Researcher profile

Benjamin Hoover

Benjamin Hoover contributes to research discovery and scholarly infrastructure.

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Published work

4 published item(s)

preprint2026arXiv

What Time Is It? How Data Geometry Makes Time Conditioning Optional for Flow Matching

Recent work has shown that models flow matching models can be trained without explicit time conditioning, challenging the standard view that the interpolation time is needed to disambiguate velocity targets. But why should a time-blind model work at all? Decomposing the time-blind flow matching loss, we identify two sources of irreducible error: a coupling variance, which arises from ambiguous velocity targets induced by how noise and data points are paired, and the time-blindness gap, which is the additional error caused by ignoring time. This gap shows that time-blind training is strictly harder than conventional training, reinforcing the puzzle that time-blind models work so well in practice. We resolve this tension by showing that the geometry of high-dimensional data makes time identifiable directly from noisy observations. When data concentrates near a $k$-dimensional subspace, time can be recovered from the statistical structure of noisy interpolants in directions orthogonal to the data; under a spiked-covariance model, this yields a closed-form estimator that recovers $t$ from a single observation $z$ at rate $O(1/\sqrt{d-k})$ for ambient dimension $d$. As a consequence, we prove that the time-blindness gap is asymptotically negligible relative to the coupling variance. We empirically demonstrate our identifiability result on real-world data and show that changing the coupling has a much larger effect on loss and sample quality than removing time conditioning across CIFAR-10, CelebA-HQ, and FFHQ. These results explain why time-blind flow matching works and show that the main practical lever is the choice of coupling, not explicit time conditioning.

preprint2022arXiv

Interactive and Visual Prompt Engineering for Ad-hoc Task Adaptation with Large Language Models

State-of-the-art neural language models can now be used to solve ad-hoc language tasks through zero-shot prompting without the need for supervised training. This approach has gained popularity in recent years, and researchers have demonstrated prompts that achieve strong accuracy on specific NLP tasks. However, finding a prompt for new tasks requires experimentation. Different prompt templates with different wording choices lead to significant accuracy differences. PromptIDE allows users to experiment with prompt variations, visualize prompt performance, and iteratively optimize prompts. We developed a workflow that allows users to first focus on model feedback using small data before moving on to a large data regime that allows empirical grounding of promising prompts using quantitative measures of the task. The tool then allows easy deployment of the newly created ad-hoc models. We demonstrate the utility of PromptIDE (demo at http://prompt.vizhub.ai) and our workflow using several real-world use cases.

preprint2022arXiv

Shared Interest: Measuring Human-AI Alignment to Identify Recurring Patterns in Model Behavior

Saliency methods -- techniques to identify the importance of input features on a model's output -- are a common step in understanding neural network behavior. However, interpreting saliency requires tedious manual inspection to identify and aggregate patterns in model behavior, resulting in ad hoc or cherry-picked analysis. To address these concerns, we present Shared Interest: metrics for comparing model reasoning (via saliency) to human reasoning (via ground truth annotations). By providing quantitative descriptors, Shared Interest enables ranking, sorting, and aggregating inputs, thereby facilitating large-scale systematic analysis of model behavior. We use Shared Interest to identify eight recurring patterns in model behavior, such as cases where contextual features or a subset of ground truth features are most important to the model. Working with representative real-world users, we show how Shared Interest can be used to decide if a model is trustworthy, uncover issues missed in manual analyses, and enable interactive probing.

preprint2020arXiv

CogMol: Target-Specific and Selective Drug Design for COVID-19 Using Deep Generative Models

The novel nature of SARS-CoV-2 calls for the development of efficient de novo drug design approaches. In this study, we propose an end-to-end framework, named CogMol (Controlled Generation of Molecules), for designing new drug-like small molecules targeting novel viral proteins with high affinity and off-target selectivity. CogMol combines adaptive pre-training of a molecular SMILES Variational Autoencoder (VAE) and an efficient multi-attribute controlled sampling scheme that uses guidance from attribute predictors trained on latent features. To generate novel and optimal drug-like molecules for unseen viral targets, CogMol leverages a protein-molecule binding affinity predictor that is trained using SMILES VAE embeddings and protein sequence embeddings learned unsupervised from a large corpus. CogMol framework is applied to three SARS-CoV-2 target proteins: main protease, receptor-binding domain of the spike protein, and non-structural protein 9 replicase. The generated candidates are novel at both molecular and chemical scaffold levels when compared to the training data. CogMol also includes insilico screening for assessing toxicity of parent molecules and their metabolites with a multi-task toxicity classifier, synthetic feasibility with a chemical retrosynthesis predictor, and target structure binding with docking simulations. Docking reveals favorable binding of generated molecules to the target protein structure, where 87-95 % of high affinity molecules showed docking free energy < -6 kcal/mol. When compared to approved drugs, the majority of designed compounds show low parent molecule and metabolite toxicity and high synthetic feasibility. In summary, CogMol handles multi-constraint design of synthesizable, low-toxic, drug-like molecules with high target specificity and selectivity, and does not need target-dependent fine-tuning of the framework or target structure information.