Understanding the consequences of mutation for molecular fitness and function is a fundamental problem in biology. Recently, generative probabilistic models have emerged as a powerful tool for estimating fitness from evolutionary sequence data, with accuracy sufficient to predict both laboratory measurements of function and disease risk in humans, and to design novel functional proteins. Existing techniques rest on an assumed relationship between density estimation and fitness estimation, a relationship that we interrogate in this article. We prove that fitness is not identifiable from observational sequence data alone, placing fundamental limits on our ability to disentangle fitness landscapes from phylogenetic history. We show on real datasets that perfect density estimation in the limit of infinite data would, with high confidence, result in poor fitness estimation; current models perform accurate fitness estimation because of, not despite, misspecification. Our results challenge the conventional wisdom that bigger models trained on bigger datasets will inevitably lead to better fitness estimation, and suggest novel estimation strategies going forward.

We introduce Resilient Multiple Choice Learning (rMCL), an extension of the MCL approach for conditional distribution estimation in regression settings where multiple targets may be sampled for each training input. Multiple Choice Learning is a simple framework to tackle multimodal density estimation, using the WinnerTakes-All (WTA) loss for a set of hypotheses. In regression settings, the existing MCL variants focus on merging the hypotheses, thereby eventually sacrificing the diversity of the predictions. In contrast, our method relies on a novel learned scoring scheme underpinned by a mathematical framework based on Voronoi tessellations of the output space, from which we can derive a probabilistic interpretation. After empirically validating rMCL with experiments on synthetic data, we further assess its merits on the sound source localization task, demonstrating its practical usefulness and the relevance of its interpretation.

Previous works have validated that text generation APIs can be stolen through imitation attacks, causing IP violations. In order to protect the IP of text generation APIs, recent work has introduced a watermarking algorithm and utilized the null-hypothesis test as a post-hoc ownership verification on the imitation models. However, we find that it is possible to detect those watermarks via sufficient statistics of the frequencies of candidate watermarking words. To address this drawback, in this paper, we propose a novel Conditional wATERmarking framework (CATER) for protecting the IP of text generation APIs. An optimization method is proposed to decide the watermarking rules that can minimize the distortion of overall word distributions while maximizing the change of conditional word selections. Theoretically, we prove that it is infeasible for even the savviest attacker (they know how CATER works) to reveal the used watermarks from a large pool of potential word pairs based on statistical inspection. Empirically, we observe that high-order conditions lead to an exponential growth of suspicious (unused) watermarks, making our crafted watermarks more stealthy. In addition, CATER can effectively identify IP infringement under architectural mismatch and cross-domain imitation attacks, with negligible impairments on the generation quality of victim APIs. We envision our work as a milestone for stealthily protecting the IP of text generation APIs.

Solving inverse problems, such as parameter estimation and optimal control, is a vital part of science. Many experiments repeatedly collect data and rely on machine learning algorithms to quickly infer solutions to the associated inverse problems. We find that state-of-the-art training techniques are not well-suited to many problems that involve physical processes. The highly nonlinear behavior, common in physical processes, results in strongly varying gradients that lead first-order optimizers like SGD or Adam to compute suboptimal optimization directions. We propose a novel hybrid training approach that combines higherorder optimization methods with machine learning techniques. We take updates from a scale-invariant inverse problem solver and embed them into the gradientdescent-based learning pipeline, replacing the regular gradient of the physical process. We demonstrate the capabilities of our method on a variety of canonical physical systems, showing that it yields significant improvements on a wide range of optimization and learning problems.