Kevin Yang

Eric Wallace, Nicholas Tomlin, Albert Xu et al. · berkeley

We present the Berkeley Crossword Solver, a state-of-the-art approach for automatically solving crossword puzzles. Our system works by generating answer candidates for each crossword clue using neural question answering models and then combines loopy belief propagation with local search to find full puzzle solutions. Compared to existing approaches, our system improves exact puzzle accuracy from 71% to 82% on crosswords from The New York Times and obtains 99.9% letter accuracy on themeless puzzles. Additionally, in 2021, a hybrid of our system and the existing Dr.Fill system outperformed all human competitors for the first time at the American Crossword Puzzle Tournament. To facilitate research on question answering and crossword solving, we analyze our system's remaining errors and release a dataset of over six million question-answer pairs.

Tengxiao Liu, Deepak Nathani, Zekun Li et al.

Recent progress in large language model (LLM) reasoning has focused on domains like mathematics and coding, where abundant high-quality data and objective evaluation metrics are readily available. In contrast, progress in LLM reasoning models remains limited in scientific domains such as medicine and materials science due to limited dataset coverage and the inherent complexity of open-ended scientific questions. To address these challenges, we introduce WildSci, a new dataset of domain-specific science questions automatically synthesized from peer-reviewed literature, covering 9 scientific disciplines and 26 subdomains. By framing complex scientific reasoning tasks in a multiple-choice format, we enable scalable training with well-defined reward signals. We further apply reinforcement learning to finetune models on these data and analyze the resulting training dynamics, including domain-specific performance changes, response behaviors, and generalization trends. Experiments on a suite of scientific benchmarks demonstrate the effectiveness of our dataset and approach. We release WildSci to enable scalable and sustainable research in scientific reasoning, available at https://huggingface.co/datasets/JustinTX/WildSci.

Kevin Yang, Tianjun Zhang, Chris Cummins et al.

Path planning, the problem of efficiently discovering high-reward trajectories, often requires optimizing a high-dimensional and multimodal reward function. Popular approaches like CEM and CMA-ES greedily focus on promising regions of the search space and may get trapped in local maxima. DOO and VOOT balance exploration and exploitation, but use space partitioning strategies independent of the reward function to be optimized. Recently, LaMCTS empirically learns to partition the search space in a reward-sensitive manner for black-box optimization. In this paper, we develop a novel formal regret analysis for when and why such an adaptive region partitioning scheme works. We also propose a new path planning method LaP3 which improves the function value estimation within each sub-region, and uses a latent representation of the search space. Empirically, LaP3 outperforms existing path planning methods in 2D navigation tasks, especially in the presence of difficult-to-escape local optima, and shows benefits when plugged into the planning components of model-based RL such as PETS. These gains transfer to highly multimodal real-world tasks, where we outperform strong baselines in compiler phase ordering by up to 39% on average across 9 tasks, and in molecular design by up to 0.4 on properties on a 0-1 scale. Code is available at https://github.com/yangkevin2/neurips2021-lap3.

Lior Hirschfeld, Kyle Swanson, Kevin Yang et al.

Uncertainty quantification (UQ) is an important component of molecular property prediction, particularly for drug discovery applications where model predictions direct experimental design and where unanticipated imprecision wastes valuable time and resources. The need for UQ is especially acute for neural models, which are becoming increasingly standard yet are challenging to interpret. While several approaches to UQ have been proposed in the literature, there is no clear consensus on the comparative performance of these models. In this paper, we study this question in the context of regression tasks. We systematically evaluate several methods on five benchmark datasets using multiple complementary performance metrics. Our experiments show that none of the methods we tested is unequivocally superior to all others, and none produces a particularly reliable ranking of errors across multiple datasets. While we believe these results show that existing UQ methods are not sufficient for all common use-cases and demonstrate the benefits of further research, we conclude with a practical recommendation as to which existing techniques seem to perform well relative to others.

Kevin Yang, Wengong Jin, Kyle Swanson et al.

Generative models in molecular design tend to be richly parameterized, data-hungry neural models, as they must create complex structured objects as outputs. Estimating such models from data may be challenging due to the lack of sufficient training data. In this paper, we propose a surprisingly effective self-training approach for iteratively creating additional molecular targets. We first pre-train the generative model together with a simple property predictor. The property predictor is then used as a likelihood model for filtering candidate structures from the generative model. Additional targets are iteratively produced and used in the course of stochastic EM iterations to maximize the log-likelihood that the candidate structures are accepted. A simple rejection (re-weighting) sampler suffices to draw posterior samples since the generative model is already reasonable after pre-training. We demonstrate significant gains over strong baselines for both unconditional and conditional molecular design. In particular, our approach outperforms the previous state-of-the-art in conditional molecular design by over 10% in absolute gain. Finally, we show that our approach is useful in other domains as well, such as program synthesis.

Kevin Yang, Kyle Swanson, Wengong Jin et al.

Advancements in neural machinery have led to a wide range of algorithmic solutions for molecular property prediction. Two classes of models in particular have yielded promising results: neural networks applied to computed molecular fingerprints or expert-crafted descriptors, and graph convolutional neural networks that construct a learned molecular representation by operating on the graph structure of the molecule. However, recent literature has yet to clearly determine which of these two methods is superior when generalizing to new chemical space. Furthermore, prior research has rarely examined these new models in industry research settings in comparison to existing employed models. In this paper, we benchmark models extensively on 19 public and 16 proprietary industrial datasets spanning a wide variety of chemical endpoints. In addition, we introduce a graph convolutional model that consistently matches or outperforms models using fixed molecular descriptors as well as previous graph neural architectures on both public and proprietary datasets. Our empirical findings indicate that while approaches based on these representations have yet to reach the level of experimental reproducibility, our proposed model nevertheless offers significant improvements over models currently used in industrial workflows.

Wengong Jin, Kevin Yang, Regina Barzilay et al.

We view molecular optimization as a graph-to-graph translation problem. The goal is to learn to map from one molecular graph to another with better properties based on an available corpus of paired molecules. Since molecules can be optimized in different ways, there are multiple viable translations for each input graph. A key challenge is therefore to model diverse translation outputs. Our primary contributions include a junction tree encoder-decoder for learning diverse graph translations along with a novel adversarial training method for aligning distributions of molecules. Diverse output distributions in our model are explicitly realized by low-dimensional latent vectors that modulate the translation process. We evaluate our model on multiple molecular optimization tasks and show that our model outperforms previous state-of-the-art baselines.