Biomarker identification is critical for precise disease diagnosis and understanding disease pathogenesis in omics data analysis, like using fold change and regression analysis. Graph neural networks (GNNs) have been the dominant deep learning model for analyzing graph-structured data. However, we found two major limitations of existing GNNs in omics data analysis, i.e., limited-prediction (diagnosis) accuracy and limited-reproducible biomarker identification capacity across multiple datasets. The root of the challenges is the unique graph structure of biological signaling pathways, which consists of a large number of targets and intensive and complex signaling interactions among these targets. To resolve these two challenges, in this study, we presented a novel GNN model architecture, named PathFormer, which systematically integrate signaling network, priori knowledge and omics data to rank biomarkers and predict disease diagnosis. In the comparison results, PathFormer outperformed existing GNN models significantly in terms of highly accurate prediction capability ( 30% accuracy improvement in disease diagnosis compared with existing GNN models) and high reproducibility of biomarker ranking across different datasets. The improvement was confirmed using two independent Alzheimer's Disease (AD) and cancer transcriptomic datasets. The PathFormer model can be directly applied to other omics data analysis studies.

We characterize the learning dynamics of stochastic gradient descent (SGD) when continuous symmetry exists in the loss function, where the divergence between SGD and gradient descent is dramatic. We show that depending on how the symmetry affects the learning dynamics, we can divide a family of symmetry into two classes. For one class of symmetry, SGD naturally converges to solutions that have a balanced and aligned gradient noise. For the other class of symmetry, SGD will almost always diverge. Then, we show that our result remains applicable and can help us understand the training dynamics even when the symmetry is not present in the loss function. Our main result is universal in the sense that it only depends on the existence of the symmetry and is independent of the details of the loss function. We demonstrate that the proposed theory offers an explanation of progressive sharpening and flattening and can be applied to common practical problems such as representation normalization, matrix factorization, and the use of warmup.

Online linear programming plays an important role in both revenue management and resource allocation, and recent research has focused on developing efficient first-order online learning algorithms. Despite the empirical success of first-order methods, they typically achieve a regret no better than $\mathcal{O}(\sqrt{T})$, which is suboptimal compared to the $\mathcal{O}(\log T)$ bound guaranteed by the state-of-the-art linear programming (LP)-based online algorithms. This paper establishes several important facts about online linear programming, which unveils the challenge for first-order-method-based online algorithms to achieve beyond $\mathcal{O}(\sqrt{T})$ regret. To address the challenge, we introduce a new algorithmic framework that decouples learning from decision-making. More importantly, for the first time, we show that first-order methods can attain regret $\mathcal{O}(T^{1/3})$ with this new framework. Lastly, we conduct numerical experiments to validate our theoretical findings.

The rapid growth of technology has meant that computer learning has increasingly integrated artificial intelligence techniques in order to develop more personalized educational systems. These systems are known as Intelligent Tutoring systems (ITS). MetaTutorES (Cerezo, Esteban, et al., 2020; Cerezo, Fernández, et al., 2020), a Spanish adaptation of MetaTutor (Azevedo, 2009) is an ITS designed to detect, model, trace, and foster students' self-regulated learning while learning various science topics (e.g., by modeling and scaffolding metacognitive monitoring, facilitating the use of effective learning strategies, and setting and coordinating relevant learning goals). The system uses human-like avatar technology that allows pedagogical agents to track student behavior and provide interaction on this basis. Tracking students' behavior is also a powerful research tool used to collect data on students' cognitive, metacognitive, affective, and motivational processes deployed during learning (Azevedo et al., 2011; Greene & Azevedo, 2010; Harley et al., 2014). These different data sources can be fused and mined to to reveal learning-related information such as student performance.

We introduce event-keyed summarization (EKS), a novel task that marries traditional summarization and document-level event extraction, with the goal of generating a contextualized summary for a specific event, given a document and an extracted event structure. We introduce a dataset for this task, MUCSUM, consisting of summaries of all events in the classic MUC-4 dataset, along with a set of baselines that comprises both pretrained LM standards in the summarization literature, as well as larger frontier models. We show that ablations that reduce EKS to traditional summarization or structure-to-text yield inferior summaries of target events and that MUCSUM is a robust benchmark for this task. Lastly, we conduct a human evaluation of both reference and model summaries, and provide some detailed analysis of the results.

The study of energetics necessarily involves numerous scientific domains, spanning shock physics and detonation science, fluid dynamics, material science, thermodynamics, and chemical synthesis. The plethora of sub-disciplines of math, physics, chemistry, and engineering pose a challenge to practitioners who would wish to amass an expertise of energetics. Furthermore, maintaining awareness of advancements in energetics research is complicated by the exponential rate at which new research is published across scientific disciplines, including energetics. Thus, the development of automated and intelligent approaches for extracting knowledge from papers, reports, textbooks, and patents related to energetics could aid researchers and accelerate progress in energetics science. Natural Language Processing (NLP) is a sub-field of linguistics, computer science, and Machine Learning (ML) involving the interactions between computers and human (natural) languages. NLP techniques are used to analyze and generate human language, allowing computers to read, interpret, and understand text and speech. In the context of energetics research, NLP can be used to analyze large volumes of textual data, such as scientific papers, technical reports, and patents, in order to extract relevant information about the concepts that underlie and explain energetics phenomenon. Furthermore, NLP can enable natural language understanding that could be further applied to text mining journal articles and performing numerous natural language tasks such as classification, summarization, and recommendation. Overall, the use of NLP in energetics research has the potential to enhance our understanding of energetic materials and phenomenon, and assist in the development novel propellants, explosives, and pyrotechnics.

Current advancements in technology have focused the attention of the quantum computing community toward exploring the potential of near-term devices whose computing power surpasses that of classical computers in practical applications. An unresolved central question revolves around whether the inherent noise in these devices can be overcome or whether any potential quantum advantage would be limited. There is no doubt that crosstalk is one of the main sources of noise in noisy intermediate-scale quantum (NISQ) systems, and it poses a fundamental challenge to hardware designs. Crosstalk between parallel instructions can corrupt quantum states and cause incorrect program execution. In this study, we present a comprehensive analysis of the crosstalk error effect on NISQ computers. Our approach is extremely straightforward and practical for characterizing the crosstalk error of various multi-qubit devices. In particular, we combine the randomized benchmarking (RB) and simultaneous randomized benchmarking (SRB) protocol to characterize the crosstalk error from the correlation controlled-NOT (CNOT) gate. We demonstrate this protocol experimentally on 5- \& 7-qubit devices. Our results demonstrate the crosstalk error model of two different IBM quantum devices over the experimental week and compare the error variation against the machine, number of qubits, quantum volume, processor, and topology of the IBM quantum devices. We then confirm the improvement in the circuit fidelity on different benchmarks by up to 3.06x via inserting an instruction barrier, as compared with an IBM quantum noisy device which offers near-optimal crosstalk mitigation in practice. Most importantly, we provide insight to ensure that the quantum operation can perform its quantum magic undisturbed.

In the rapidly evolving field of text generation, the demand for more precise control mechanisms has become increasingly apparent. To address this need, we present a novel methodology, LIFI, which offers a lightweight approach with fine-grained control for controlled text generation. Unlike previous studies that train pre-trained language models to follow discrete, categorical, and exclusive control codes, LIFI learns controlled text generation under the guidance of continuous, relative, and nonexclusive control codes. These fine-grained codes are automatically derived from an attribute classifier, initially trained with a small amount of labeled data and subsequently employed to label abundant unlabeled data, thus garnering more extensive supervision signals. Moreover, to achieve efficient control, we incorporate the fine-grained control codes with adapters, a parameter- and compute-efficient way to steer a pre-trained language model. We evaluate LIFI on two conventional tasks -- sentiment control and topic control -- and one newly proposed task -- stylistic novel writing. Comprehensive experimental results validate the effectiveness of our proposed methods, demonstrating substantial performance improvements over existing baselines.

Decoding methods play an indispensable role in converting language models from next-token predictors into practical task solvers. Prior research on decoding methods, primarily focusing on task-specific models, may not extend to the current era of general-purpose large language models (LLMs). Moreover, the recent influx of decoding strategies has further complicated this landscape. This paper provides a comprehensive and multifaceted analysis of various decoding methods within the context of LLMs, evaluating their performance, robustness to hyperparameter changes, and decoding speeds across a wide range of tasks, models, and deployment environments. Our findings reveal that decoding method performance is notably task-dependent and influenced by factors such as alignment, model size, and quantization. Intriguingly, sensitivity analysis exposes that certain methods achieve superior performance at the cost of extensive hyperparameter tuning, highlighting the trade-off between attaining optimal results and the practicality of implementation in varying contexts.

The irreducible complexity of natural phenomena has led Graph Neural Networks to be employed as a standard model to perform representation learning tasks on graph-structured data. While their capacity to capture local and global patterns is remarkable, the implications associated with long-range and higher-order dependencies pose considerable challenges to such models. This work starts with a theoretical framework to reveal the impact of network's width, depth, and graph topology on the over-squashing phenomena in message-passing neural networks. Then, the work drifts towards, higher-order interactions and multi-relational inductive biases via Topological Neural Networks. Such models propagate messages through higher-dimensional structures, providing shortcuts or additional routes for information flow. With this construction, the underlying computational graph is no longer coupled with the input graph structure, thus mitigating the aforementioned bottlenecks while accounting also for higher-order interactions. Inspired by Graph Attention Networks, two topological attention networks are proposed: Simplicial and Cell Attention Networks. The rationale behind these architecture is to leverage the extended notion of neighbourhoods provided by the arrangement of groups of nodes within a simplicial or cell complex to design anisotropic aggregations able to measure the importance of the information coming from different regions of the domain. By doing so, they capture dependencies that conventional Graph Neural Networks might miss. Finally, a multi-way communication scheme is introduced with Enhanced Cellular Isomorphism Networks, which augment topological message passing schemes to enable a direct interactions among groups of nodes arranged in ring-like structures.