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Publications
Effects of gene dosage on cognitive ability: A function-based association study across brain and non-brain processes
Genomic Copy Number Variants (CNVs) that increase risk for neurodevelopmental disorders are also associated with lower cognitive ability in … (voir plus)general population cohorts. Studies have focussed on a small set of recurrent CNVs, but burden analyses suggested that the vast majority of CNVs affecting cognitive ability are too rare to reach variant-level association. As a result, the full range of gene-dosage-sensitive biological processes linked to cognitive ability remains unknown. To investigate this issue, we identified all CNVs >50 kilobases in 258k individuals from 6 general population cohorts with assessments of general cognitive abilities. We performed a CNV-GWAS and functional burden analyses, which tested 6502 gene-sets defined by tissue and cell-type transcriptomics as well as gene ontology disrupted by all rare coding CNVs. CNV-GWAS identified a novel duplication at 2q12.3 associated with higher performance in cognitive ability. Among the 864 gene-sets associated with cognitive ability, only 11% showed significant effects for both deletions and duplication. Accordingly, we systematically observed negative correlations between deletion and duplication effect sizes across all levels of biological observations. We quantified the preferential effects of deletions versus duplication using tagDS, a new normalized metric. Cognitive ability was preferentially affected by cortical, presynaptic, and negative-regulation gene-sets when duplicated. In contrast, preferential effects of deletions were observed for subcortical, post-synaptic, and positive-regulation gene-sets. A large proportion of gene-sets assigned to non-brain organs were associated with cognitive ability due to low tissue specificity genes, which were associated with higher sensitive to haploinsufficiency. Overall, most biological functions associated with cognitive ability are divided into those sensitive to either deletion or duplications.
Neural Algorithmic Reasoning (NAR) is a research area focused on designing neural architectures that can reliably capture classical computat… (voir plus)ion, usually by learning to execute algorithms. A typical approach is to rely on Graph Neural Network (GNN) architectures, which encode inputs in high-dimensional latent spaces that are repeatedly transformed during the execution of the algorithm. In this work we perform a detailed analysis of the structure of the latent space induced by the GNN when executing algorithms. We identify two possible failure modes: (i) loss of resolution, making it hard to distinguish similar values; (ii) inability to deal with values outside the range observed during training. We propose to solve the first issue by relying on a softmax aggregator, and propose to decay the latent space in order to deal with out-of-range values. We show that these changes lead to improvements on the majority of algorithms in the standard CLRS-30 benchmark when using the state-of-the-art Triplet-GMPNN processor. Our code is available at https://github.com/mirjanic/nar-latent-spaces
2024-04-17
Proceedings of the Second Learning on Graphs Conference (publié)
Large language models (LLMs) excel at few-shot in-context learning (ICL) -- learning from a few examples provided in context at inference, w… (voir plus)ithout any weight updates. Newly expanded context windows allow us to investigate ICL with hundreds or thousands of examples -- the many-shot regime. Going from few-shot to many-shot, we observe significant performance gains across a wide variety of generative and discriminative tasks. While promising, many-shot ICL can be bottlenecked by the available amount of human-generated examples. To mitigate this limitation, we explore two new settings: Reinforced and Unsupervised ICL. Reinforced ICL uses model-generated chain-of-thought rationales in place of human examples. Unsupervised ICL removes rationales from the prompt altogether, and prompts the model only with domain-specific questions. We find that both Reinforced and Unsupervised ICL can be quite effective in the many-shot regime, particularly on complex reasoning tasks. Finally, we demonstrate that, unlike few-shot learning, many-shot learning is effective at overriding pretraining biases, can learn high-dimensional functions with numerical inputs, and performs comparably to fine-tuning. We also find that inference cost increases linearly in the many-shot regime, and frontier LLMs benefit from many-shot ICL to varying degrees. Our analysis also reveals the limitations of next-token prediction loss as an indicator of downstream ICL performance.
Large language models (LLMs) excel at few-shot in-context learning (ICL) -- learning from a few examples provided in context at inference, w… (voir plus)ithout any weight updates. Newly expanded context windows allow us to investigate ICL with hundreds or thousands of examples -- the many-shot regime. Going from few-shot to many-shot, we observe significant performance gains across a wide variety of generative and discriminative tasks. While promising, many-shot ICL can be bottlenecked by the available amount of human-generated examples. To mitigate this limitation, we explore two new settings: Reinforced and Unsupervised ICL. Reinforced ICL uses model-generated chain-of-thought rationales in place of human examples. Unsupervised ICL removes rationales from the prompt altogether, and prompts the model only with domain-specific questions. We find that both Reinforced and Unsupervised ICL can be quite effective in the many-shot regime, particularly on complex reasoning tasks. Finally, we demonstrate that, unlike few-shot learning, many-shot learning is effective at overriding pretraining biases, can learn high-dimensional functions with numerical inputs, and performs comparably to fine-tuning. We also find that inference cost increases linearly in the many-shot regime, and frontier LLMs benefit from many-shot ICL to varying degrees. Our analysis also reveals the limitations of next-token prediction loss as an indicator of downstream ICL performance.
Large language models (LLMs) excel at few-shot in-context learning (ICL) -- learning from a few examples provided in context at inference, w… (voir plus)ithout any weight updates. Newly expanded context windows allow us to investigate ICL with hundreds or thousands of examples -- the many-shot regime. Going from few-shot to many-shot, we observe significant performance gains across a wide variety of generative and discriminative tasks. While promising, many-shot ICL can be bottlenecked by the available amount of human-generated examples. To mitigate this limitation, we explore two new settings: Reinforced and Unsupervised ICL. Reinforced ICL uses model-generated chain-of-thought rationales in place of human examples. Unsupervised ICL removes rationales from the prompt altogether, and prompts the model only with domain-specific questions. We find that both Reinforced and Unsupervised ICL can be quite effective in the many-shot regime, particularly on complex reasoning tasks. Finally, we demonstrate that, unlike few-shot learning, many-shot learning is effective at overriding pretraining biases, can learn high-dimensional functions with numerical inputs, and performs comparably to fine-tuning. We also find that inference cost increases linearly in the many-shot regime, and frontier LLMs benefit from many-shot ICL to varying degrees. Our analysis also reveals the limitations of next-token prediction loss as an indicator of downstream ICL performance.
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
