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Proteins are fundamental components of biological systems and can be represented through various modalities, including sequences, structures, and textual descriptions. Despite the advances in deep learning and scientific large language models (LLMs) for protein research, current methodologies predominantly focus on limited specialized tasks -- often predicting one protein modality from another. These approaches restrict the understanding and generation of multimodal protein data. In contrast, large multimodal models have demonstrated potential capabilities in generating any-to-any content like text, images, and videos, thus enriching user interactions across various domains. Integrating these multimodal model technologies into protein research offers significant promise by potentially transforming how proteins are studied. To this end, we introduce HelixProtX, a system built upon the large multimodal model, aiming to offer a comprehensive solution to protein research by supporting any-to-any protein modality generation. Unlike existing methods, it allows for the transformation of any input protein modality into any desired protein modality. The experimental results affirm the advanced capabilities of HelixProtX, not only in generating functional descriptions from amino acid sequences but also in executing critical tasks such as designing protein sequences and structures from textual descriptions. Preliminary findings indicate that HelixProtX consistently achieves superior accuracy across a range of protein-related tasks, outperforming existing state-of-the-art models. By integrating multimodal large models into protein research, HelixProtX opens new avenues for understanding protein biology, thereby promising to accelerate scientific discovery.

The study evaluates the efficacy of Conversational Artificial Intelligence (CAI) in rectifying cognitive biases and recognizing affect in human-AI interactions, which is crucial for digital mental health interventions. Cognitive biases (systematic deviations from normative thinking) affect mental health, intensifying conditions like depression and anxiety. Therapeutic chatbots can make cognitive-behavioral therapy (CBT) more accessible and affordable, offering scalable and immediate support. The research employs a structured methodology with clinical-based virtual case scenarios simulating typical user-bot interactions. Performance and affect recognition were assessed across two categories of cognitive biases: theory of mind biases (anthropomorphization of AI, overtrust in AI, attribution to AI) and autonomy biases (illusion of control, fundamental attribution error, just-world hypothesis). A qualitative feedback mechanism was used with an ordinal scale to quantify responses based on accuracy, therapeutic quality, and adherence to CBT principles. Therapeutic bots (Wysa, Youper) and general-use LLMs (GTP 3.5, GTP 4, Gemini Pro) were evaluated through scripted interactions, double-reviewed by cognitive scientists and a clinical psychologist. Statistical analysis showed therapeutic bots were consistently outperformed by non-therapeutic bots in bias rectification and in 4 out of 6 biases in affect recognition. The data suggests that non-therapeutic chatbots are more effective in addressing some cognitive biases.

Multimodal emotion recognition systems rely heavily on the full availability of modalities, suffering significant performance declines when modal data is incomplete. To tackle this issue, we present the Cross-Modal Alignment, Reconstruction, and Refinement (CM-ARR) framework, an innovative approach that sequentially engages in cross-modal alignment, reconstruction, and refinement phases to handle missing modalities and enhance emotion recognition. This framework utilizes unsupervised distribution-based contrastive learning to align heterogeneous modal distributions, reducing discrepancies and modeling semantic uncertainty effectively. The reconstruction phase applies normalizing flow models to transform these aligned distributions and recover missing modalities. The refinement phase employs supervised point-based contrastive learning to disrupt semantic correlations and accentuate emotional traits, thereby enriching the affective content of the reconstructed representations. Extensive experiments on the IEMOCAP and MSP-IMPROV datasets confirm the superior performance of CM-ARR under conditions of both missing and complete modalities. Notably, averaged across six scenarios of missing modalities, CM-ARR achieves absolute improvements of 2.11% in WAR and 2.12% in UAR on the IEMOCAP dataset, and 1.71% and 1.96% in WAR and UAR, respectively, on the MSP-IMPROV dataset.

Retrieval-augmented Generation (RAG) systems have been actively studied and deployed across various industries to query on domain-specific knowledge base. However, evaluating these systems presents unique challenges due to the scarcity of domain-specific queries and corresponding ground truths, as well as a lack of systematic approaches to diagnosing the cause of failure cases -- whether they stem from knowledge deficits or issues related to system robustness. To address these challenges, we introduce GRAMMAR (GRounded And Modular Methodology for Assessment of RAG), an evaluation framework comprising two key elements: 1) a data generation process that leverages relational databases and LLMs to efficiently produce scalable query-answer pairs for evaluation. This method facilitates the separation of query logic from linguistic variations, enabling the testing of hypotheses related to non-robust textual forms; and 2) an evaluation framework that differentiates knowledge gaps from robustness and enables the identification of defective modules. Our empirical results underscore the limitations of current reference-free evaluation approaches and the reliability of GRAMMAR to accurately identify model vulnerabilities. For implementation details, refer to our GitHub repository: //github.com/xinzhel/grammar.

We present IntrinsicAvatar, a novel approach to recovering the intrinsic properties of clothed human avatars including geometry, albedo, material, and environment lighting from only monocular videos. Recent advancements in human-based neural rendering have enabled high-quality geometry and appearance reconstruction of clothed humans from just monocular videos. However, these methods bake intrinsic properties such as albedo, material, and environment lighting into a single entangled neural representation. On the other hand, only a handful of works tackle the problem of estimating geometry and disentangled appearance properties of clothed humans from monocular videos. They usually achieve limited quality and disentanglement due to approximations of secondary shading effects via learned MLPs. In this work, we propose to model secondary shading effects explicitly via Monte-Carlo ray tracing. We model the rendering process of clothed humans as a volumetric scattering process, and combine ray tracing with body articulation. Our approach can recover high-quality geometry, albedo, material, and lighting properties of clothed humans from a single monocular video, without requiring supervised pre-training using ground truth materials. Furthermore, since we explicitly model the volumetric scattering process and ray tracing, our model naturally generalizes to novel poses, enabling animation of the reconstructed avatar in novel lighting conditions.

Biometric systems based on brain activity have been proposed as an alternative to passwords or to complement current authentication techniques. By leveraging the unique brainwave patterns of individuals, these systems offer the possibility of creating authentication solutions that are resistant to theft, hands-free, accessible, and potentially even revocable. However, despite the growing stream of research in this area, faster advance is hindered by reproducibility problems. Issues such as the lack of standard reporting schemes for performance results and system configuration, or the absence of common evaluation benchmarks, make comparability and proper assessment of different biometric solutions challenging. Further, barriers are erected to future work when, as so often, source code is not published open access. To bridge this gap, we introduce NeuroIDBench, a flexible open source tool to benchmark brainwave-based authentication models. It incorporates nine diverse datasets, implements a comprehensive set of pre-processing parameters and machine learning algorithms, enables testing under two common adversary models (known vs unknown attacker), and allows researchers to generate full performance reports and visualizations. We use NeuroIDBench to investigate the shallow classifiers and deep learning-based approaches proposed in the literature, and to test robustness across multiple sessions. We observe a 37.6% reduction in Equal Error Rate (EER) for unknown attacker scenarios (typically not tested in the literature), and we highlight the importance of session variability to brainwave authentication. All in all, our results demonstrate the viability and relevance of NeuroIDBench in streamlining fair comparisons of algorithms, thereby furthering the advancement of brainwave-based authentication through robust methodological practices.

Kernels are a fundamental technical primitive in machine learning. In recent years, kernel-based methods such as Gaussian processes are becoming increasingly important in applications where quantifying uncertainty is of key interest. In settings that involve structured data defined on graphs, meshes, manifolds, or other related spaces, defining kernels with good uncertainty-quantification behavior, and computing their value numerically, is less straightforward than in the Euclidean setting. To address this difficulty, we present GeometricKernels, a software package which implements the geometric analogs of classical Euclidean squared exponential - also known as heat - and Mat\'ern kernels, which are widely-used in settings where uncertainty is of key interest. As a byproduct, we obtain the ability to compute Fourier-feature-type expansions, which are widely used in their own right, on a wide set of geometric spaces. Our implementation supports automatic differentiation in every major current framework simultaneously via a backend-agnostic design. In this companion paper to the package and its documentation, we outline the capabilities of the package and present an illustrated example of its interface. We also include a brief overview of the theory the package is built upon and provide some historic context in the appendix.

Chain-of-thought reasoning, a cognitive process fundamental to human intelligence, has garnered significant attention in the realm of artificial intelligence and natural language processing. However, there still remains a lack of a comprehensive survey for this arena. To this end, we take the first step and present a thorough survey of this research field carefully and widely. We use X-of-Thought to refer to Chain-of-Thought in a broad sense. In detail, we systematically organize the current research according to the taxonomies of methods, including XoT construction, XoT structure variants, and enhanced XoT. Additionally, we describe XoT with frontier applications, covering planning, tool use, and distillation. Furthermore, we address challenges and discuss some future directions, including faithfulness, multi-modal, and theory. We hope this survey serves as a valuable resource for researchers seeking to innovate within the domain of chain-of-thought reasoning.

Believable proxies of human behavior can empower interactive applications ranging from immersive environments to rehearsal spaces for interpersonal communication to prototyping tools. In this paper, we introduce generative agents--computational software agents that simulate believable human behavior. Generative agents wake up, cook breakfast, and head to work; artists paint, while authors write; they form opinions, notice each other, and initiate conversations; they remember and reflect on days past as they plan the next day. To enable generative agents, we describe an architecture that extends a large language model to store a complete record of the agent's experiences using natural language, synthesize those memories over time into higher-level reflections, and retrieve them dynamically to plan behavior. We instantiate generative agents to populate an interactive sandbox environment inspired by The Sims, where end users can interact with a small town of twenty five agents using natural language. In an evaluation, these generative agents produce believable individual and emergent social behaviors: for example, starting with only a single user-specified notion that one agent wants to throw a Valentine's Day party, the agents autonomously spread invitations to the party over the next two days, make new acquaintances, ask each other out on dates to the party, and coordinate to show up for the party together at the right time. We demonstrate through ablation that the components of our agent architecture--observation, planning, and reflection--each contribute critically to the believability of agent behavior. By fusing large language models with computational, interactive agents, this work introduces architectural and interaction patterns for enabling believable simulations of human behavior.

A fundamental goal of scientific research is to learn about causal relationships. However, despite its critical role in the life and social sciences, causality has not had the same importance in Natural Language Processing (NLP), which has traditionally placed more emphasis on predictive tasks. This distinction is beginning to fade, with an emerging area of interdisciplinary research at the convergence of causal inference and language processing. Still, research on causality in NLP remains scattered across domains without unified definitions, benchmark datasets and clear articulations of the remaining challenges. In this survey, we consolidate research across academic areas and situate it in the broader NLP landscape. We introduce the statistical challenge of estimating causal effects, encompassing settings where text is used as an outcome, treatment, or as a means to address confounding. In addition, we explore potential uses of causal inference to improve the performance, robustness, fairness, and interpretability of NLP models. We thus provide a unified overview of causal inference for the computational linguistics community.