Masked autoencoders are scalable learners of cellular morphology

Inferring biological relationships from cellular phenotypes in high-content microscopy screens provides significant opportunity and challenge in biological research. Prior results have shown that deep vision models can capture biological signal better than hand-crafted features. This work explores how weakly supervised and self-supervised deep learning approaches scale when training larger models on larger datasets. Our results show that both CNN- and ViT-based masked autoencoders significantly outperform weakly supervised models. At the high-end of our scale, a ViT-L/8 trained on over 3.5-billion unique crops sampled from 95-million microscopy images achieves relative improvements as high as 28% over our best weakly supervised models at inferring known biological relationships curated from public databases.

Deconstructing word embedding algorithms

Word embeddings are reliable feature representations of words used to obtain high quality results for various NLP applications. Uncontextualized word embeddings are used in many NLP tasks today, especially in resource-limited settings where high memory capacity and GPUs are not available. Given the historical success of word embeddings in NLP, we propose a retrospective on some of the most well-known word embedding algorithms. In this work, we deconstruct Word2vec, GloVe, and others, into a common form, unveiling some of the common conditions that seem to be required for making performant word embeddings. We believe that the theoretical findings in this paper can provide a basis for more informed development of future models.

Learning Efficient Task-Specific Meta-Embeddings with Word Prisms

Word embeddings are trained to predict word cooccurrence statistics, which leads them to possess different lexical properties (syntactic, semantic, etc.) depending on the notion of context defined at training time. These properties manifest when querying the embedding space for the most similar vectors, and when used at the input layer of deep neural networks trained to solve downstream NLP problems. Meta-embeddings combine multiple sets of differently trained word embeddings, and have been shown to successfully improve intrinsic and extrinsic performance over equivalent models which use just one set of source embeddings. We introduce word prisms: a simple and efficient meta-embedding method that learns to combine source embeddings according to the task at hand. Word prisms learn orthogonal transformations to linearly combine the input source embeddings, which allows them to be very efficient at inference time. We evaluate word prisms in comparison to other meta-embedding methods on six extrinsic evaluations and observe that word prisms offer improvements in performance on all tasks.

Deconstructing and reconstructing word embedding algorithms

Uncontextualized word embeddings are reliable feature representations of words used to obtain high quality results for various NLP applications. Given the historical success of word embeddings in NLP, we propose a retrospective on some of the most well-known word embedding algorithms. In this work, we deconstruct Word2vec, GloVe, and others, into a common form, unveiling some of the necessary and sufficient conditions required for making performant word embeddings. We find that each algorithm: (1) fits vector-covector dot products to approximate pointwise mutual information (PMI); and, (2) modulates the loss gradient to balance weak and strong signals. We demonstrate that these two algorithmic features are sufficient conditions to construct a novel word embedding algorithm, Hilbert-MLE. We find that its embeddings obtain equivalent or better performance against other algorithms across 17 intrinsic and extrinsic datasets.

Word Embedding Algorithms as Generalized Low Rank Models and their Canonical Form

Word embedding algorithms produce very reliable feature representations of words that are used by neural network models across a constantly growing multitude of NLP tasks. As such, it is imperative for NLP practitioners to understand how their word representations are produced, and why they are so impactful. The present work presents the Simple Embedder framework, generalizing the state-of-the-art existing word embedding algorithms (including Word2vec (SGNS) and GloVe) under the umbrella of generalized low rank models. We derive that both of these algorithms attempt to produce embedding inner products that approximate pointwise mutual information (PMI) statistics in the corpus. Once cast as Simple Embedders, comparison of these models reveals that these successful embedders all resemble a straightforward maximum likelihood estimate (MLE) of the PMI parametrized by the inner product (between embeddings). This MLE induces our proposed novel word embedding model, Hilbert-MLE, as the canonical representative of the Simple Embedder framework. We empirically compare these algorithms with evaluations on 17 different datasets. Hilbert-MLE consistently observes second-best performance on every extrinsic evaluation (news classification, sentiment analysis, POS-tagging, and supersense tagging), while the first-best model depends varying on the task. Moreover, Hilbert-MLE consistently observes the least variance in results with respect to the random initialization of the weights in bidirectional LSTMs. Our empirical results demonstrate that Hilbert-MLE is a very consistent word embedding algorithm that can be reliably integrated into existing NLP systems to obtain high-quality results.

Clustering-Oriented Representation Learning with Attractive-Repulsive Loss

The standard loss function used to train neural network classifiers, categorical cross-entropy (CCE), seeks to maximize accuracy on the training 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.

Resolving Event Coreference with Supervised Representation Learning and Clustering-Oriented Regularization

We present an approach to event coreference resolution by developing a general framework for clustering that uses supervised representation learning. We propose a neural network architecture with novel Clustering-Oriented Regularization (CORE) terms in the objective function. These terms encourage the model to create embeddings of event mentions that are amenable to clustering. We then use agglomerative clustering on these embeddings to build event coreference chains. For both within- and cross-document coreference on the ECB+ corpus, our model obtains better results than models that require significantly more pre-annotated information. This work provides insight and motivating results for a new general approach to solving coreference and clustering problems with representation learning.