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
La science, un droit humain. Mettre en œuvre le principe d’une science participative, équitable et accessible à tous
In this work, we consider the problem of autonomously discovering behavioral abstractions, or options, for reinforcement learning agents. We… (voir plus) propose an algorithm that focuses on the termination function, as opposed to - as is common - the policy. The termination function is usually trained to optimize a control objective: an option ought to terminate if another has better value. We offer a different, information-theoretic perspective, and propose that terminations should focus instead on the compressibility of the option’s encoding - arguably a key reason for using abstractions.To achieve this algorithmically, we leverage the classical options framework, and learn the option transition model as a “critic” for the termination function. Using this model, we derive gradients that optimize the desired criteria. We show that the resulting options are non-trivial, intuitively meaningful, and useful for learning.
In current practice, the behavior of Machine-Learned Components (MLCs) is not sufficiently specified by the predefined requirements. Instead… (voir plus), they "learn" existing patterns from the available training data, and make predictions for unseen data when deployed. On the surface, their ability to extract patterns and to behave accordingly is specifically useful for hard-to-specify concepts in certain safety critical domains (e.g., the definition of a pedestrian in a pedestrian detection component in a vehicle). However, the lack of requirements specifications on their behaviors makes further software engineering tasks challenging for such components. This is especially concerning for tasks such as safety assessment and assurance. In this position paper, we call for more attention from the requirements engineering community on supporting the specification of requirements for MLCs in safety critical domains. Towards that end, we propose an approach to improve the process of requirements specification in which an MLC is developed and operates by explicitly specifying domain-related concepts. Our approach extracts a universally accepted benchmark for hard-to-specify concepts (e.g., "pedestrian") and can be used to identify gaps in the associated dataset and the constructed machine-learned model.
2019-01-01
2019 IEEE 27th International Requirements Engineering Conference Workshops (REW) (publié)
Semantic parsing is the task of converting natural language utterances into machine interpretable meaning representations which can be execu… (voir plus)ted against a real-world environment such as a database. Scaling semantic parsing to arbitrary domains faces two interrelated challenges: obtaining broad coverage training data effectively and cheaply; and developing a model that generalizes to compositional utterances and complex intentions. We address these challenges with a framework which allows to elicit training data from a domain ontology and bootstrap a neural parser which recursively builds derivations of logical forms. In our framework meaning representations are described by sequences of natural language templates, where each template corresponds to a decomposed fragment of the underlying meaning representation. Although artificial, templates can be understood and paraphrased by humans to create natural utterances, resulting in parallel triples of utterances, meaning representations, and their decompositions. These allow us to train a neural semantic parser which learns to compose rules in deriving meaning representations. We crowdsource training data on six domains, covering both single-turn utterances which exhibit rich compositionality, and sequential utterances where a complex task is procedurally performed in steps. We then develop neural semantic parsers which perform such compositional tasks. In general, our approach allows to deploy neural semantic parsers quickly and cheaply from a given domain ontology.
The standard loss function used to train neural network classifiers, categorical cross-entropy (CCE), seeks to maximize accuracy on the trai… (voir plus)ning data; building useful representations is not a necessary byproduct of this objective. In this work, we propose clustering-oriented representation learning (COREL) as an alternative to CCE in the context of a generalized attractive-repulsive loss framework. COREL has the consequence of building latent representations that collectively exhibit the quality of natural clustering within the latent space of the final hidden layer, according to a predefined similarity function. Despite being simple to implement, COREL variants outperform or perform equivalently to CCE in a variety of scenarios, including image and news article classification using both feed-forward and convolutional neural networks. Analysis of the latent spaces created with different similarity functions facilitates insights on the different use cases COREL variants can satisfy, where the Cosine-COREL variant makes a consistently clusterable latent space, while Gaussian-COREL consistently obtains better classification accuracy than CCE.
This paper presents a new method for learning typed entailment graphs from text. We extract predicate-argument structures from multiple-sour… (voir plus)ce news corpora, and compute local distributional similarity scores to learn entailments between predicates with typed arguments (e.g., person contracted disease). Previous work has used transitivity constraints to improve local decisions, but these constraints are intractable on large graphs. We instead propose a scalable method that learns globally consistent similarity scores based on new soft constraints that consider both the structures across typed entailment graphs and inside each graph. Learning takes only a few hours to run over 100K predicates and our results show large improvements over local similarity scores on two entailment data sets. We further show improvements over paraphrases and entailments from the Paraphrase Database, and prior state-of-the-art entailment graphs. We show that the entailment graphs improve performance in a downstream task.
2018-12-01
Transactions of the Association for Computational Linguistics (publié)
In this work, we present a specific case study where we aim to design effective treatment allocation strategies and validate these using a m… (voir plus)ouse model of skin cancer. Collecting data for modelling treatments effectiveness on animal models is an expensive and time consuming process. Moreover, acquiring this information during the full range of disease stages is hard to achieve with a conventional random treatment allocation procedure, as poor treatments cause deterioration of subject health. We therefore aim to design an adaptive allocation strategy to improve the efficiency of data collection by allocating more samples for exploring promising treatments. We cast this application as a contextual bandit problem and introduce a simple and practical algorithm for exploration-exploitation in this framework. The work builds on a recent class of approaches for non-contextual bandits that relies on subsampling to compare treatment options using an equivalent amount of information. On the technical side, we extend the subsampling strategy to the case of bandits with context, by applying subsampling within Gaussian Process regression. On the experimental side, preliminary results using 10 mice with skin tumours suggest that the proposed approach extends by more than 50% the subjects life duration compared with baseline strategies: no treatment, random treatment allocation, and constant chemotherapeutic agent. By slowing the tumour growth rate, the adaptive procedure gathers information about treatment effectiveness on a broader range of tumour volumes, which is crucial for eventually deriving sequential pharmacological treatment strategies for cancer.
2018-11-29
Proceedings of the 3rd Machine Learning for Healthcare Conference (publié)
Entropy regularization is commonly used to improve policy optimization in reinforcement learning. It is believed to help with \emph{explorat… (voir plus)ion} by encouraging the selection of more stochastic policies. In this work, we analyze this claim using new visualizations of the optimization landscape based on randomly perturbing the loss function. We first show that even with access to the exact gradient, policy optimization is difficult due to the geometry of the objective function. Then, we qualitatively show that in some environments, a policy with higher entropy can make the optimization landscape smoother, thereby connecting local optima and enabling the use of larger learning rates. This paper presents new tools for understanding the optimization landscape, shows that policy entropy serves as a regularizer, and highlights the challenge of designing general-purpose policy optimization algorithms.
To achieve general artificial intelligence, reinforcement learning (RL) agents should learn not only to optimize returns for one specific ta… (voir plus)sk but also to constantly build more complex skills and scaffold their knowledge about the world, without forgetting what has already been learned. In this paper, we discuss the desired characteristics of environments that can support the training and evaluation of lifelong reinforcement learning agents, review existing environments from this perspective, and propose recommendations for devising suitable environments in the future.
We present two architectures for multi-task learning with neural sequence models. Our approach allows the relationships between different ta… (voir plus)sks to be learned dynamically, rather than using an ad-hoc pre-defined structure as in previous work. We adopt the idea from message-passing graph neural networks and propose a general \textbf{graph multi-task learning} framework in which different tasks can communicate with each other in an effective and interpretable way. We conduct extensive experiments in text classification and sequence labeling to evaluate our approach on multi-task learning and transfer learning. The empirical results show that our models not only outperform competitive baselines but also learn interpretable and transferable patterns across tasks.
Identifying the Best Machine Learning Algorithms for Brain Tumor Segmentation, Progression Assessment, and Overall Survival Prediction in the BRATS Challenge
Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneo… (voir plus)us histologic sub-regions, i.e., peritumoral edematous/invaded tissue, necrotic core, active and non-enhancing core. This intrinsic heterogeneity is also portrayed in their radio-phenotype, as their sub-regions are depicted by varying intensity profiles disseminated across multi-parametric magnetic resonance imaging (mpMRI) scans, reflecting varying biological properties. Their heterogeneous shape, extent, and location are some of the factors that make these tumors difficult to resect, and in some cases inoperable. The amount of resected tumoris a factor also considered in longitudinal scans, when evaluating the apparent tumor for potential diagnosis of progression. Furthermore, there is mounting evidence that accurate segmentation of the various tumor sub-regions can offer the basis for quantitative image analysis towards prediction of patient overall survival. This study assesses thestate-of-the-art machine learning (ML) methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i.e., 2012-2018. Specifically, we focus on i) evaluating segmentations of the various glioma sub-regions in pre-operative mpMRI scans, ii) assessing potential tumor progression by virtue of longitudinal growth of tumor sub-regions, beyond use of the RECIST/RANO criteria, and iii) predicting the overall survival from pre-operative mpMRI scans of patients that underwent gross tota lresection. Finally, we investigate the challenge of identifying the best ML algorithms for each of these tasks, considering that apart from being diverse on each instance of the challenge, the multi-institutional mpMRI BraTS dataset has also been a continuously evolving/growing dataset.
The NLP and ML communities have long been interested in developing models capable of common-sense reasoning, and recent works have significa… (voir plus)ntly improved the state of the art on benchmarks like the Winograd Schema Challenge (WSC). Despite these advances, the complexity of tasks designed to test common-sense reasoning remains under-analyzed. In this paper, we make a case study of the Winograd Schema Challenge and, based on two new measures of instance-level complexity, design a protocol that both clarifies and qualifies the results of previous work. Our protocol accounts for the WSC's limited size and variable instance difficulty, properties common to other common-sense benchmarks. Accounting for these properties when assessing model results may prevent unjustified conclusions.