Towards scientific discovery with dictionary learning: Extracting biological concepts from microscopy foundation models

Dictionary learning (DL) has emerged as a powerful interpretability tool for large language models. By extracting known concepts (e.g., Golden-Gate Bridge) from human-interpretable data (e.g., text), sparse DL can elucidate a model's inner workings. In this work, we ask if DL can also be used to discover unknown concepts from less human-interpretable scientific data (e.g., cell images), ultimately enabling modern approaches to scientific discovery. As a first step, we use DL algorithms to study microscopy foundation models trained on multi-cell image data, where little prior knowledge exists regarding which high-level concepts should arise. We show that sparse dictionaries indeed extract biologically-meaningful concepts such as cell type and genetic perturbation type. We also propose a new DL algorithm, Iterative Codebook Feature Learning~(ICFL), and combine it with a pre-processing step that uses PCA whitening from a control dataset. In our experiments, we demonstrate that both ICFL and PCA improve the selectivity of extracted features compared to TopK sparse autoencoders.

Copyright-Protected Language Generation via Adaptive Model Fusion

The risk of language models reproducing copyrighted material from their training data has led to the development of various protective measures. Among these, inference-time strategies that impose constraints via post-processing have shown promise in addressing the complexities of copyright regulation. However, they often incur prohibitive computational costs or suffer from performance trade-offs. To overcome these limitations, we introduce Copyright-Protecting Model Fusion (CP-Fuse), a novel approach that combines models trained on disjoint sets of copyrighted material during inference. In particular, CP-Fuse adaptively aggregates the model outputs to minimize the reproduction of copyrighted content, adhering to a crucial balancing property that prevents the regurgitation of memorized data. Through extensive experiments, we show that CP-Fuse significantly reduces the reproduction of protected material without compromising the quality of text and code generation. Moreover, its post-hoc nature allows seamless integration with other protective measures, further enhancing copyright safeguards. Lastly, we show that CP-Fuse is robust against common techniques for extracting training data.

ViTally Consistent: Scaling Biological Representation Learning for Cell Microscopy

Large-scale cell microscopy screens are used in drug discovery and molecular biology research to study the effects of millions of chemical and genetic perturbations on cells. To use these images in downstream analysis, we need models that can map each image into a feature space that represents diverse biological phenotypes consistently, in the sense that perturbations with similar biological effects have similar representations. In this work, we present the largest foundation model for cell microscopy data to date, a new 1.9 billion-parameter ViT-G/8 MAE trained on over 8 billion microscopy image crops. Compared to a previous published ViT-L/8 MAE, our new model achieves a 60% improvement in linear separability of genetic perturbations and obtains the best overall performance on whole-genome biological relationship recall and replicate consistency benchmarks. Beyond scaling, we developed two key methods that improve performance: (1) training on a curated and diverse dataset; and, (2) using biologically motivated linear probing tasks to search across each transformer block for the best candidate representation of whole-genome screens. We find that many self-supervised vision transformers, pretrained on either natural or microscopy images, yield significantly more biologically meaningful representations of microscopy images in their intermediate blocks than in their typically used final blocks. More broadly, our approach and results provide insights toward a general strategy for successfully building foundation models for large-scale biological data.

Strong Copyright Protection for Language Models via Adaptive Model Fusion

The risk of language models unintentionally reproducing copyrighted material from their training data has led to the development of various protective measures. In this paper, we propose model fusion as an effective solution to safeguard against copyright infringement. In particular, we introduce Copyright-Protecting Fusion (CP-Fuse), an algorithm that adaptively combines language models to minimize the reproduction of protected materials. CP-Fuse is inspired by the recently proposed Near-Access Free (NAF) framework and additionally incorporates a desirable balancing property that we demonstrate prevents the reproduction of memorized training data. Our results show that CP-Fuse significantly reduces the memorization of copyrighted content while maintaining high-quality text and code generation. Furthermore, we demonstrate how CP-Fuse can be integrated with other techniques for enhanced protection.

Detecting critical treatment effect bias in small subgroups

Randomized trials are considered the gold standard for making informed decisions in medicine, yet they often lack generalizability to the patient populations in clinical practice. Observational studies, on the other hand, cover a broader patient population but are prone to various biases. Thus, before using an observational study for decision-making, it is crucial to benchmark its treatment effect estimates against those derived from a randomized trial. We propose a novel strategy to benchmark observational studies beyond the average treatment effect. First, we design a statistical test for the null hypothesis that the treatment effects estimated from the two studies, conditioned on a set of relevant features, differ up to some tolerance. We then estimate an asymptotically valid lower bound on the maximum bias strength for any subgroup in the observational study. Finally, we validate our benchmarking strategy in a real-world setting and show that it leads to conclusions that align with established medical knowledge.

Privacy-preserving data release leveraging optimal transport and particle gradient descent

We present a novel approach for differentially private data synthesis of protected tabular datasets, a relevant task in highly sensitive domains such as healthcare and government. Current state-of-the-art methods predominantly use marginal-based approaches, where a dataset is generated from private estimates of the marginals. In this paper, we introduce PrivPGD, a new generation method for marginal-based private data synthesis, leveraging tools from optimal transport and particle gradient descent. Our algorithm outperforms existing methods on a large range of datasets while being highly scalable and offering the flexibility to incorporate additional domain-specific constraints.

Hidden yet quantifiable: A lower bound for confounding strength using randomized trials

In the era of fast-paced precision medicine, observational studies play a major role in properly evaluating new treatments in clinical practice. Yet, unobserved confounding can significantly compromise causal conclusions drawn from non-randomized data. We propose a novel strategy that leverages randomized trials to quantify unobserved confounding. First, we design a statistical test to detect unobserved confounding with strength above a given threshold. Then, we use the test to estimate an asymptotically valid lower bound on the unobserved confounding strength. We evaluate the power and validity of our statistical test on several synthetic and semi-synthetic datasets. Further, we show how our lower bound can correctly identify the absence and presence of unobserved confounding in a real-world setting.

Strong inductive biases provably prevent harmless interpolation

Classical wisdom suggests that estimators should avoid fitting noise to achieve good generalization. In contrast, modern overparameterized models can yield small test error despite interpolating noise -- a phenomenon often called "benign overfitting" or "harmless interpolation". This paper argues that the degree to which interpolation is harmless hinges upon the strength of an estimator's inductive bias, i.e., how heavily the estimator favors solutions with a certain structure: while strong inductive biases prevent harmless interpolation, weak inductive biases can even require fitting noise to generalize well. Our main theoretical result establishes tight non-asymptotic bounds for high-dimensional kernel regression that reflect this phenomenon for convolutional kernels, where the filter size regulates the strength of the inductive bias. We further provide empirical evidence of the same behavior for deep neural networks with varying filter sizes and rotational invariance.

Tight bounds for maximum $\ell_1$-margin classifiers

Popular iterative algorithms such as boosting methods and coordinate descent on linear models converge to the maximum $\ell_1$-margin classifier, a.k.a. sparse hard-margin SVM, in high dimensional regimes where the data is linearly separable. Previous works consistently show that many estimators relying on the $\ell_1$-norm achieve improved statistical rates for hard sparse ground truths. We show that surprisingly, this adaptivity does not apply to the maximum $\ell_1$-margin classifier for a standard discriminative setting. In particular, for the noiseless setting, we prove tight upper and lower bounds for the prediction error that match existing rates of order $\frac{\|\wgt\|_1^{2/3}}{n^{1/3}}$ for general ground truths. To complete the picture, we show that when interpolating noisy observations, the error vanishes at a rate of order $\frac{1}{\sqrt{\log(d/n)}}$. We are therefore first to show benign overfitting for the maximum $\ell_1$-margin classifier.

Fast rates for noisy interpolation require rethinking the effects of inductive bias

Good generalization performance on high-dimensional data crucially hinges on a simple structure of the ground truth and a corresponding strong inductive bias of the estimator. Even though this intuition is valid for regularized models, in this paper we caution against a strong inductive bias for interpolation in the presence of noise: Our results suggest that, while a stronger inductive bias encourages a simpler structure that is more aligned with the ground truth, it also increases the detrimental effect of noise. Specifically, for both linear regression and classification with a sparse ground truth, we prove that minimum $\ell_p$-norm and maximum $\ell_p$-margin interpolators achieve fast polynomial rates up to order $1/n$ for $p > 1$ compared to a logarithmic rate for $p = 1$. Finally, we provide experimental evidence that this trade-off may also play a crucial role in understanding non-linear interpolating models used in practice.