Advances in deep learning models have revolutionized the study of biomolecule systems and their mechanisms. Graph representation learning, in particular, is important for accurately capturing the geometric information of biomolecules at different levels. This paper presents a comprehensive review of the methodologies used to represent biological molecules and systems as computer-recognizable objects, such as sequences, graphs, and surfaces. Moreover, it examines how geometric deep learning models, with an emphasis on graph-based techniques, can analyze biomolecule data to enable drug discovery, protein characterization, and biological system analysis. The study concludes with an overview of the current state of the field, highlighting the challenges that exist and the potential future research directions.

In this thesis, we argue that (order-) lattice-based multi-agent information systems constitute a broad class of networked multi-agent systems in which relational data is passed between nodes. Mathematically modeled as lattice-valued sheaves, we initiate a discrete Hodge theory with a Laplace operator, analogous to the graph Laplacian and the graph connection Laplacian, acting on assignments of data to the nodes of a Tarski sheaf. The Hodge-Tarski theorem (the main theorem) relates the fixed point theory of this operator, called the Tarski Laplacian in deference to the Tarski Fixed Point Theorem, to the global sections (consistent global states) of the sheaf. We present novel applications to signal processing and multi-agent semantics and supply a plethora of examples throughout.

Neural networks (NNs) playing the role of controllers have demonstrated impressive empirical performances on challenging control problems. However, the potential adoption of NN controllers in real-life applications also gives rise to a growing concern over the safety of these neural-network controlled systems (NNCSs), especially when used in safety-critical applications. In this work, we present POLAR-Express, an efficient and precise formal reachability analysis tool for verifying the safety of NNCSs. POLAR-Express uses Taylor model arithmetic to propagate Taylor models (TMs) across a neural network layer-by-layer to compute an overapproximation of the neural-network function. It can be applied to analyze any feed-forward neural network with continuous activation functions. We also present a novel approach to propagate TMs more efficiently and precisely across ReLU activation functions. In addition, POLAR-Express provides parallel computation support for the layer-by-layer propagation of TMs, thus significantly improving the efficiency and scalability over its earlier prototype POLAR. Across the comparison with six other state-of-the-art tools on a diverse set of benchmarks, POLAR-Express achieves the best verification efficiency and tightness in the reachable set analysis.

Automatic translation from signed to spoken languages is an interdisciplinary research domain, lying on the intersection of computer vision, machine translation and linguistics. Nevertheless, research in this domain is performed mostly by computer scientists in isolation. As the domain is becoming increasingly popular - the majority of scientific papers on the topic of sign language translation have been published in the past three years - we provide an overview of the state of the art as well as some required background in the different related disciplines. We give a high-level introduction to sign language linguistics and machine translation to illustrate the requirements of automatic sign language translation. We present a systematic literature review to illustrate the state of the art in the domain and then, harking back to the requirements, lay out several challenges for future research. We find that significant advances have been made on the shoulders of spoken language machine translation research. However, current approaches are often not linguistically motivated or are not adapted to the different input modality of sign languages. We explore challenges related to the representation of sign language data, the collection of datasets, the need for interdisciplinary research and requirements for moving beyond research, towards applications. Based on our findings, we advocate for interdisciplinary research and to base future research on linguistic analysis of sign languages. Furthermore, the inclusion of deaf and hearing end users of sign language translation applications in use case identification, data collection and evaluation is of the utmost importance in the creation of useful sign language translation models. We recommend iterative, human-in-the-loop, design and development of sign language translation models.

Recent advances in the areas of Multimodal Machine Learning and Artificial Intelligence (AI) have led to the development of challenging tasks at the intersection of Computer Vision, Natural Language Processing, and Robotics. Whereas many approaches and previous survey pursuits have characterised one or two of these dimensions, there has not been a holistic analysis at the center of all three. Moreover, even when combinations of these topics are considered, more focus is placed on describing, e.g., current architectural methods, as opposed to also illustrating high-level challenges and opportunities for the field. In this survey paper, we discuss Embodied Vision-Language Planning (EVLP) tasks, a family of prominent embodied navigation and manipulation problems that jointly leverage computer vision and natural language for interaction in physical environments. We propose a taxonomy to unify these tasks and provide an in-depth analysis and comparison of the current and new algorithmic approaches, metrics, simulators, and datasets used for EVLP tasks. Finally, we present the core challenges that we believe new EVLP works should seek to address, and we advocate for task construction that enables model generalisability and furthers real-world deployment.

Abstract--Continuous Integration (CI) has become a wellestablished software development practice for automatically and continuously integrating code changes during software development. An increasing number of Machine Learning (ML) based approaches for automation of CI phases are being reported in the literature. It is timely and relevant to provide a Systemization of Knowledge (SoK) of ML-based approaches for CI phases. Our systematic analysis also highlights the deficiencies of the existing ML-based solutions that can be improved for advancing the state-of-the-art. Given the variety of employed techniques in applying ML solutions in CI, and growing interest in this domain, it is In recent years, the software development industry has seen necessary to systematically identify state-of-the-art practices a significant shift towards the adoption of Continuous Integration used for automating CI tasks through ML methods.

Large language models have introduced exciting new opportunities and challenges in designing and developing new AI-assisted writing support tools. Recent work has shown that leveraging this new technology can transform writing in many scenarios such as ideation during creative writing, editing support, and summarization. However, AI-supported expository writing--including real-world tasks like scholars writing literature reviews or doctors writing progress notes--is relatively understudied. In this position paper, we argue that developing AI supports for expository writing has unique and exciting research challenges and can lead to high real-world impacts. We characterize expository writing as evidence-based and knowledge-generating: it contains summaries of external documents as well as new information or knowledge. It can be seen as the product of authors' sensemaking process over a set of source documents, and the interplay between reading, reflection, and writing opens up new opportunities for designing AI support. We sketch three components for AI support design and discuss considerations for future research.

We study an online joint assortment-inventory optimization problem, in which we assume that the choice behavior of each customer follows the Multinomial Logit (MNL) choice model, and the attraction parameters are unknown a priori. The retailer makes periodic assortment and inventory decisions to dynamically learn from the realized demands about the attraction parameters while maximizing the expected total profit over time. In this paper, we propose a novel algorithm that can effectively balance the exploration and exploitation in the online decision-making of assortment and inventory. Our algorithm builds on a new estimator for the MNL attraction parameters, a novel approach to incentivize exploration by adaptively tuning certain known and unknown parameters, and an optimization oracle to static single-cycle assortment-inventory planning problems with given parameters. We establish a regret upper bound for our algorithm and a lower bound for the online joint assortment-inventory optimization problem, suggesting that our algorithm achieves nearly optimal regret rate, provided that the static optimization oracle is exact. Then we incorporate more practical approximate static optimization oracles into our algorithm, and bound from above the impact of static optimization errors on the regret of our algorithm. At last, we perform numerical studies to demonstrate the effectiveness of our proposed algorithm.

We present CAMELS-ASTRID, the third suite of hydrodynamical simulations in the Cosmology and Astrophysics with MachinE Learning (CAMELS) project, along with new simulation sets that extend the model parameter space based on the previous frameworks of CAMELS-TNG and CAMELS-SIMBA, to provide broader training sets and testing grounds for machine-learning algorithms designed for cosmological studies. CAMELS-ASTRID employs the galaxy formation model following the ASTRID simulation and contains 2,124 hydrodynamic simulation runs that vary 3 cosmological parameters ($\Omega_m$, $\sigma_8$, $\Omega_b$) and 4 parameters controlling stellar and AGN feedback. Compared to the existing TNG and SIMBA simulation suites in CAMELS, the fiducial model of ASTRID features the mildest AGN feedback and predicts the least baryonic effect on the matter power spectrum. The training set of ASTRID covers a broader variation in the galaxy populations and the baryonic impact on the matter power spectrum compared to its TNG and SIMBA counterparts, which can make machine-learning models trained on the ASTRID suite exhibit better extrapolation performance when tested on other hydrodynamic simulation sets. We also introduce extension simulation sets in CAMELS that widely explore 28 parameters in the TNG and SIMBA models, demonstrating the enormity of the overall galaxy formation model parameter space and the complex non-linear interplay between cosmology and astrophysical processes. With the new simulation suites, we show that building robust machine-learning models favors training and testing on the largest possible diversity of galaxy formation models. We also demonstrate that it is possible to train accurate neural networks to infer cosmological parameters using the high-dimensional TNG-SB28 simulation set.

In recent years, deep learning models have demonstrated remarkable success in various domains, such as computer vision, natural language processing, and speech recognition. However, the generalization capabilities of these models can be negatively impacted by the limitations of their feature fusion techniques. This paper introduces an innovative approach, Adaptive Feature Fusion (AFF), to enhance the generalization of deep learning models by dynamically adapting the fusion process of feature representations. The proposed AFF framework is designed to incorporate fusion layers into existing deep learning architectures, enabling seamless integration and improved performance. By leveraging a combination of data-driven and model-based fusion strategies, AFF is able to adaptively fuse features based on the underlying data characteristics and model requirements. This paper presents a detailed description of the AFF framework, including the design and implementation of fusion layers for various architectures. Extensive experiments are conducted on multiple benchmark datasets, with the results demonstrating the superiority of the AFF approach in comparison to traditional feature fusion techniques. The analysis showcases the effectiveness of AFF in enhancing generalization capabilities, leading to improved performance across different tasks and applications. Finally, the paper discusses various real-world use cases where AFF can be employed, providing insights into its practical applicability. The conclusion highlights the potential for future research directions, including the exploration of advanced fusion strategies and the extension of AFF to other machine learning paradigms.