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Scaling deep learning models has been at the heart of recent revolutions in language modelling and image generation. Practitioners have obse… (voir plus)rved a strong relationship between model size, dataset size, and performance. However, structure-based architectures such as Graph Neural Networks (GNNs) are yet to show the benefits of scale mainly due to the lower efficiency of sparse operations, large data requirements, and lack of clarity about the effectiveness of various architectures. We address this drawback of GNNs by studying their scaling behavior. Specifically, we analyze message-passing networks, graph Transformers, and hybrid architectures on the largest public collection of 2D molecular graphs. For the first time, we observe that GNNs benefit tremendously from the increasing scale of depth, width, number of molecules, number of labels, and the diversity in the pretraining datasets. We further demonstrate strong finetuning scaling behavior on 38 highly competitive downstream tasks, outclassing previous large models. This gives rise to MolGPS, a new graph foundation model that allows to navigate the chemical space, outperforming the previous state-of-the-arts on 26 out the 38 downstream tasks. We hope that our work paves the way for an era where foundational GNNs drive pharmaceutical drug discovery.
Featurizing microscopy images for use in biological research remains a significant challenge, especially for large-scale experiments spannin… (voir plus)g millions of images. This work explores the scaling properties of weakly supervised classifiers and self-supervised masked autoencoders (MAEs) when training with increasingly larger model backbones and microscopy datasets. Our results show that ViT-based MAEs outperform weakly supervised classifiers on a variety of tasks, achieving as much as a 11.5% relative improvement when recalling known biological relationships curated from public databases. Additionally, we develop a new channel-agnostic MAE architecture (CA-MAE) that allows for inputting images of different numbers and orders of channels at inference time. We demonstrate that CA-MAEs effectively generalize by inferring and evaluating on a microscopy image dataset (JUMP-CP) generated under different experimental conditions with a different channel structure than our pretraining data (RPI-93M). Our findings motivate continued research into scaling self-supervised learning on microscopy data in order to create powerful foundation models of cellular biology that have the potential to catalyze advancements in drug discovery and beyond. Relevant code and select models released with this work can be found at: https://github.com/recursionpharma/maes_microscopy.
Featurizing microscopy images for use in biological research remains a significant challenge, especially for large-scale experiments spannin… (voir plus)g millions of images. This work explores the scaling properties of weakly supervised classifiers and self-supervised masked autoencoders (MAEs) when training with increasingly larger model backbones and microscopy datasets. Our results show that ViT-based MAEs outperform weakly supervised classifiers on a variety of tasks, achieving as much as a 11.5% relative improvement when recalling known biological relationships curated from public databases. Additionally, we develop a new channel-agnostic MAE architecture (CA-MAE) that allows for inputting images of different numbers and orders of channels at inference time. We demonstrate that CA-MAEs effectively generalize by inferring and evaluating on a microscopy image dataset (JUMP-CP) generated under different experimental conditions with a different channel structure than our pretraining data (RPI-93M). Our findings motivate continued research into scaling self-supervised learning on microscopy data in order to create powerful foundation models of cellular biology that have the potential to catalyze advancements in drug discovery and beyond. Relevant code and select models released with this work can be found at: https://github.com/recursionpharma/maes_microscopy.
Featurizing microscopy images for use in biological research remains a significant challenge, especially for large-scale experiments spannin… (voir plus)g millions of images. This work explores the scaling properties of weakly supervised classifiers and self-supervised masked autoencoders (MAEs) when training with increasingly larger model backbones and microscopy datasets. Our results show that ViT-based MAEs outperform weakly supervised classifiers on a variety of tasks, achieving as much as a 11.5% relative improvement when recalling known biological relationships curated from public databases. Additionally, we develop a new channel-agnostic MAE architecture (CA-MAE) that allows for inputting images of different numbers and orders of channels at inference time. We demonstrate that CA-MAEs effectively generalize by inferring and evaluating on a microscopy image dataset (JUMP-CP) generated under different experimental conditions with a different channel structure than our pretraining data (RPI-93M). Our findings motivate continued research into scaling self-supervised learning on microscopy data in order to create powerful foundation models of cellular biology that have the potential to catalyze advancements in drug discovery and beyond. Relevant code and select models released with this work can be found at: https://github.com/recursionpharma/maes_microscopy.
This work identifies 18 foundational challenges in assuring the alignment and safety of large language models (LLMs). These challenges are o… (voir plus)rganized into three different categories: scientific understanding of LLMs, development and deployment methods, and sociotechnical challenges. Based on the identified challenges, we pose
This work identifies 18 foundational challenges in assuring the alignment and safety of large language models (LLMs). These challenges are o… (voir plus)rganized into three different categories: scientific understanding of LLMs, development and deployment methods, and sociotechnical challenges. Based on the identified challenges, we pose
This work identifies 18 foundational challenges in assuring the alignment and safety of large language models (LLMs). These challenges are o… (voir plus)rganized into three different categories: scientific understanding of LLMs, development and deployment methods, and sociotechnical challenges. Based on the identified challenges, we pose
This work identifies 18 foundational challenges in assuring the alignment and safety of large language models (LLMs). These challenges are o… (voir plus)rganized into three different categories: scientific understanding of LLMs, development and deployment methods, and sociotechnical challenges. Based on the identified challenges, we pose
This work identifies 18 foundational challenges in assuring the alignment and safety of large language models (LLMs). These challenges are o… (voir plus)rganized into three different categories: scientific understanding of LLMs, development and deployment methods, and sociotechnical challenges. Based on the identified challenges, we pose
Weakly Supervised Object Localization (WSOL) allows training deep learning models for classification and localization (LOC) using only globa… (voir plus)l class-level labels. The absence of bounding box (bbox) supervision during training raises challenges in the literature for hyper-parameter tuning, model selection, and evaluation. WSOL methods rely on a validation set with bbox annotations for model selection, and a test set with bbox annotations for threshold estimation for producing bboxes from localization maps. This approach, however, is not aligned with the WSOL setting as these annotations are typically unavailable in real-world scenarios. Our initial empirical analysis shows a significant decline in LOC performance when model selection and threshold estimation rely solely on class labels and the image itself, respectively, compared to using manual bbox annotations. This highlights the importance of incorporating bbox labels for optimal model performance. In this paper, a new WSOL evaluation protocol is proposed that provides LOC information without the need for manual bbox annotations. In particular, we generated noisy pseudo-boxes from a pretrained off-the-shelf region proposal method such as Selective Search, CLIP, and RPN for model selection. These bboxes are also employed to estimate the threshold from LOC maps, circumventing the need for test-set bbox annotations. Our experiments with several WSOL methods on ILSVRC and CUB datasets show that using the proposed pseudo-bboxes for validation facilitates the model selection and threshold estimation, with LOC performance comparable to those selected using GT bboxes on the validation set and threshold estimation on the test set. It also outperforms models selected using class-level labels, and then dynamically thresholded based solely on LOC maps.
