We introduce Concept Bottleneck Protein Language Models (CB-pLM), a generative masked language model with a layer where each neuron corresponds to an interpretable concept. Our architecture offers three key benefits: i) Control: We can intervene on concept values to precisely control the properties of generated proteins, achieving a 3 times larger change in desired concept values compared to baselines. ii) Interpretability: A linear mapping between concept values and predicted tokens allows transparent analysis of the model's decision-making process. iii) Debugging: This transparency facilitates easy debugging of trained models. Our models achieve pre-training perplexity and downstream task performance comparable to traditional masked protein language models, demonstrating that interpretability does not compromise performance. While adaptable to any language model, we focus on masked protein language models due to their importance in drug discovery and the ability to validate our model's capabilities through real-world experiments and expert knowledge. We scale our CB-pLM from 24 million to 3 billion parameters, making them the largest Concept Bottleneck Models trained and the first capable of generative language modeling.

The increasing rates of global urbanization and vehicle usage are leading to a shift of mobility to the third dimension-through Advanced Air Mobility (AAM)-offering a promising solution for faster, safer, cleaner, and more efficient transportation. As air transportation continues to evolve with more automated and autonomous systems, advancements in AAM require a deep understanding of human-computer interaction and human-AI collaboration to ensure safe and effective operations in complex urban and regional environments. There has been a significant increase in publications regarding these emerging applications; thus, there is a need to review developments in this area. This paper comprehensively reviews the current state of research on human-computer interaction and human-AI collaboration in AAM. Specifically, we focus on AAM applications related to the design of human-machine interfaces for various uses, including pilot training, air traffic management, and the integration of AI-assisted decision-making systems with immersive technologies such as extended, virtual, mixed, and augmented reality devices. Additionally, we provide a comprehensive analysis of the challenges AAM encounters in integrating human-computer frameworks, including unique challenges associated with these interactions, such as trust in AI systems and safety concerns. Finally, we highlight emerging opportunities and propose future research directions to bridge the gap between human factors and technological advancements in AAM.

It took over 15 years and more than 1,000 remotely operated vehicle (ROV) expeditions, but researchers aboard the NOAA Ocean Exploration Trust's Nautilus finally spotted their research vessel's namesake in the wild. On December 3, operators of the ship's Hercules ROV located four specimens of Palau nautilus (Nautilus belauensis) during the Nautilus Exploration Program's ongoing, 17-day survey in the Palau National Marine Sanctuary. While the team recorded these particular examples swimming 220-to-375 meters (roughly 721-to-1,230 ft) below the Pacific Ocean's surface, the pelagic marine mollusk cephalopods can survive at depths approaching 2,500 feet. Their spiral-shelled bodies belong to one of Earth's oldest families of animals, with fossil records indicating the squid relatives have changed comparatively little even after nearly 500 million years. Although their sight is limited due to rudimentary eyes that lack solid lenses, nine known nautilus species instead rely heavily on their olfactory senses to find food and mates.

In recent years, large language models (LLMs) have been widely adopted in political science tasks such as election prediction, sentiment analysis, policy impact assessment, and misinformation detection. Meanwhile, the need to systematically understand how LLMs can further revolutionize the field also becomes urgent. In this work, we--a multidisciplinary team of researchers spanning computer science and political science--present the first principled framework termed Political-LLM to advance the comprehensive understanding of integrating LLMs into computational political science. Specifically, we first introduce a fundamental taxonomy classifying the existing explorations into two perspectives: political science and computational methodologies. In particular, from the political science perspective, we highlight the role of LLMs in automating predictive and generative tasks, simulating behavior dynamics, and improving causal inference through tools like counterfactual generation; from a computational perspective, we introduce advancements in data preparation, fine-tuning, and evaluation methods for LLMs that are tailored to political contexts. We identify key challenges and future directions, emphasizing the development of domain-specific datasets, addressing issues of bias and fairness, incorporating human expertise, and redefining evaluation criteria to align with the unique requirements of computational political science. Political-LLM seeks to serve as a guidebook for researchers to foster an informed, ethical, and impactful use of Artificial Intelligence in political science. Our online resource is available at: http://political-llm.org/. Corresponding authors: Yushun Dong (yd24f@fsu.edu) is with the Department of Computer Science, Florida State University; Yue Zhao (yzhao010@usc.edu) is with the Department of Computer Science, University of Southern California; Fred Gui (pgui@lsu.edu) is with the Department of Political Science, Louisiana State University; Catherine Chen (catherinechen@lsu.edu) is with the Manship School of Mass Communication and the Department of Political Science, Louisiana State University.

The remarkable performance of large language models (LLMs) in content generation, coding, and common-sense reasoning has spurred widespread integration into many facets of society. However, integration of LLMs raises valid questions on their reliability and trustworthiness, given their propensity to generate hallucinations: plausible, factually-incorrect responses, which are expressed with striking confidence. Previous work has shown that hallucinations and other non-factual responses generated by LLMs can be detected by examining the uncertainty of the LLM in its response to the pertinent prompt, driving significant research efforts devoted to quantifying the uncertainty of LLMs. This survey seeks to provide an extensive review of existing uncertainty quantification methods for LLMs, identifying their salient features, along with their strengths and weaknesses. We present existing methods within a relevant taxonomy, unifying ostensibly disparate methods to aid understanding of the state of the art. Furthermore, we highlight applications of uncertainty quantification methods for LLMs, spanning chatbot and textual applications to embodied artificial intelligence applications in robotics. We conclude with open research challenges in uncertainty quantification of LLMs, seeking to motivate future research.

As natural disasters become increasingly frequent, the need for efficient and equitable evacuation planning has become more critical. This paper proposes a data-driven, reinforcement learning-based framework to optimize bus-based evacuations with an emphasis on improving both efficiency and equity. We model the evacuation problem as a Markov Decision Process solved by reinforcement learning, using real-time transit data from General Transit Feed Specification and transportation networks extracted from OpenStreetMap. The reinforcement learning agent dynamically reroutes buses from their scheduled location to minimize total passengers' evacuation time while prioritizing equity-priority communities. Simulations on the San Francisco Bay Area transportation network indicate that the proposed framework achieves significant improvements in both evacuation efficiency and equitable service distribution compared to traditional rule-based and random strategies. These results highlight the potential of reinforcement learning to enhance system performance and urban resilience during emergency evacuations, offering a scalable solution for real-world applications in intelligent transportation systems.

Self-supervised learning has become a popular and effective approach for enhancing time series forecasting, enabling models to learn universal representations from unlabeled data. However, effectively capturing both the global sequence dependence and local detail features within time series data remains challenging. To address this, we propose a novel generative self-supervised method called TimeDART, denoting Diffusion Auto-regressive Transformer for Time series forecasting. In TimeDART, we treat time series patches as basic modeling units. Specifically, we employ an self-attention based Transformer encoder to model the dependencies of inter-patches. Additionally, we introduce diffusion and denoising mechanisms to capture the detail locality features of intra-patch. Notably, we design a cross-attention-based denoising decoder that allows for adjustable optimization difficulty in the self-supervised task, facilitating more effective self-supervised pre-training. Furthermore, the entire model is optimized in an auto-regressive manner to obtain transferable representations. Extensive experiments demonstrate that TimeDART achieves state-of-the-art fine-tuning performance compared to the most advanced competitive methods in forecasting tasks. Time series forecasting (Harvey, 1990; Hamilton, 2020; Box et al., 2015; Cheng et al., 2024b) is crucial in a wide array of domains, including finance (Black & Scholes, 1973), healthcare (Cheng et al., 2024c), energy management (Zhou et al., 2024). Accurate predictions of future data points could enable better decision-making, resource allocation, and risk management, ultimately leading to significant operational improvements and strategic advantages. Among the various methods developed for time series forecasting (Miller et al., 2024), deep neural networks (Ding et al., 2024; Jin et al., 2023; Cao et al., 2023; Cheng et al., 2024b) have emerged as a popular and effective solution paradigm. To further enhance the performance of time series forecasting, self-supervised learning has become an increasingly popular research paradigm (Nie et al., 2022).

This week, OpenAI launched what its chief executive, Sam Altman, called "the smartest model in the world"--a generative-AI program whose capabilities are supposedly far greater, and more closely approximate how humans think, than those of any such software preceding it. The start-up has been building toward this moment since September 12, a day that, in OpenAI's telling, set the world on a new path toward superintelligence. That was when the company previewed early versions of a series of AI models, known as o1, constructed with novel methods that the start-up believes will propel its programs to unseen heights. Mark Chen, then OpenAI's vice president of research, told me a few days later that o1 is fundamentally different from the standard ChatGPT because it can "reason," a hallmark of human intelligence. Shortly thereafter, Altman pronounced "the dawn of the Intelligence Age," in which AI helps humankind fix the climate and colonize space. As of yesterday afternoon, the start-up has released the first complete version of o1, with fully fledged reasoning powers, to the public.

Adapting foundation models for specific purposes has become a standard approach to build machine learning systems for downstream applications. Yet, it is an open question which mechanisms take place during adaptation. Here we develop a new Sparse Autoencoder (SAE) for the CLIP vision transformer, named PatchSAE, to extract interpretable concepts at granular levels (e.g. shape, color, or semantics of an object) and their patch-wise spatial attributions. We explore how these concepts influence the model output in downstream image classification tasks and investigate how recent state-of-the-art prompt-based adaptation techniques change the association of model inputs to these concepts. While activations of concepts slightly change between adapted and non-adapted models, we find that the majority of gains on common adaptation tasks can be explained with the existing concepts already present in the non-adapted foundation model. This work provides a concrete framework to train and use SAEs for Vision Transformers and provides insights into explaining adaptation mechanisms.

Topological signals are variables or features associated with both nodes and edges of a network. Recently, in the context of Topological Machine Learning, great attention has been devoted to signal processing of such topological signals. Most of the previous topological signal processing algorithms treat node and edge signals separately and work under the hypothesis that the true signal is smooth and/or well approximated by a harmonic eigenvector of the Hodge-Laplacian, which may be violated in practice. Here we propose Dirac-equation signal processing, a framework for efficiently reconstructing true signals on nodes and edges, also if they are not smooth or harmonic, by processing them jointly. The proposed physics-inspired algorithm is based on the spectral properties of the topological Dirac operator. It leverages the mathematical structure of the topological Dirac equation to boost the performance of the signal processing algorithm. We discuss how the relativistic dispersion relation obeyed by the topological Dirac equation can be used to assess the quality of the signal reconstruction. Finally, we demonstrate the improved performance of the algorithm with respect to previous algorithms. Specifically, we show that Dirac-equation signal processing can also be used efficiently if the true signal is a non-trivial linear combination of more than one eigenstate of the Dirac equation, as it generally occurs for real signals.