One of the grand challenges of cell biology is inferring the gene regulatory network (GRN) which describes interactions between genes and their products that control gene expression and cellular function. We can treat this as a causal discovery problem but with two non-standard challenges: (1) regulatory networks are inherently cyclic so we should not model a GRN as a directed acyclic graph (DAG), and (2) observations have significant measurement noise so for typical sample sizes, there will always be a large equivalence class of graphs that are likely given the data, and we want methods that capture this uncertainty. Existing methods either focus on challenge (1), identifying cyclic structure from dynamics, or on challenge (2) learning complex Bayesian posteriors over directed acyclic graphs, but not both. In this paper we leverage the fact that it is possible to estimate the ``velocity'' of the expression of a gene with RNA velocity techniques to develop an approach that addresses both challenges. Because we have access to velocity information, we can treat the Bayesian structure learning problem as a problem of sparse identification of a dynamical system, capturing cyclic feedback loops through time. We leverage Generative Flow Networks (GFlowNets) to estimate the posterior distribution over the combinatorial space of possible sparse dependencies. Our results indicate that our method learns posteriors that better encapsulate the distributions of cyclic structures compared to counterpart state-of-the-art Bayesian structure learning approaches.

Working memory (WM), a fundamental cognitive process facilitating the temporary storage, integration, manipulation, and retrieval of information, plays a vital role in reasoning and decision-making tasks. Robust benchmark datasets that capture the multifaceted nature of WM are crucial for the effective development and evaluation of AI WM models. Here, we introduce a comprehensive Working Memory (WorM) benchmark dataset for this purpose. WorM comprises 10 tasks and a total of 1 million trials, assessing 4 functionalities, 3 domains, and 11 behavioral and neural characteristics of WM. We jointly trained and tested state-of-the-art recurrent neural networks and transformers on all these tasks. We also include human behavioral benchmarks as an upper bound for comparison. Our results suggest that AI models replicate some characteristics of WM in the brain, most notably primacy and recency effects, and neural clusters and correlates specialized for different domains and functionalities of WM. In the experiments, we also reveal some limitations in existing models to approximate human behavior. This dataset serves as a valuable resource for communities in cognitive psychology, neuroscience, and AI, offering a standardized framework to compare and enhance WM models, investigate WM's neural underpinnings, and develop WM models with human-like capabilities.

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We present the Minigrid and Miniworld libraries which provide a suite of goal-oriented 2D and 3D environments. The libraries were explicitly created with a minimalistic design paradigm to allow users to rapidly develop new environments for a wide range of research-specific needs. As a result, both have received widescale adoption by the RL community, facilitating research in a wide range of areas. In this paper, we outline the design philosophy, environment details, and their world generation API. We also showcase the additional capabilities brought by the unified API between Minigrid and Miniworld through case studies on transfer learning (for both RL agents and humans) between the different observation spaces.

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In the field of natural language processing, the prevalent approach involves fine-tuning pretrained language models (PLMs) using local samples. Recent research has exposed the susceptibility of PLMs to backdoor attacks, wherein the adversaries can embed malicious prediction behaviors by manipulating a few training samples. In this study, our objective is to develop a backdoor-resistant tuning procedure that yields a backdoor-free model, no matter whether the fine-tuning dataset contains poisoned samples. To this end, we propose and integrate an \emph{honeypot module} into the original PLM, specifically designed to absorb backdoor information exclusively. Our design is motivated by the observation that lower-layer representations in PLMs carry sufficient backdoor features while carrying minimal information about the original tasks. Consequently, we can impose penalties on the information acquired by the honeypot module to inhibit backdoor creation during the fine-tuning process of the stem network. Comprehensive experiments conducted on benchmark datasets substantiate the effectiveness and robustness of our defensive strategy. Notably, these results indicate a substantial reduction in the attack success rate ranging from 10\% to 40\% when compared to prior state-of-the-art methods.

Vision transformers (ViTs) are top-performing models on many computer vision benchmarks and can accurately predict human behavior on object recognition tasks. However, researchers question the value of using ViTs as models of biological learning because ViTs are thought to be more "data hungry" than brains, with ViTs requiring more training data than brains to reach similar levels of performance. To test this assumption, we directly compared the learning abilities of ViTs and animals, by performing parallel controlled-rearing experiments on ViTs and newborn chicks. We first raised chicks in impoverished visual environments containing a single object, then simulated the training data available in those environments by building virtual animal chambers in a video game engine. We recorded the first-person images acquired by agents moving through the virtual chambers and used those images to train self-supervised ViTs that leverage time as a teaching signal, akin to biological visual systems. When ViTs were trained "through the eyes" of newborn chicks, the ViTs solved the same view-invariant object recognition tasks as the chicks. Thus, ViTs were not more data hungry than newborn chicks: both learned view-invariant object representations in impoverished visual environments. The flexible and generic attention-based learning mechanism in ViTs--combined with the embodied data streams available to newborn animals--appears sufficient to drive the development of animal-like object recognition.

Exploration is essential in reinforcement learning, particularly in environments where external rewards are sparse. Here we focus on exploration with intrinsic rewards, where the agent transiently augments the external rewards with self-generated intrinsic rewards. Although the study of intrinsic rewards has a long history, existing methods focus on composing the intrinsic reward based on measures of future prospects of states, ignoring the information contained in the retrospective structure of transition sequences. Here we argue that the agent can utilise retrospective information to generate explorative behaviour with structure-awareness, facilitating efficient exploration based on global instead of local information. We propose Successor-Predecessor Intrinsic Exploration (SPIE), an exploration algorithm based on a novel intrinsic reward combining prospective and retrospective information. We show that SPIE yields more efficient and ethologically plausible exploratory behaviour in environments with sparse rewards and bottleneck states than competing methods. We also implement SPIE in deep reinforcement learning agents, and show that the resulting agent achieves stronger empirical performance than existing methods on sparse-reward Atari games.

Several recent works have studied the societal effects of AI; these include issues such as fairness, robustness, and safety. In many of these objectives, a learner seeks to minimize its worst-case loss over a set of predefined distributions (known as uncertainty sets), with usual examples being perturbed versions of the empirical distribution. In other words, the aforementioned problems can be written as min-max problems over these uncertainty sets. In this work, we provide a general framework for studying these problems, which we refer to as Responsible AI (RAI) games. We provide two classes of algorithms for solving these games: (a) game-play based algorithms, and (b) greedy stagewise estimation algorithms. The former class is motivated by online learning and game theory, whereas the latter class is motivated by the classical statistical literature on boosting, and regression. We empirically demonstrate the applicability and competitive performance of our techniques for solving several RAI problems, particularly around subpopulation shift.