In the problem of \emph{active sequential hypothesis testing} (ASHT), a learner seeks to identify the \emph{true} hypothesis from among a known set of hypotheses. The learner is given a set of actions and knows the random distribution of the outcome of any action under any true hypothesis. Given a target error $\delta> 0$, the goal is to sequentially select the fewest number of actions so as to identify the true hypothesis with probability at least $1 - \delta$. Motivated by applications in which the number of hypotheses or actions is massive (e.g., genomics-based cancer detection), we propose efficient (greedy, in fact) algorithms and provide the first approximation guarantees for ASHT, under two types of adaptivity. Both of our guarantees are independent of the number of actions and logarithmic in the number of hypotheses. We numerically evaluate the performance of our algorithms using both synthetic and real-world DNA mutation data, demonstrating that our algorithms outperform previously proposed heuristic policies by large margins.

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.

Multiple sequence alignments (MSAs) of proteins encode rich biological information and have been workhorses in bioinformatic methods for tasks like protein design and protein structure prediction for decades. Recent breakthroughs like AlphaFold2 that use transformers to attend directly over large quantities of raw MSAs have reaffirmed their importance. Generation of MSAs is highly computationally intensive, however, and no datasets comparable to those used to train AlphaFold2 have been made available to the research community, hindering progress in machine learning for proteins. To remedy this problem, we introduce OpenProteinSet, an open-source corpus of more than 16 million MSAs, associated structural homologs from the Protein Data Bank, and AlphaFold2 protein structure predictions. We have previously demonstrated the utility of OpenProteinSet by successfully retraining AlphaFold2 on it. We expect OpenProteinSet to be broadly useful as training and validation data for 1) diverse tasks focused on protein structure, function, and design and 2) large-scale multimodal machine learning research.

Blackbox adversarial attacks can be categorized into transfer-and query-based attacks. Transfer methods do not require any feedback from the victim model, but provide lower success rates compared to query-based methods. Query attacks often require a large number of queries for success. To achieve the best of both approaches, recent efforts have tried to combine them, but still require hundreds of queries to achieve high success rates (especially for targeted attacks). In this paper, we propose a novel method for Blackbox Attacks via Surrogate Ensemble Search (BASES) that can generate highly successful blackbox attacks using an extremely small number of queries.

A critical yet frequently overlooked challenge in the field of deepfake detection is the lack of a standardized, unified, comprehensive benchmark. This issue leads to unfair performance comparisons and potentially misleading results. Specifically, there is a lack of uniformity in data processing pipelines, resulting in inconsistent data inputs for detection models. Additionally, there are noticeable differences in experimental settings, and evaluation strategies and metrics lack standardization. To fill this gap, we present the first comprehensive benchmark for deepfake detection, called \textit{DeepfakeBench}, which offers three key contributions: 1) a unified data management system to ensure consistent input across all detectors, 2) an integrated framework for state-of-the-art methods implementation, and 3) standardized evaluation metrics and protocols to promote transparency and reproducibility. Featuring an extensible, modular-based codebase, \textit{DeepfakeBench} contains 15 state-of-the-art detection methods, 9 deepfake datasets, a series of deepfake detection evaluation protocols and analysis tools, as well as comprehensive evaluations. Moreover, we provide new insights based on extensive analysis of these evaluations from various perspectives (\eg, data augmentations, backbones). We hope that our efforts could facilitate future research and foster innovation in this increasingly critical domain.

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. We applied the CogMol framework 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 the 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.

Federated Learning (FL) is a novel approach enabling several clients holding sensitive data to collaboratively train machine learning models, without centralizing data. The cross-silo FL setting corresponds to the case of few ($2$--$50$) reliable clients, each holding medium to large datasets, and is typically found in applications such as healthcare, finance, or industry. While previous works have proposed representative datasets for cross-device FL, few realistic healthcare cross-silo FL datasets exist, thereby slowing algorithmic research in this critical application. In this work, we propose a novel cross-silo dataset suite focused on healthcare, FLamby (Federated Learning AMple Benchmark of Your cross-silo strategies), to bridge the gap between theory and practice of cross-silo FL.FLamby encompasses 7 healthcare datasets with natural splits, covering multiple tasks, modalities, and data volumes, each accompanied with baseline training code. As an illustration, we additionally benchmark standard FL algorithms on all datasets.Our flexible and modular suite allows researchers to easily download datasets, reproduce results and re-use the different components for their research.

There are multiple scales of abstraction from which we can describe the same image, depending on whether we are focusing on fine-grained details or a more global attribute of the image. In brain mapping, learning to automatically parse images to build representations of both small-scale features (e.g., the presence of cells or blood vessels) and global properties of an image (e.g., which brain region the image comes from) is a crucial and open challenge. However, most existing datasets and benchmarks for neuroanatomy consider only a single downstream task at a time. To bridge this gap, we introduce a new dataset, annotations, and multiple downstream tasks that provide diverse ways to readout information about brain structure and architecture from the same image. Our multi-task neuroimaging benchmark (MTNeuro) is built on volumetric, micrometer-resolution X-ray microtomography images spanning a large thalamocortical section of mouse brain, encompassing multiple cortical and subcortical regions. We generated a number of different prediction challenges and evaluated several supervised and self-supervised models for brain-region prediction and pixel-level semantic segmentation of microstructures. Our experiments not only highlight the rich heterogeneity of this dataset, but also provide insights into how self-supervised approaches can be used to learn representations that capture multiple attributes of a single image and perform well on a variety of downstream tasks. Datasets, code, and pre-trained baseline models are provided at: https://mtneuro.github.io/.

Machine learning has successfully framed many sequential decision making problems as either supervised prediction, or optimal decision-making policy identification via reinforcement learning. In data-constrained offline settings, both approaches may fail as they assume fully optimal behavior or rely on exploring alternatives that may not exist. We introduce an inherently different approach that identifies dead-ends of a state space. We focus on patient condition in the intensive care unit, where a medical dead-end indicates that a patient will expire, regardless of all potential future treatment sequences. We postulate treatment security as avoiding treatments with probability proportional to their chance of leading to dead-ends, present a formal proof, and frame discovery as an RL problem. We then train three independent deep neural models for automated state construction, dead-end discovery and confirmation. Our empirical results discover that dead-ends exist in real clinical data among septic patients, and further reveal gaps between secure treatments and those administered.

In this paper, we study both multi-armed and contextual bandit problems in censored environments. Our goal is to estimate the performance loss due to censorship in the context of classical algorithms designed for uncensored environments. Our main contributions include the introduction of a broad class of censorship models and their analysis in terms of the effective dimension of the problem -- a natural measure of its underlying statistical complexity and main driver of the regret bound. In particular, the effective dimension allows us to maintain the structure of the original problem at first order, while embedding it in a bigger space, and thus naturally leads to results analogous to uncensored settings. Our analysis involves a continuous generalization of the Elliptical Potential Inequality, which we believe is of independent interest. We also discover an interesting property of decision-making under censorship: a transient phase during which initial misspecification of censorship is self-corrected at an extra cost; followed by a stationary phase that reflects the inherent slowdown of learning governed by the effective dimension. Our results are useful for applications of sequential decision-making models where the feedback received depends on strategic uncertainty (e.g., agents' willingness to follow a recommendation) and/or random uncertainty (e.g., loss or delay in arrival of information).