The biomedical imaging world is notorious for working with small amounts of data, frustrating state-of-the-art efforts in the computer vision and deep learning worlds. With large datasets, it is easier to make progress we have seen from the natural image distribution. It is the same with microscopy videos of neuron cells moving in a culture. This problem presents several challenges as it can be difficult to grow and maintain the culture for days, and it is expensive to acquire the materials and equipment. In this work, we explore how to alleviate this data scarcity problem by synthesizing the videos. We, therefore, take the recent work of the video diffusion model to synthesize videos of cells from our training dataset. We then analyze the model's strengths and consistent shortcomings to guide us on improving video generation to be as high-quality as possible. To improve on such a task, we propose modifying the denoising function and adding motion information (dense optical flow) so that the model has more context regarding how video frames transition over time and how each pixel changes over time.

Array programming provides a powerful, compact, expressive syntax for accessing, manipulating, and operating on data in vectors, matrices, and higher-dimensional arrays [1]. NumPy is the primary array programming library for the Python language [2,3,4,5]. It plays an essential role in research analysis pipelines in fields as diverse as physics, chemistry, astronomy, geoscience, biology, psychology, material science, engineering, finance, and economics. For example, in astronomy, NumPy was an important part of the software stack used in the discovery of gravitational waves [6] and the first imaging of a black hole [7].Here we show how a few fundamental array concepts lead to a simple and powerful programming paradigm for organizing, exploring, and analyzing scientific data. NumPy is the foundation upon which the entire scientific Python universe is constructed. It is so pervasive that several projects, targeting audiences with specialized needs, have developed their own NumPy-like interfaces and array objects. Because of its central position in the ecosystem, NumPy increasingly plays the role of an interoperability layer between these new array computation libraries.

Machine learning methods have seen increased application to geospatial environmental problems, such as precipitation nowcasting, haze forecasting, and crop yield prediction. However, many of the machine learning methods applied to mosquito population and disease forecasting do not inherently take into account the underlying spatial structure of the given data. In our work, we apply a spatially aware graph neural network model consisting of GraphSAGE layers to forecast the presence of West Nile virus in Illinois, to aid mosquito surveillance and abatement efforts within the state. More generally, we show that graph neural networks applied to irregularly sampled geospatial data can exceed the performance of a range of baseline methods including logistic regression, XGBoost, and fully-connected neural networks.

We introduce a language generation task grounded in a popular video game environment. KNUDGE (KNowledge Constrained User-NPC Dialogue GEneration) involves generating dialogue trees conditioned on an ontology captured in natural language passages providing quest and entity specifications. KNUDGE is constructed from side quest dialogues drawn directly from game data of Obsidian Entertainment's The Outer Worlds, leading to real-world complexities in generation: (1) dialogues are branching trees as opposed to linear chains of utterances; (2) utterances must remain faithful to the game lore--character personas, backstories, and entity relationships; and (3) a dialogue must accurately reveal new quest-related details to the human player. We report results for supervised and in-context learning techniques, finding there is significant room for future work on creating realistic game-quality dialogues.

Recent work in open-domain question answering (ODQA) has shown that adversarial poisoning of the input contexts can cause large drops in accuracy for production systems. However, little to no work has proposed methods to defend against these attacks. To do so, we introduce a new method that uses query augmentation to search for a diverse set of retrieved passages that could answer the original question. We integrate these new passages into the model through the design of a novel confidence method, comparing the predicted answer to its appearance in the retrieved contexts (what we call Confidence from Answer Redundancy, e.g. CAR). Together these methods allow for a simple but effective way to defend against poisoning attacks and provide gains of 5-20% exact match across varying levels of data poisoning.

The findable, accessible, interoperable, and reusable (FAIR) data principles have provided a framework for examining, evaluating, and improving how we share data with the aim of facilitating scientific discovery. Efforts have been made to generalize these principles to research software and other digital products. Artificial intelligence (AI) models -- algorithms that have been trained on data rather than explicitly programmed -- are an important target for this because of the ever-increasing pace with which AI is transforming scientific and engineering domains. In this paper, we propose a practical definition of FAIR principles for AI models and create a FAIR AI project template that promotes adherence to these principles. We demonstrate how to implement these principles using a concrete example from experimental high energy physics: a graph neural network for identifying Higgs bosons decaying to bottom quarks. We study the robustness of these FAIR AI models and their portability across hardware architectures and software frameworks, and report new insights on the interpretability of AI predictions by studying the interplay between FAIR datasets and AI models. Enabled by publishing FAIR AI models, these studies pave the way toward reliable and automated AI-driven scientific discovery.

Athletes routinely undergo fitness evaluations to evaluate their training progress. Typically, these evaluations require a trained professional who utilizes specialized equipment like force plates. For the assessment, athletes perform drop and squat jumps, and key variables are measured, e.g. velocity, flight time, and time to stabilization, to name a few. However, amateur athletes may not have access to professionals or equipment that can provide these assessments. Here, we investigate the feasibility of estimating key variables using video recordings. We focus on jump velocity as a starting point because it is highly correlated with other key variables and is important for determining posture and lower-limb capacity. We find that velocity can be estimated with a high degree of precision across a range of athletes, with an average R-value of 0.71 (SD = 0.06).

We study the problem of finding elements in the intersection of an arbitrary conic variety in $\mathbb{F}^n$ with a given linear subspace (where $\mathbb{F}$ can be the real or complex field). This problem captures a rich family of algorithmic problems under different choices of the variety. The special case of the variety consisting of rank-1 matrices already has strong connections to central problems in different areas like quantum information theory and tensor decompositions. This problem is known to be NP-hard in the worst-case, even for the variety of rank-1 matrices. Surprisingly, despite these hardness results we give efficient algorithms that solve this problem for "typical" subspaces. Here, the subspace $U \subseteq \mathbb{F}^n$ is chosen generically of a certain dimension, potentially with some generic elements of the variety contained in it. Our main algorithmic result is a polynomial time algorithm that recovers all the elements of $U$ that lie in the variety, under some mild non-degeneracy assumptions on the variety. As corollaries, we obtain the following results: $\bullet$ Uniqueness results and polynomial time algorithms for generic instances of a broad class of low-rank decomposition problems that go beyond tensor decompositions. Here, we recover a decomposition of the form $\sum_{i=1}^R v_i \otimes w_i$, where the $v_i$ are elements of the given variety $X$. This implies new algorithmic results even in the special case of tensor decompositions. $\bullet$ Polynomial time algorithms for several entangled subspaces problems in quantum entanglement, including determining $r$-entanglement, complete entanglement, and genuine entanglement of a subspace. While all of these problems are NP-hard in the worst case, our algorithm solves them in polynomial time for generic subspaces of dimension up to a constant multiple of the maximum possible.

Unlike the typical classification setting where each instance is associated with a single class, in multi-label learning each instance is associated with multiple classes simultaneously. Therefore the learning task in this setting is to predict the subset of classes to which each instance belongs. This work examines the application of a recently developed framework called Conformal Prediction (CP) to the multi-label learning setting. CP complements the predictions of machine learning algorithms with reliable measures of confidence. As a result the proposed approach instead of just predicting the most likely subset of classes for a new unseen instance, also indicates the likelihood of each predicted subset being correct. This additional information is especially valuable in the multi-label setting where the overall uncertainty is extremely high.

Previous work has shown that a neural network with the rectified linear unit (ReLU) activation function leads to a convex polyhedral decomposition of the input space. These decompositions can be represented by a dual graph with vertices corresponding to polyhedra and edges corresponding to polyhedra sharing a facet, which is a subgraph of a Hamming graph. This paper illustrates how one can utilize the dual graph to detect and analyze adversarial attacks in the context of digital images. When an image passes through a network containing ReLU nodes, the firing or non-firing at a node can be encoded as a bit ($1$ for ReLU activation, $0$ for ReLU non-activation). The sequence of all bit activations identifies the image with a bit vector, which identifies it with a polyhedron in the decomposition and, in turn, identifies it with a vertex in the dual graph. We identify ReLU bits that are discriminators between non-adversarial and adversarial images and examine how well collections of these discriminators can ensemble vote to build an adversarial image detector. Specifically, we examine the similarities and differences of ReLU bit vectors for adversarial images, and their non-adversarial counterparts, using a pre-trained ResNet-50 architecture. While this paper focuses on adversarial digital images, ResNet-50 architecture, and the ReLU activation function, our methods extend to other network architectures, activation functions, and types of datasets.