Peu importe la taille : démocratiser la découverte de protéines avec l'IA
Des chercheurs de Mila ont créé un puissant modèle de langage protéique à source ouverte plus compact et efficace afin de démocratiser la découverte de protéines.
La prochaine cohorte de notre programme, conçu pour fournir aux participant·e·s une compréhension fondamentale des technologies de l'IA, se déroulera à Ottawa les 28 et 29 novembre.
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Publications
Self-Supervised Learning from Images with a Joint-Embedding Predictive Architecture
This paper demonstrates an approach for learning highly semantic image representations without relying on hand-crafted data-augmentations. W… (voir plus)e introduce the Image-based Joint-Embedding Predictive Architecture (I-JEPA), a non-generative approach for self-supervised learning from images. The idea behind I-JEPA is simple: from a single context block, predict the representations of various target blocks in the same image. A core design choice to guide I-JEPA towards producing semantic representations is the masking strategy; specifically, it is crucial to (a) sample target blocks with sufficiently large scale (semantic), and to (b) use a sufficiently informative (spatially distributed) context block. Empirically, when combined with Vision Transformers, we find I-JEPA to be highly scalable. For instance, we train a ViT-Huge/14 on ImageNet using 16 A100 GPUs in under 72 hours to achieve strong downstream performance across a wide range of tasks, from linear classification to object counting and depth prediction.
2023-06-17
2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) (publié)
Recently, a number of iterative learning methods have been introduced to improve generalization. These typically rely on training for longer… (voir plus) periods of time in exchange for improved generalization. LLF (later-layer-forgetting) is a state-of-the-art method in this category. It strengthens learning in early layers by periodically re-initializing the last few layers of the network. Our principal innovation in this work is to use Simulated annealing in EArly Layers (SEAL) of the network in place of re-initialization of later layers. Essentially, later layers go through the normal gradient descent process, while the early layers go through short stints of gradient ascent followed by gradient descent. Extensive experiments on the popular Tiny-ImageNet dataset benchmark and a series of transfer learning and few-shot learning tasks show that we outperform LLF by a significant margin. We further show that, compared to normal training, LLF features, although improving on the target task, degrade the transfer learning performance across all datasets we explored. In comparison, our method outperforms LLF across the same target datasets by a large margin. We also show that the prediction depth of our method is significantly lower than that of LLF and normal training, indicating on average better prediction performance. 11The code to reproduce our results is publicly available at: https://github.com/amiiir-sarfi/SEAL
2023-06-17
2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) (publié)
We present a neural technique for learning to select a local sub-region around a point which can be used for mesh parameterization. The moti… (voir plus)vation for our framework is driven by interactive workflows used for decaling, texturing, or painting on surfaces. Our key idea is to incorporate segmentation probabilities as weights of a classical parameterization method, implemented as a novel differentiable parameterization layer within a neural network framework. We train a segmentation network to select 3D regions that are parameterized into 2D and penalized by the resulting distortion, giving rise to segmentations which are distortion-aware. Following training, a user can use our system to interactively select a point on the mesh and obtain a large, meaningful region around the selection which induces a low-distortion parameterization. Our code11https://github.com/threedle/DA-Wand and project22https://threedle.github.io/DA-Wand/ are publicly available.
2023-06-17
2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) (publié)
Modern deep learning systems do not generalize well when the test data distribution is slightly different to the training data distribution.… (voir plus) While much promising work has been accomplished to address this fragility, a systematic study of the role of optimizers and their out-of-distribution generalization performance has not been undertaken. In this study, we examine the performance of popular first-order optimizers for different classes of distributional shift under empirical risk minimization and invariant risk minimization. We address this question for image and text classification using DomainBed, WILDS, and Backgrounds Challenge as testbeds for studying different types of shifts---namely correlation and diversity shift. We search over a wide range of hyperparameters and examine classification accuracy (in-distribution and out-of-distribution) for over 20,000 models. We arrive at the following findings, which we expect to be helpful for practitioners: i) adaptive optimizers (e.g., Adam) perform worse than non-adaptive optimizers (e.g., SGD, momentum SGD) on out-of-distribution performance. In particular, even though there is no significant difference in in-distribution performance, we show a measurable difference in out-of-distribution performance. ii) in-distribution performance and out-of-distribution performance exhibit three types of behavior depending on the dataset---linear returns, increasing returns, and diminishing returns. For example, in the training of natural language data using Adam, fine-tuning the performance of in-distribution performance does not significantly contribute to the out-of-distribution generalization performance.
Motivation: Recent advances in deep learning model development have enabled more accurate prediction of drug response in cancer. However, th… (voir plus)e black-box nature of these models still remains a hurdle in their adoption for precision cancer medicine. Recent efforts have focused on making these models interpretable by incorporating signaling pathway information in model architecture. While these models improve interpretability, it is unclear whether this higher interpretability comes at the cost of less accurate predictions, or a prediction improvement can also be obtained. Results: In this study, we comprehensively and systematically assessed four state-of-the-art interpretable models developed for drug response prediction to answer this question using three pathway collections. Our results showed that models that explicitly incorporate pathway information in the form of a latent layer perform worse compared to models that incorporate this information implicitly. Moreover, in most evaluation setups the best performance is achieved using a simple black-box model. In addition, replacing the signaling pathways with randomly generated pathways shows a comparable performance for the majority of these interpretable models. Our results suggest that new interpretable models are necessary to improve the drug response prediction performance. In addition, the current study provides different baseline models and evaluation setups necessary for such new models to demonstrate their superior prediction performance. Availability and Implementation: Implementation of all methods are provided in https://github.com/Emad-COMBINE-lab/InterpretableAI_for_DRP. Generated uniform datasets are in https://zenodo.org/record/7101665#.YzS79HbMKUk. Contact: amin.emad@mcgill.ca Supplementary Information: Online-only supplementary data is available at the journal’s website.
In this paper, we explore effective prompting techniques to enhance zero- and few-shot Visual Question Answering (VQA) performance in contem… (voir plus)porary Vision-Language Models (VLMs). Central to our investigation is the role of question templates in guiding VLMs to generate accurate answers. We identify that specific templates significantly influence VQA outcomes, underscoring the need for strategic template selection. Another pivotal aspect of our study is augmenting VLMs with image captions, providing them with additional visual cues alongside direct image features in VQA tasks. Surprisingly, this augmentation significantly improves the VLMs' performance in many cases, even though VLMs"see"the image directly! We explore chain-of-thought (CoT) reasoning and find that while standard CoT reasoning causes drops in performance, advanced methods like self-consistency can help recover it. Furthermore, we find that text-only few-shot examples enhance VLMs' alignment with the task format, particularly benefiting models prone to verbose zero-shot answers. Lastly, to mitigate the challenges associated with evaluating free-form open-ended VQA responses using string-matching based VQA metrics, we introduce a straightforward LLM-guided pre-processing technique to adapt the model responses to the expected ground-truth answer distribution. In summary, our research sheds light on the intricacies of prompting strategies in VLMs for VQA, emphasizing the synergistic use of captions, templates, and pre-processing to enhance model efficacy.
Across a variety of ranking tasks, researchers use reciprocal rank to measure the effectiveness for users interested in exactly one relevant… (voir plus) item. Despite its widespread use, evidence suggests that reciprocal rank is brittle when discriminating between systems. This brittleness, in turn, is compounded in modern evaluation settings where current, high-precision systems may be difficult to distinguish. We address the lack of sensitivity of reciprocal rank by introducing and connecting it to the concept of best-case retrieval, an evaluation method focusing on assessing the quality of a ranking for the most satisfied possible user across possible recall requirements. This perspective allows us to generalize reciprocal rank and define a new preference-based evaluation we call lexicographic precision or lexiprecision. By mathematical construction, we ensure that lexiprecision preserves differences detected by reciprocal rank, while empirically improving sensitivity and robustness across a broad set of retrieval and recommendation tasks.