to address this. We elaborate upon the Concordia framework that simulates offline, `real life' activity by adding online interactions to the simulation through social media with the integration of a Mastodon server. We improve simulation efficiency and information flow, and add a set of measurement tools, particularly longitudinal surveys. We demonstrate the simulator with a tailored example in which we track agents' political positions and show how partisan manipulation of agents can affect election results.
The optimal training of a vision transformer for brain encoding depends on three factors: model size, data size, and computational resources… (voir plus). This study investigates these three pillars, focusing on the effects of data scaling, model scaling, and high-performance computing on brain encoding results. Using VideoGPT to extract efficient spatiotemporal features from videos and training a Ridge model to predict brain activity based on these features, we conducted benchmark experiments with varying data sizes (10k, 100k, 1M, 6M) and different model configurations of GPT-2, including hidden layer dimensions, number of layers, and number of attention heads. We also evaluated the effects of training models with 32-bit vs 16-bit floating point representations. Our results demonstrate that increasing the hidden layer dimensions significantly improves brain encoding performance, as evidenced by higher Pearson correlation coefficients across all subjects. In contrast, the number of attention heads does not have a significant effect on the encoding results. Additionally, increasing the number of layers shows some improvement in brain encoding correlations, but the trend is not as consistent as that observed with hidden layer dimensions. The data scaling results show that larger training datasets lead to improved brain encoding performance, with the highest Pearson correlation coefficients observed for the largest dataset size (6M). These findings highlight that the effects of data scaling are more significant compared to model scaling in enhancing brain encoding performance. Furthermore, we explored the impact of floating-point precision by comparing 32-bit and 16-bit representations. Training with 16-bit precision yielded the same brain encoding accuracy as 32-bit, while reducing training time by 1.17 times, demonstrating its efficiency for high-performance computing tasks.
The optimal training of a vision transformer for brain encoding depends on three factors: model size, data size, and computational resources… (voir plus). This study investigates these three pillars, focusing on the effects of data scaling, model scaling, and high-performance computing on brain encoding results. Using VideoGPT to extract efficient spatiotemporal features from videos and training a Ridge model to predict brain activity based on these features, we conducted benchmark experiments with varying data sizes (10k, 100k, 1M, 6M) and different model configurations of GPT-2, including hidden layer dimensions, number of layers, and number of attention heads. We also evaluated the effects of training models with 32-bit vs 16-bit floating point representations. Our results demonstrate that increasing the hidden layer dimensions significantly improves brain encoding performance, as evidenced by higher Pearson correlation coefficients across all subjects. In contrast, the number of attention heads does not have a significant effect on the encoding results. Additionally, increasing the number of layers shows some improvement in brain encoding correlations, but the trend is not as consistent as that observed with hidden layer dimensions. The data scaling results show that larger training datasets lead to improved brain encoding performance, with the highest Pearson correlation coefficients observed for the largest dataset size (6M). These findings highlight that the effects of data scaling are more significant compared to model scaling in enhancing brain encoding performance. Furthermore, we explored the impact of floating-point precision by comparing 32-bit and 16-bit representations. Training with 16-bit precision yielded the same brain encoding accuracy as 32-bit, while reducing training time by 1.17 times, demonstrating its efficiency for high-performance computing tasks.
Real-time aerial image segmentation plays an important role in the environmental perception of Uncrewed Aerial Vehicles (UAVs). We introduce… (voir plus) BlabberSeg, an optimized Vision-Language Model built on CLIPSeg for on-board, real-time processing of aerial images by UAVs. BlabberSeg improves the efficiency of CLIPSeg by reusing prompt and model features, reducing computational overhead while achieving real-time open-vocabulary aerial segmentation. We validated BlabberSeg in a safe landing scenario using the Dynamic Open-Vocabulary Enhanced SafE-Landing with Intelligence (DOVESEI) framework, which uses visual servoing and open-vocabulary segmentation. BlabberSeg reduces computational costs significantly, with a speed increase of 927.41% (16.78 Hz) on a NVIDIA Jetson Orin AGX (64GB) compared with the original CLIPSeg (1.81Hz), achieving real-time aerial segmentation with negligible loss in accuracy (2.1% as the ratio of the correctly segmented area with respect to CLIPSeg). BlabberSeg's source code is open and available online.
Model merging aims to efficiently combine the weights of multiple expert models, each trained on a specific task, into a single multi-task m… (voir plus)odel, with strong performance across all tasks. When applied to all but the last layer of weights, existing methods -- such as Task Arithmetic, TIES-merging, and TALL mask merging -- work well to combine expert models obtained by fine-tuning a common foundation model, operating within a"local"neighborhood of the foundation model. This work explores the more challenging scenario of"non-local"merging, which we find arises when an expert model changes significantly during pretraining or where the expert models do not even share a common foundation model. We observe that standard merging techniques often fail to generalize effectively in this non-local setting, even when accounting for permutation symmetries using standard techniques. We identify that this failure is, in part, due to"variance collapse", a phenomenon identified also in the setting of linear mode connectivity by Jordan et al. (2023). To address this, we propose a multi-task technique to re-scale and shift the output activations of the merged model for each task, aligning its output statistics with those of the corresponding task-specific expert models. Our experiments demonstrate that this correction significantly improves the performance of various model merging approaches in non-local settings, providing a strong baseline for future research on this problem.
Adversarial perturbations aim to deceive neural networks into predicting inaccurate results. For visual object trackers, adversarial attacks… (voir plus) have been developed to generate perturbations by manipulating the outputs. However, transformer trackers predict a specific bounding box instead of an object candidate list, which limits the applicability of many existing attack scenarios. To address this issue, we present a novel white-box approach to attack visual object trackers with transformer backbones using only one bounding box. From the tracker predicted bounding box, we generate a list of adversarial bounding boxes and compute the adversarial loss for those bounding boxes. Experimental results demonstrate that our simple yet effective attack outperforms existing attacks against several robust transformer trackers, including TransT-M, ROMTrack, and MixFormer, on popular benchmark tracking datasets such as GOT-10k, UAV123, and VOT2022STS.
Machine unlearning is gaining increasing attention as a way to remove adversarial data poisoning attacks from already trained models and to … (voir plus)comply with privacy and AI regulations. The objective is to unlearn the effect of undesired data from a trained model while maintaining performance on the remaining data. This paper introduces HyperForget, a novel machine unlearning framework that leverages hypernetworks– neural networks that generate parameters for other networks– to dynamically sample models that lack knowledge of targeted data while preserving essential capabilities. Leveraging diffusion models, we implement two Diffusion HyperForget Networks and used them to sample unlearned models in Proof-of-Concept experiments. The unlearned models obtained zero accuracy on the forget set, while preserving good accuracy on the retain sets, highlighting the potential of HyperForget for dynamic targeted data removal and a promising direction for developing adaptive machine unlearning algorithms.
The intricate structural and functional architecture of the brain enables a wide range of cognitive processes ranging from perception and ac… (voir plus)tion to higher-order abstract thinking. Despite important progress, the relationship between the brain’s structural and functional properties is not yet fully established. In particular, the way the brain’s anatomy shapes its electrophysiological dynamics remains elusive. The electroencephalography (EEG) activity recorded during naturalistic tasks is thought to exhibit patterns of coupling with the underlying brain structure that vary as a function of behavior. Yet these patterns have not yet been sufficiently quantified. We address this gap by jointly examining individual Diffusion-Weighted Imaging (DWI) scans and continuous EEG recorded during video-watching and resting state, using a Graph Signal Processing (GSP) framework. By decomposing the structural graph into Eigenmodes and expressing the EEG activity as an extension of anatomy, GSP provides a way to quantify the structure-function coupling. We elucidate how the structure shapes function during naturalistic tasks such as movie-watching and how this association is modulated by tasks. We quantify the coupling relationship in a region-, time-, frequency-resolved manner. First of all, our findings indicate that the EEG activity in the sensorimotor cortex is strongly coupled with brain structure, while the activity in higher-order systems is less constrained by anatomy, i.e., shows more flexibility. In addition, we found that watching videos was associated with stronger structure-function coupling in the sensorimotor cortex, as compared to resting-state data. Second, time-resolved analysis revealed that the unimodal systems undergo minimal temporal fluctuation in structure-function association, and the transmodal system displays highest temporal fluctuations, with the exception of PCC seeing low fluctuations. Lastly, our frequency-resolved analysis revealed a consistent topography across different EEG rhythms, suggesting a similar relationship with the anatomical structure across frequency bands. Together, this unprecedented characterization of the link between structure and function using continuous EEG during naturalistic behavior underscores the role of anatomy in shaping ongoing cognitive processes. Taken together, by combining the temporal and spectral resolution of EEG and the methodological advantages of GSP, our work sheds new light onto the anatomo-functional organization of the brain.
