Phylogenetic inference, grounded in molecular evolution models, is essential for understanding the evolutionary relationships in biological data. Accounting for the uncertainty of phylogenetic tree variables, which include tree topologies and evolutionary distances on branches, is crucial for accurately inferring species relationships from molecular data and tasks requiring variable marginalization. Variational Bayesian methods are key to developing scalable, practical models; however, it remains challenging to conduct phylogenetic inference without restricting the combinatorially vast number of possible tree topologies. In this work, we introduce a novel, fully differentiable formulation of phylogenetic inference that leverages a unique representation of topological distributions in continuous geometric spaces. Through practical considerations on design spaces and control variates for gradient estimations, our approach, GeoPhy, enables variational inference without limiting the topological candidates. In experiments using real benchmark datasets, GeoPhy significantly outperformed other approximate Bayesian methods that considered whole topologies.
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Foundation models that incorporate language, vision, and more recently actions have revolutionized the ability to harness internet scale data to reason about useful tasks. However, one of the key challenges of training embodied foundation models is the lack of data grounded in the physical world. In this paper, we propose AutoRT, a system that leverages existing foundation models to scale up the deployment of operational robots in completely unseen scenarios with minimal human supervision. AutoRT leverages vision-language models (VLMs) for scene understanding and grounding, and further uses large language models (LLMs) for proposing diverse and novel instructions to be performed by a fleet of robots. Guiding data collection by tapping into the knowledge of foundation models enables AutoRT to effectively reason about autonomy tradeoffs and safety while significantly scaling up data collection for robot learning. We demonstrate AutoRT proposing instructions to over 20 robots across multiple buildings and collecting 77k real robot episodes via both teleoperation and autonomous robot policies. We experimentally show that such "in-the-wild" data collected by AutoRT is significantly more diverse, and that AutoRT's use of LLMs allows for instruction following data collection robots that can align to human preferences.
This study explores the impact of peer acknowledgement on learner engagement and implicit psychological attributes in written annotations on an online social reading platform. Participants included 91 undergraduates from a large North American University. Using log file data, we analyzed the relationship between learners' received peer acknowledgement and their subsequent annotation behaviours using cross-lag regression. Higher peer acknowledgements correlate with increased initiation of annotations and responses to peer annotations. By applying text mining techniques and calculating Shapley values to analyze 1,969 social annotation entries, we identified prominent psychological themes within three dimensions (i.e., affect, cognition, and motivation) that foster peer acknowledgment in digital social annotation. These themes include positive affect, openness to learning and discussion, and expression of motivation. The findings assist educators in improving online learning communities and provide guidance to technology developers in designing effective prompts, drawing from both implicit psychological cues and explicit learning behaviours.
Insufficient modeling of human preferences within the reward model is a major obstacle for leveraging human feedback to improve translation quality. Fortunately, quality estimation (QE), which predicts the quality of a given translation without reference, has achieved impressive alignment with human evaluations in the last two years. In this work, we investigate the potential of employing the QE model as the reward model (the QE-based reward model) to predict human preferences for feedback training. We first identify the overoptimization problem during QE-based feedback training, manifested as an increase in reward while translation quality declines. We examine the problem and argue that the vulnerability of the QE model might lead to high rewards for incorrect translations, resulting in overoptimization and error propagation. To address the problem, we adopt a simple yet effective method that uses heuristic rules to detect the incorrect translations and assigns a penalty term to the QE-based rewards for the detected incorrect translations. Experimental results show that the proposed QE-based feedback training achieves consistent and significant improvements across various settings, further verified through human preference studies. Our subsequent analysis demonstrates the high data efficiency of the proposed QE-based feedback training: the proposed approach using a small amount of monolingual data can outperform systems using larger parallel corpora.
Recent advances in large language models elicit reasoning in a chain-of-thought that allows models to decompose problems in a human-like fashion. Though this paradigm improves multi-step reasoning ability in language models, it is limited by being unimodal and applied mainly to question-answering tasks. We claim that incorporating visual augmentation into reasoning is essential, especially for complex, imaginative tasks. Consequently, we introduce VCoT, a novel method that leverages chain-of-thought prompting with vision-language grounding to recursively bridge the logical gaps within sequential data. Our method uses visual guidance to generate synthetic multimodal infillings that add consistent and novel information to reduce the logical gaps for downstream tasks that can benefit from temporal reasoning, as well as provide interpretability into models' multi-step reasoning. We apply VCoT to the Visual Storytelling and WikiHow summarization datasets and demonstrate through human evaluation that VCoT offers novel and consistent synthetic data augmentation beating chain-of-thought baselines, which can be used to enhance downstream performance.
Understanding and recognizing emotions are important and challenging issues in the metaverse era. Understanding, identifying, and predicting fear, which is one of the fundamental human emotions, in virtual reality (VR) environments plays an essential role in immersive game development, scene development, and next-generation virtual human-computer interaction applications. In this article, we used VR horror games as a medium to analyze fear emotions by collecting multi-modal data (posture, audio, and physiological signals) from 23 players. We used an LSTM-based model to predict fear with accuracies of 65.31% and 90.47% under 6-level classification (no fear and five different levels of fear) and 2-level classification (no fear and fear), respectively. We constructed a multi-modal natural behavior dataset of immersive human fear responses (VRMN-bD) and compared it with existing relevant advanced datasets. The results show that our dataset has fewer limitations in terms of collection method, data scale and audience scope. We are unique and advanced in targeting multi-modal datasets of fear and behavior in VR stand-up interactive environments. Moreover, we discussed the implications of this work for communities and applications. The dataset and pre-trained model are available at //github.com/KindOPSTAR/VRMN-bD.
Computational complexity is a key limitation of genomic analyses. Thus, over the last 30 years, researchers have proposed numerous fast heuristic methods that provide computational relief. Comparing genomic sequences is one of the most fundamental computational steps in most genomic analyses. Due to its high computational complexity, optimized exact and heuristic algorithms are still being developed. We find that these methods are highly sensitive to the underlying data, its quality, and various hyperparameters. Despite their wide use, no in-depth analysis has been performed, potentially falsely discarding genetic sequences from further analysis and unnecessarily inflating computational costs. We provide the first analysis and benchmark of this heterogeneity. We deliver an actionable overview of the 11 most widely used state-of-the-art methods for comparing genomic sequences. We also inform readers about their advantages and downsides using thorough experimental evaluation and different real datasets from all major manufacturers (i.e., Illumina, ONT, and PacBio). SequenceLab is publicly available at //github.com/CMU-SAFARI/SequenceLab.
Stochastic generators are useful for estimating climate impacts on various sectors. Projecting climate risk in various sectors, e.g. energy systems, requires generators that are accurate (statistical resemblance to ground-truth), reliable (do not produce erroneous examples), and efficient. Leveraging data from the North American Land Data Assimilation System, we introduce TemperatureGAN, a Generative Adversarial Network conditioned on months, locations, and time periods, to generate 2m above ground atmospheric temperatures at an hourly resolution. We propose evaluation methods and metrics to measure the quality of generated samples. We show that TemperatureGAN produces high-fidelity examples with good spatial representation and temporal dynamics consistent with known diurnal cycles.
Recently, the astonishing performance of large language models (LLMs) in natural language comprehension and generation tasks triggered lots of exploration of using them as central controllers to build agent systems. Multiple studies focus on bridging the LLMs to external tools to extend the application scenarios. However, the current LLMs' perceiving tool-use ability is limited to a single text query, which may result in ambiguity in understanding the users' real intentions. LLMs are expected to eliminate that by perceiving the visual- or auditory-grounded instructions' information. Therefore, in this paper, we propose Tool-LMM, a system incorporating open-source LLMs and multi-modal encoders so that the learnt LLMs can be conscious of multi-modal input instruction and then select the function-matched tool correctly. To facilitate the evaluation of the model's capability, we collect a dataset featured by consisting of multi-modal input tools from HuggingFace. Another important feature of our dataset is that our dataset also contains multiple potential choices for the same instruction due to the existence of identical functions and synonymous functions, which provides more potential solutions for the same query. The experiments reveal that our LMM is capable of recommending appropriate tools for multi-modal instructions. Codes and data are available at //github.com/Tool-LMM/Tool-LMM.
In pace with developments in the research field of artificial intelligence, knowledge graphs (KGs) have attracted a surge of interest from both academia and industry. As a representation of semantic relations between entities, KGs have proven to be particularly relevant for natural language processing (NLP), experiencing a rapid spread and wide adoption within recent years. Given the increasing amount of research work in this area, several KG-related approaches have been surveyed in the NLP research community. However, a comprehensive study that categorizes established topics and reviews the maturity of individual research streams remains absent to this day. Contributing to closing this gap, we systematically analyzed 507 papers from the literature on KGs in NLP. Our survey encompasses a multifaceted review of tasks, research types, and contributions. As a result, we present a structured overview of the research landscape, provide a taxonomy of tasks, summarize our findings, and highlight directions for future work.
We consider the problem of explaining the predictions of graph neural networks (GNNs), which otherwise are considered as black boxes. Existing methods invariably focus on explaining the importance of graph nodes or edges but ignore the substructures of graphs, which are more intuitive and human-intelligible. In this work, we propose a novel method, known as SubgraphX, to explain GNNs by identifying important subgraphs. Given a trained GNN model and an input graph, our SubgraphX explains its predictions by efficiently exploring different subgraphs with Monte Carlo tree search. To make the tree search more effective, we propose to use Shapley values as a measure of subgraph importance, which can also capture the interactions among different subgraphs. To expedite computations, we propose efficient approximation schemes to compute Shapley values for graph data. Our work represents the first attempt to explain GNNs via identifying subgraphs explicitly and directly. Experimental results show that our SubgraphX achieves significantly improved explanations, while keeping computations at a reasonable level.
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