The discovery of dynamical systems is crucial across a range of fields, including pharmacology, epidemiology, and physical sciences.

Models trained with self-supervised learning objectives have recently matched or surpassed models trained with traditional supervised object recognition in their ability to predict neural responses of object-selective neurons in the primate visual system. A self-supervised learning objective is arguably a more biologically plausible organizing principle, as the optimization does not require a large number of labeled examples. However, typical self-supervised objectives may result in network representations that are overly invariant to changes in the input. Here, we show that a representation with structured variability to the input transformations is better aligned with known features of visual perception and neural computation. We introduce a novel framework for converting standard invariant SSL losses into contrastive-equivariant versions that encourage preserving aspects of the input transformation without supervised access to the transformation parameters. We further demonstrate that our proposed method systematically increases models' ability to predict responses in macaque inferior temporal cortex. Our results demonstrate the promise of incorporating known features of neural computation into task-optimization for building better models of visual cortex.

High-throughput image analysis in the biomedical domain has gained significant attention in recent years, driving advancements in drug discovery, disease prediction, and personalized medicine. Organoids, specifically, are an active area of research, providing excellent models for human organs and their functions. Automating the quantification of organoids in microscopy images would provide an effective solution to overcome substantial manual quantification bottlenecks, particularly in high-throughput image analysis. However, there is a notable lack of open biomedical datasets, in contrast to other domains, such as autonomous driving, and, notably, only few of them have attempted to quantify annotation uncertainty. In this work, we present MultiOrg a comprehensive organoid dataset tailored for object detection tasks with uncertainty quantification. This dataset comprises over 400 high-resolution 2d microscopy images and curated annotations of more than 60,000 organoids. Most importantly, it includes three label sets for the test data, independently annotated by two experts at distinct time points. We additionally provide a benchmark for organoid detection, and make the best model available through an easily installable, interactive plugin for the popular image visualization tool Napari, to perform organoid quantification.

Analyzing inter-individual variability of physiological functions is particularly appealing in medical and biological contexts to describe or quantify health conditions. Such analysis can be done by comparing individuals to a reference one with time series as biomedical data.This paper introduces an unsupervised representation learning (URL) algorithm for time series tailored to inter-individual studies. The idea is to represent time series as deformations of a reference time series. The deformations are diffeomorphisms parameterized and learned by our method called TS-LDDMM. Once the deformations and the reference time series are learned, the vector representations of individual time series are given by the parametrization of their corresponding deformation. At the crossroads between URL for time series and shape analysis, the proposed algorithm handles irregularly sampled multivariate time series of variable lengths and provides shape-based representations of temporal data.In this work, we establish a representation theorem for the graph of a time series and derive its consequences on the LDDMM framework. We showcase the advantages of our representation compared to existing methods using synthetic data and real-world examples motivated by biomedical applications.

Decision-making in large-scale games is an essential research area in artificial intelligence (AI) with significant real-world impact. However, the limited access to realistic large-scale game environments has hindered research progress in this area. In this paper, we present AuctionNet, a benchmark for bid decision-making in large-scale ad auctions derived from a real-world online advertising platform. AuctionNet is composed of three parts: an ad auction environment, a pre-generated dataset based on the environment, and performance evaluations of several baseline bid decision-making algorithms. More specifically, the environment effectively replicates the integrity and complexity of real-world ad auctions through the interaction of several modules: the ad opportunity generation module employs deep generative networks to bridge the gap between simulated and real-world data while mitigating the risk of sensitive data exposure; the bidding module implements diverse auto-bidding agents trained with different decision-making algorithms; and the auction module is anchored in the classic Generalized Second Price (GSP) auction but also allows for customization of auction mechanisms as needed.

Large Vision-Language Models (LVLMs) are capable of handling diverse data types such as imaging, text, and physiological signals, and can be applied in various fields. In the medical field, LVLMs have a high potential to offer substantial assistance for diagnosis and treatment. Before that, it is crucial to develop benchmarks to evaluate LVLMs' effectiveness in various medical applications. Current benchmarks are often built upon specific academic literature, mainly focusing on a single domain, and lacking varying perceptual granularities. Thus, they face specific challenges, including limited clinical relevance, incomplete evaluations, and insufficient guidance for interactive LVLMs. To address these limitations, we developed the GMAI-MMBench, the most comprehensive general medical AI benchmark with well-categorized data structure and multi-perceptual granularity to date.

In this paper, we reconstruct naturalistic images directly from macaque brain signals using a convolutional neural network (CNN) based decoder. We investigate the ability of this CNN-based decoding technique to differentiate among neuronal populations from areas V1, V4, and IT, revealing distinct readout characteristics for each. This research marks a progression from low-level to high-level brain signals, thereby enriching the existing framework for utilizing CNN-based decoders to decode brain activity. Our results demonstrate high-precision reconstructions of naturalistic images, highlighting the efficiency of CNN-based decoders in advancing our knowledge of how the brain's representations translate into pixels. Additionally, we present a novel space-time-resolved decoding technique, demonstrating how temporal resolution in decoding can advance our understanding of neural representations. Moreover, we introduce a learned receptive field layer that sheds light on the CNN-based model's data processing during training, enhancing understanding of its structure and interpretive capacity.

Vehicle Routing Problems (VRPs) can model many real-world scenarios and often involve complex constraints. While recent neural methods excel in constructing solutions based on feasibility masking, they struggle with handling complex constraints, especially when obtaining the masking itself is NP-hard. In this paper, we propose a novel Proactive Infeasibility Prevention (PIP) framework to advance the capabilities of neural methods towards more complex VRPs. Our PIP integrates the Lagrangian multiplier as a basis to enhance constraint awareness and introduces preventative infeasibility masking to proactively steer the solution construction process. Moreover, we present PIP-D, which employs an auxiliary decoder and two adaptive strategies to learn and predict these tailored masks, potentially enhancing performance while significantly reducing computational costs during training. To verify our PIP designs, we conduct extensive experiments on the highly challenging Traveling Salesman Problem with Time Window (TSPTW), and TSP with Draft Limit (TSPDL) variants under different constraint hardness levels. Notably, our PIP is generic to boost many neural methods, and exhibits both a significant reduction in infeasible rate and a substantial improvement in solution quality.

Gene therapies have the potential to treat disease by delivering therapeutic genetic cargo to disease-associated cells. One limitation to their widespread use is the lack of short regulatory sequences, or promoters, that differentially induce the expression of delivered genetic cargo in target cells, minimizing side effects in other cell types. Such cell-type-specific promoters are difficult to discover using existing methods, requiring either manual curation or access to large datasets of promoter-driven expression from both targeted and untargeted cells. Model-based optimization (MBO) has emerged as an effective method to design biological sequences in an automated manner, and has recently been used in promoter design methods. However, these methods have only been tested using large training datasets that are expensive to collect, and focus on designing promoters for markedly different cell types, overlooking the complexities associated with designing promoters for closely related cell types that share similar regulatory features. Therefore, we introduce a comprehensive framework for utilizing MBO to design promoters in a data-efficient manner, with an emphasis on discovering promoters for similar cell types. We use conservative objective models (COMs) for MBO and highlight practical considerations such as best practices for improving sequence diversity, getting estimates of model uncertainty, and choosing the optimal set of sequences for experimental validation. Using three leukemia cell lines (Jurkat, K562, and THP1), we show that our approach discovers many novel cell-type-specific promoters after experimentally validating the designed sequences. For K562 cells, in particular, we discover a promoter that has 75.85\% higher cell-type-specificity than the best promoter from the initial dataset used to train our models.

Can a physicist make only a finite number of errors in the eternal quest to uncover the law of nature?This millennium-old philosophical problem, known as inductive inference, lies at the heart of epistemology.Despite its significance to understanding human reasoning, a rigorous justification of inductive inference has remained elusive.At a high level, inductive inference asks whether one can make at most finite errors amidst an infinite sequence of observations, when deducing the correct hypothesis from a given hypothesis class.Historically, the only theoretical guarantee has been that if the hypothesis class is countable, inductive inference is possible, as exemplified by Solomonoff induction for learning Turing machines.In this paper, we provide a tight characterization of inductive inference by establishing a novel link to online learning theory.As our main result, we prove that inductive inference is possible if and only if the hypothesis class is a countable union of online learnable classes, potentially with an uncountable size, no matter the observations are adaptively chosen or iid sampled.Moreover, the same condition is also sufficient and necessary in the agnostic setting, where any hypothesis class meeting this criterion enjoys an $\tilde{O}(\sqrt{T})$ regret bound for any time step $T$, while others require an arbitrarily slow rate of regret.Our main technical tool is a novel non-uniform online learning framework, which may be of independent interest.Our main technical tool is a novel non-uniform online learning framework, which may be of independent interest.