Latent variable models such as the Variational Auto-Encoder (VAE) have become a go-to tool for analyzing biological data, especially in the field of single-cell genomics. One remaining challenge is the interpretability of latent variables as biological processes that define a cell's identity. Outside of biological applications, this problem is commonly referred to as learning disentangled representations. Although several disentanglement-promoting variants of the VAE were introduced, and applied to single-cell genomics data, this task has been shown to be infeasible from independent and identically distributed measurements, without additional structure. Instead, recent methods propose to leverage non-stationary data, as well as the sparse mechanism shift assumption in order to learn disentangled representations with a causal semantic. Here, we extend the application of these methodological advances to the analysis of single-cell genomics data with genetic or chemical perturbations. More precisely, we propose a deep generative model of single-cell gene expression data for which each perturbation is treated as a stochastic intervention targeting an unknown, but sparse, subset of latent variables. We benchmark these methods on simulated single-cell data to evaluate their performance at latent units recovery, causal target identification and out-of-domain generalization. Finally, we apply those approaches to two real-world large-scale gene perturbation data sets and find that models that exploit the sparse mechanism shift hypothesis surpass contemporary methods on a transfer learning task. We implement our new model and benchmarks using the scvi-tools library, and release it as open-source software at \url{https://github.com/Genentech/sVAE}.

因果推断的一个共同主题是学习观察到的变量（也称为因果发现）之间的因果关系。考虑到大量候选因果图和搜索空间的组合性质，这通常是一项艰巨的任务。也许出于这个原因，到目前为止，大多数研究都集中在相对较小的因果图上，并具有多达数百个节点。但是，诸如生物学之类的领域的最新进展使生成实验数据集，并进行了数千种干预措施，然后进行了数千个变量的丰富分析，从而增加了机会和迫切需要大量因果图模型。在这里，我们介绍了因子定向无环图（F-DAG）的概念，是将搜索空间限制为非线性低级别因果相互作用模型的一种方法。将这种新颖的结构假设与最近的进步相结合，弥合因果发现与连续优化之间的差距，我们在数千个变量上实现了因果发现。此外，作为统计噪声对此估计程序的影响的模型，我们根据随机图研究了F-DAG骨架的边缘扰动模型，并量化了此类扰动对F-DAG等级的影响。该理论分析表明，一组候选F-DAG比整个DAG空间小得多，因此在很难评估基础骨架的高维度中更统计学上的稳定性。我们提出了因子图（DCD-FG）的可区分因果发现，这是对高维介入数据的F-DAG约束因果发现的可扩展实现。 DCD-FG使用高斯非线性低级结构方程模型，并且在模拟中的最新方法以及最新的大型单细胞RNA测序数据集中，与最新方法相比显示出显着改善遗传干预措施。

Contrastive representation learning has proven to be an effective self-supervised learning method for images and videos. Most successful approaches are based on Noise Contrastive Estimation (NCE) and use different views of an instance as positives that should be contrasted with other instances, called negatives, that are considered as noise. However, several instances in a dataset are drawn from the same distribution and share underlying semantic information. A good data representation should contain relations between the instances, or semantic similarity and dissimilarity, that contrastive learning harms by considering all negatives as noise. To circumvent this issue, we propose a novel formulation of contrastive learning using semantic similarity between instances called Similarity Contrastive Estimation (SCE). Our training objective is a soft contrastive one that brings the positives closer and estimates a continuous distribution to push or pull negative instances based on their learned similarities. We validate empirically our approach on both image and video representation learning. We show that SCE performs competitively with the state of the art on the ImageNet linear evaluation protocol for fewer pretraining epochs and that it generalizes to several downstream image tasks. We also show that SCE reaches state-of-the-art results for pretraining video representation and that the learned representation can generalize to video downstream tasks.

The optimal layout of a complex system such as aerospace vehicles consists in placing a given number of components in a container in order to minimize one or several objectives under some geometrical or functional constraints. This paper presents an extended formulation of this problem as a variable-size design space (VSDS) problem to take into account a large number of architectural choices and components allocation during the design process. As a representative example of such systems, considering the layout of a satellite module, the VSDS aspect translates the fact that the optimizer has to choose between several subdivisions of the components. For instance, one large tank of fuel might be placed as well as two smaller tanks or three even smaller tanks for the same amount of fuel. In order to tackle this NP-hard problem, a genetic algorithm enhanced by an adapted hidden-variables mechanism is proposed. This latter is illustrated on a toy case and an aerospace application case representative to real world complexity to illustrate the performance of the proposed algorithms. The results obtained using the proposed mechanism are reported and analyzed.

Machine Learning for Source Code (ML4Code) is an active research field in which extensive experimentation is needed to discover how to best use source code's richly structured information. With this in mind, we introduce JEMMA, an Extensible Java Dataset for ML4Code Applications, which is a large-scale, diverse, and high-quality dataset targeted at ML4Code. Our goal with JEMMA is to lower the barrier to entry in ML4Code by providing the building blocks to experiment with source code models and tasks. JEMMA comes with a considerable amount of pre-processed information such as metadata, representations (e.g., code tokens, ASTs, graphs), and several properties (e.g., metrics, static analysis results) for 50,000 Java projects from the 50KC dataset, with over 1.2 million classes and over 8 million methods. JEMMA is also extensible allowing users to add new properties and representations to the dataset, and evaluate tasks on them. Thus, JEMMA becomes a workbench that researchers can use to experiment with novel representations and tasks operating on source code. To demonstrate the utility of the dataset, we also report results from two empirical studies on our data, ultimately showing that significant work lies ahead in the design of context-aware source code models that can reason over a broader network of source code entities in a software project, the very task that JEMMA is designed to help with.

Scaling up neural networks has led to remarkable performance across a wide range of tasks. Moreover, performance often follows reliable scaling laws as a function of training set size, model size, and compute, which offers valuable guidance as large-scale experiments are becoming increasingly expensive. However, previous work on scaling laws has primarily used private data \& models or focused on uni-modal language or vision learning. To address these limitations, we investigate scaling laws for contrastive language-image pre-training (CLIP) with the public LAION dataset and the open-source OpenCLIP repository. Our large-scale experiments involve models trained on up to two billion image-text pairs and identify power law scaling for multiple downstream tasks including zero-shot classification, retrieval, linear probing, and end-to-end fine-tuning. We find that the training distribution plays a key role in scaling laws as the OpenAI and OpenCLIP models exhibit different scaling behavior despite identical model architectures and similar training recipes. We open-source our evaluation workflow and all models, including the largest public CLIP models, to ensure reproducibility and make scaling laws research more accessible. Source code and instructions to reproduce this study will be available at https://github.com/LAION-AI/scaling-laws-openclip

In this paper, we investigate the problem of multi-domain translation: given an element $a$ of domain $A$, we would like to generate a corresponding $b$ sample in another domain $B$, and vice versa. Acquiring supervision in multiple domains can be a tedious task, also we propose to learn this translation from one domain to another when supervision is available as a pair $(a,b)\sim A\times B$ and leveraging possible unpaired data when only $a\sim A$ or only $b\sim B$ is available. We introduce a new unified framework called Latent Space Mapping (\model) that exploits the manifold assumption in order to learn, from each domain, a latent space. Unlike existing approaches, we propose to further regularize each latent space using available domains by learning each dependency between pairs of domains. We evaluate our approach in three tasks performing i) synthetic dataset with image translation, ii) real-world task of semantic segmentation for medical images, and iii) real-world task of facial landmark detection.

The Codex model has demonstrated extraordinary competence in synthesizing code from natural language problem descriptions. However, in order to reveal unknown failure modes and hidden biases, such large-scale models must be systematically subjected to multiple and diverse evaluation studies. In this work, we evaluate the code synthesis capabilities of the Codex model based on a set of 115 Python problem statements from a popular competitive programming portal: HackerRank. Our evaluation shows that Codex is indeed proficient in Python, solving 96% of the problems in a zero-shot setting, and 100% of the problems in a few-shot setting. However, Codex exhibits clear signs of generating memorized code based on our evaluation. This is alarming, especially since the adoption and use of such models could directly impact how code is written and produced in the foreseeable future. With this in mind, we further discuss and highlight some of the prominent risks associated with large-scale models of source code. Finally, we propose a framework for code-synthesis evaluation using variations of problem statements based on mutations.

In this work we propose a novel token-based training strategy that improves Transformer-Transducer (T-T) based speaker change detection (SCD) performance. The conventional T-T based SCD model loss optimizes all output tokens equally. Due to the sparsity of the speaker changes in the training data, the conventional T-T based SCD model loss leads to sub-optimal detection accuracy. To mitigate this issue, we use a customized edit-distance algorithm to estimate the token-level SCD false accept (FA) and false reject (FR) rates during training and optimize model parameters to minimize a weighted combination of the FA and FR, focusing the model on accurately predicting speaker changes. We also propose a set of evaluation metrics that align better with commercial use cases. Experiments on a group of challenging real-world datasets show that the proposed training method can significantly improve the overall performance of the SCD model with the same number of parameters.

The spread of misinformation is a prominent problem in today's society, and many researchers in academia and industry are trying to combat it. Due to the vast amount of misinformation that is created every day, it is unrealistic to leave this task to human fact-checkers. Data scientists and researchers have been working on automated misinformation detection for years, and it is still a challenging problem today. The goal of our research is to add a new level to automated misinformation detection; classifying segments of text with persuasive writing techniques in order to produce interpretable reasoning for why an article can be marked as misinformation. To accomplish this, we present a novel annotation scheme containing many common persuasive writing tactics, along with a dataset with human annotations accordingly. For this task, we make use of a RoBERTa model for text classification, due to its high performance in NLP. We develop several language model-based baselines and present the results of our persuasive strategy label predictions as well as the improvements these intermediate labels make in detecting misinformation and producing interpretable results.