单细胞转录组学的分析通常依赖于聚类细胞，然后进行差异基因表达（DGE）来识别这些簇之间变化的基因。这些离散分析成功地确定了细胞类型和标记。但是，可能无法检测到细胞类型内部和之间的连续变化。我们提出了三种拓扑动机的数学方法，用于无监督的特征选择，这些方法可以同时在多个尺度上同时考虑离散和连续的转录模式。 eigenscores（$ \ mathrm {eig} _i $）基于其与图形laplacian的频谱分解在数据中与低频内在图案的对应相对的对应。多尺度拉普拉斯评分（MLS）是一种无监督的方法，用于在数据中定位相关量表并选择在这些相应量表上相干表达的基因。持续的瑞利商（PRQ）采用了配备过滤的数据，允许在分叉过程中具有不同作用的基因（例如伪时间）。我们通过将它们应用于已发布的单细胞转录组数据集来证明这些技术的实用性。该方法验证了先前鉴定的基因并检测具有相干表达模式的其他基因。通过研究基因信号与基础空间的几何形状之间的相互作用，这三种方法给出了基因的多维排名和它们之间关系的可视化。

语言模型既展示了定量的改进，又展示了新的定性功能，随着规模的增加。尽管它们具有潜在的变革性影响，但这些新能力的特征却很差。为了为未来的研究提供信息，为破坏性的新模型能力做准备，并改善社会有害的效果，至关重要的是，我们必须了解目前和近乎未来的能力和语言模型的局限性。为了应对这一挑战，我们介绍了超越模仿游戏基准（Big Bench）。 Big Bench目前由204个任务组成，由132家机构的442位作者贡献。任务主题是多样的，从语言学，儿童发展，数学，常识性推理，生物学，物理学，社会偏见，软件开发等等。 Big-Bench专注于被认为超出当前语言模型的功能的任务。我们评估了OpenAI的GPT型号，Google内部密集变压器体系结构和大型基础上的开关稀疏变压器的行为，跨越了数百万到数十亿个参数。此外，一个人类专家评估者团队执行了所有任务，以提供强大的基准。研究结果包括：模型性能和校准都随规模改善，但绝对的术语（以及与评估者的性能相比）；在模型类中的性能非常相似，尽管带有稀疏性。逐渐和预测的任务通常涉及大量知识或记忆成分，而在临界规模上表现出“突破性”行为的任务通常涉及多个步骤或组成部分或脆性指标；社交偏见通常会随着含糊不清的环境而随着规模而增加，但这可以通过提示来改善。

In this work we introduce reinforcement learning techniques for solving lexicographic multi-objective problems. These are problems that involve multiple reward signals, and where the goal is to learn a policy that maximises the first reward signal, and subject to this constraint also maximises the second reward signal, and so on. We present a family of both action-value and policy gradient algorithms that can be used to solve such problems, and prove that they converge to policies that are lexicographically optimal. We evaluate the scalability and performance of these algorithms empirically, demonstrating their practical applicability. As a more specific application, we show how our algorithms can be used to impose safety constraints on the behaviour of an agent, and compare their performance in this context with that of other constrained reinforcement learning algorithms.

Large-scale models combining text and images have made incredible progress in recent years. However, they can still fail at tasks requiring compositional knowledge, such as correctly picking out a red cube from a picture of multiple shapes. We examine the ability of CLIP (Radford et al., 2021), to caption images requiring compositional knowledge. We implement five compositional language models to probe the kinds of structure that CLIP may be using, and develop a novel training algorithm, Compositional Skipgram for Images (CoSI), to train these models. We look at performance in attribute-based tasks, requiring the identification of a particular combination of attribute and object (such as "red cube"), and in relational settings, where the spatial relation between two shapes (such as "cube behind sphere") must be identified. We find that in some conditions, CLIP is able to learn attribute-object labellings, and to generalize to unseen attribute-object combinations. However, we also see evidence that CLIP is not able to bind features together reliably. Moreover, CLIP is not able to reliably learn relations between objects, whereas some compositional models are able to learn these perfectly. Of the five models we developed, none were able to generalize to unseen relations.

Prior work has shown that it is possible to expand pretrained Masked Language Models (MLMs) to new languages by learning a new set of embeddings, while keeping the transformer body frozen. Despite learning a small subset of parameters, this approach is not compute-efficient, as training the new embeddings requires a full forward and backward pass over the entire model. In this work, we propose mini-model adaptation, a compute-efficient alternative that builds a shallow mini-model from a fraction of a large model's parameters. New language-specific embeddings can then be efficiently trained over the mini-model, and plugged into the aligned large model for rapid cross-lingual transfer. We explore two approaches to learn mini-models: MiniJoint, which jointly pretrains the primary model and the mini-model using a single transformer with a secondary MLM head at a middle layer; and MiniPost, where we start from a regular pretrained model and build a mini-model by extracting and freezing a few layers and learning a small number of parameters on top. Experiments on XNLI, MLQA and PAWS-X show that mini-model adaptation matches the performance of the standard approach using up to 2.4x less compute.

Despite many recent advancements in language modeling, state-of-the-art language models lack grounding in the real world and struggle with tasks involving complex reasoning. Meanwhile, advances in the symbolic reasoning capabilities of AI have led to systems that outperform humans in games like chess and Go (Silver et al., 2018). Chess commentary provides an interesting domain for bridging these two fields of research, as it requires reasoning over a complex board state and providing analyses in natural language. In this work we demonstrate how to combine symbolic reasoning engines with controllable language models to generate chess commentaries. We conduct experiments to demonstrate that our approach generates commentaries that are preferred by human judges over previous baselines.

Large-scale generative models show an impressive ability to perform a wide range of Natural Language Processing (NLP) tasks using in-context learning, where a few examples are used to describe a task to the model. For Machine Translation (MT), these examples are typically randomly sampled from the development dataset with a similar distribution as the evaluation set. However, it is unclear how the choice of these in-context examples and their ordering impacts the output translation quality. In this work, we aim to understand the properties of good in-context examples for MT in both in-domain and out-of-domain settings. We show that the translation quality and the domain of the in-context examples matter and that 1-shot noisy unrelated example can have a catastrophic impact on output quality. While concatenating multiple random examples reduces the effect of noise, a single good prompt optimized to maximize translation quality on the development dataset can elicit learned information from the pre-trained language model. Adding similar examples based on an n-gram overlap with the test source significantly and consistently improves the translation quality of the outputs, outperforming a strong kNN-MT baseline in 2 out of 4 out-of-domain datasets.

Existing language models (LMs) predict tokens with a softmax over a finite vocabulary, which can make it difficult to predict rare tokens or phrases. We introduce NPM, the first nonparametric masked language model that replaces this softmax with a nonparametric distribution over every phrase in a reference corpus. We show that NPM can be efficiently trained with a contrastive objective and an in-batch approximation to full corpus retrieval. Zero-shot evaluation on 9 closed-set tasks and 7 open-set tasks demonstrates that NPM outperforms significantly larger parametric models, either with or without a retrieve-and-generate approach. It is particularly better on dealing with rare patterns (word senses or facts), and predicting rare or nearly unseen words (e.g., non-Latin script). We release the model and code at github.com/facebookresearch/NPM.

Sampling diverse programs from a code language model and reranking with model likelihood is a popular method for code generation but it is prone to preferring degenerate solutions. Inspired by collaborative programming, we propose Coder-Reviewer reranking. We augment Coder language models from past work, which generate programs given language instructions, with Reviewer models, which evaluate the likelihood of the instruction given the generated programs. We perform an extensive study across six datasets with eight models from three model families. Experimental results show that Coder-Reviewer reranking leads to consistent and significant improvement (up to 17% absolute accuracy gain) over reranking with the Coder model only. When combined with executability filtering, Coder-Reviewer reranking can often outperform the minimum Bayes risk method. Coder-Reviewer reranking is easy to implement by prompting, can generalize to different programming languages, and works well with off-the-shelf hyperparameters.

The diverse metabolic pathways are fundamental to all living organisms, as they harvest energy, synthesize biomass components, produce molecules to interact with the microenvironment, and neutralize toxins. While discovery of new metabolites and pathways continues, the prediction of pathways for new metabolites can be challenging. It can take vast amounts of time to elucidate pathways for new metabolites; thus, according to HMDB only 60% of metabolites get assigned to pathways. Here, we present an approach to identify pathways based on metabolite structure. We extracted 201 features from SMILES annotations, and identified new metabolites from PubMed abstracts and HMDB. After applying clustering algorithms to both groups of features, we quantified correlations between metabolites, and found the clusters accurately linked 92% of known metabolites to their respective pathways. Thus, this approach could be valuable for predicting metabolic pathways for new metabolites.