Yueqi Wang

Yueqi Wang, Yoni Halpern, Shuo Chang et al.

Sequential recommenders have been widely used in industry due to their strength in modeling user preferences. While these models excel at learning a user's positive interests, less attention has been paid to learning from negative user feedback. Negative user feedback is an important lever of user control, and comes with an expectation that recommenders should respond quickly and reduce similar recommendations to the user. However, negative feedback signals are often ignored in the training objective of sequential retrieval models, which primarily aim at predicting positive user interactions. In this work, we incorporate explicit and implicit negative user feedback into the training objective of sequential recommenders in the retrieval stage using a "not-to-recommend" loss function that optimizes for the log-likelihood of not recommending items with negative feedback. We demonstrate the effectiveness of this approach using live experiments on a large-scale industrial recommender system. Furthermore, we address a challenge in measuring recommender responsiveness to negative feedback by developing a counterfactual simulation framework to compare recommender responses between different user actions, showing improved responsiveness from the modeling change.

Iddo Drori, Isht Dwivedi, Pranav Shrestha et al.

We tackle the problem of protein secondary structure prediction using a common task framework. This lead to the introduction of multiple ideas for neural architectures based on state of the art building blocks, used in this task for the first time. We take a principled machine learning approach, which provides genuine, unbiased performance measures, correcting longstanding errors in the application domain. We focus on the Q8 resolution of secondary structure, an active area for continuously improving methods. We use an ensemble of strong predictors to achieve accuracy of 70.7% (on the CB513 test set using the CB6133filtered training set). These results are statistically indistinguishable from those of the top existing predictors. In the spirit of reproducible research we make our data, models and code available, aiming to set a gold standard for purity of training and testing sets. Such good practices lower entry barriers to this domain and facilitate reproducible, extendable research.

Ruining He, Lukasz Heldt, Lichan Hong et al.

Large Language Models (LLMs) pose a new paradigm of modeling and computation for information tasks. Recommendation systems are a critical application domain poised to benefit significantly from the sequence modeling capabilities and world knowledge inherent in these large models. In this paper, we introduce PLUM, a framework designed to adapt pre-trained LLMs for industry-scale recommendation tasks. PLUM consists of item tokenization using Semantic IDs, continued pre-training (CPT) on domain-specific data, and task-specific fine-tuning for recommendation objectives. For fine-tuning, we focus particularly on generative retrieval, where the model is directly trained to generate Semantic IDs of recommended items based on user context. We conduct comprehensive experiments on large-scale internal video recommendation datasets. Our results demonstrate that PLUM achieves substantial improvements for retrieval compared to a heavily-optimized production model built with large embedding tables. We also present a scaling study for the model's retrieval performance, our learnings about CPT, a few enhancements to Semantic IDs, along with an overview of the training and inference methods that enable launching this framework to billions of users in YouTube.

Yueqi Wang, Yoonho Lee, Pallab Basu et al.

Learning community structures in graphs has broad applications across scientific domains. While graph neural networks (GNNs) have been successful in encoding graph structures, existing GNN-based methods for community detection are limited by requiring knowledge of the number of communities in advance, in addition to lacking a proper probabilistic formulation to handle uncertainty. We propose a simple framework for amortized community detection, which addresses both of these issues by combining the expressive power of GNNs with recent methods for amortized clustering. Our models consist of a graph representation backbone that extracts structural information and an amortized clustering network that naturally handles variable numbers of clusters. Both components combine into well-defined models of the posterior distribution of graph communities and are jointly optimized given labeled graphs. At inference time, the models yield parallel samples from the posterior of community labels, quantifying uncertainty in a principled way. We evaluate several models from our framework on synthetic and real datasets, and demonstrate improved performance compared to previous methods. As a separate contribution, we extend recent amortized probabilistic clustering architectures by adding attention modules, which yield further improvements on community detection tasks.

Iddo Drori, Darshan Thaker, Arjun Srivatsa et al.

Proteins are the major building blocks of life, and actuators of almost all chemical and biophysical events in living organisms. Their native structures in turn enable their biological functions which have a fundamental role in drug design. This motivates predicting the structure of a protein from its sequence of amino acids, a fundamental problem in computational biology. In this work, we demonstrate state-of-the-art protein structure prediction (PSP) results using embeddings and deep learning models for prediction of backbone atom distance matrices and torsion angles. We recover 3D coordinates of backbone atoms and reconstruct full atom protein by optimization. We create a new gold standard dataset of proteins which is comprehensive and easy to use. Our dataset consists of amino acid sequences, Q8 secondary structures, position specific scoring matrices, multiple sequence alignment co-evolutionary features, backbone atom distance matrices, torsion angles, and 3D coordinates. We evaluate the quality of our structure prediction by RMSD on the latest Critical Assessment of Techniques for Protein Structure Prediction (CASP) test data and demonstrate competitive results with the winning teams and AlphaFold in CASP13 and supersede the results of the winning teams in CASP12. We make our data, models, and code publicly available.

Ari Pakman, Yueqi Wang, Catalin Mitelut et al.

Probabilistic clustering models (or equivalently, mixture models) are basic building blocks in countless statistical models and involve latent random variables over discrete spaces. For these models, posterior inference methods can be inaccurate and/or very slow. In this work we introduce deep network architectures trained with labeled samples from any generative model of clustered datasets. At test time, the networks generate approximate posterior samples of cluster labels for any new dataset of arbitrary size. We develop two complementary approaches to this task, requiring either O(N) or O(K) network forward passes per dataset, where N is the dataset size and K the number of clusters. Unlike previous approaches, our methods sample the labels of all the data points from a well-defined posterior, and can learn nonparametric Bayesian posteriors since they do not limit the number of mixture components. As a scientific application, we present a novel approach to neural spike sorting for high-density multielectrode arrays.