The success of language models, especially transformer-based architectures, has trickled into other domains giving rise to "scientific language models" that operate on small molecules, proteins or polymers. In chemistry, language models contribute to accelerating the molecule discovery cycle as evidenced by promising recent findings in early-stage drug discovery. Here, we review the role of language models in molecular discovery, underlining their strength in de novo drug design, property prediction and reaction chemistry. We highlight valuable open-source software assets thus lowering the entry barrier to the field of scientific language modeling. Last, we sketch a vision for future molecular design that combines a chatbot interface with access to computational chemistry tools. Our contribution serves as a valuable resource for researchers, chemists, and AI enthusiasts interested in understanding how language models can and will be used to accelerate chemical discovery.
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We consider two applications where we study how dependence structure between many variables is linked to external network data. We first study the interplay between social media connectedness and the co-evolution of the COVID-19 pandemic across USA counties. We next study study how the dependence between stock market returns across firms relates to similarities in economic and policy indicators from text regulatory filings. Both applications are modelled via Gaussian graphical models where one has external network data. We develop spike-and-slab and graphical LASSO frameworks to integrate the network data, both facilitating the interpretation of the graphical model and improving inference. The goal is to detect when the network data relates to the graphical model and, if so, explain how. We found that counties strongly connected on Facebook are more likely to have similar COVID-19 evolution (positive partial correlations), accounting for various factors driving the mean. We also found that the association in stock market returns depends in a stronger fashion on economic than on policy indicators. The examples show that data integration can improve interpretation, statistical accuracy, and out-of-sample prediction, in some instances using significantly sparser graphical models.
This tutorial shows how various Bayesian survival models can be fitted using the integrated nested Laplace approximation in a clear, legible, and comprehensible manner using the INLA and INLAjoint R-packages. Such models include accelerated failure time, proportional hazards, mixture cure, competing risks, multi-state, frailty, and joint models of longitudinal and survival data, originally presented in the article "Bayesian survival analysis with BUGS" (Alvares et al., 2021). In addition, we illustrate the implementation of a new joint model for a longitudinal semicontinuous marker, recurrent events, and a terminal event. Our proposal aims to provide the reader with syntax examples for implementing survival models using a fast and accurate approximate Bayesian inferential approach.
The remarkable generative capabilities of denoising diffusion models have raised new concerns regarding the authenticity of the images we see every day on the Internet. However, the vast majority of existing deepfake detection models are tested against previous generative approaches (e.g. GAN) and usually provide only a "fake" or "real" label per image. We believe a more informative output would be to augment the per-image label with a localization map indicating which regions of the input have been manipulated. To this end, we frame this task as a weakly-supervised localization problem and identify three main categories of methods (based on either explanations, local scores or attention), which we compare on an equal footing by using the Xception network as the common backbone architecture. We provide a careful analysis of all the main factors that parameterize the design space: choice of method, type of supervision, dataset and generator used in the creation of manipulated images; our study is enabled by constructing datasets in which only one of the components is varied. Our results show that weakly-supervised localization is attainable, with the best performing detection method (based on local scores) being less sensitive to the looser supervision than to the mismatch in terms of dataset or generator.
Understanding adaptive human driving behavior, in particular how drivers manage uncertainty, is of key importance for developing simulated human driver models that can be used in the evaluation and development of autonomous vehicles. However, existing traffic psychology models of adaptive driving behavior either lack computational rigor or only address specific scenarios and/or behavioral phenomena. While models developed in the fields of machine learning and robotics can effectively learn adaptive driving behavior from data, due to their black box nature, they offer little or no explanation of the mechanisms underlying the adaptive behavior. Thus, a generalizable, interpretable, computational model of adaptive human driving behavior is still lacking. This paper proposes such a model based on active inference, a behavioral modeling framework originating in computational neuroscience. The model offers a principled solution to how humans trade progress against caution through policy selection based on the single mandate to minimize expected free energy. This casts goal-seeking and information-seeking (uncertainty-resolving) behavior under a single objective function, allowing the model to seamlessly resolve uncertainty as a means to obtain its goals. We apply the model in two apparently disparate driving scenarios that require managing uncertainty, (1) driving past an occluding object and (2) visual time sharing between driving and a secondary task, and show how human-like adaptive driving behavior emerges from the single principle of expected free energy minimization.
This study compares the performance of (1) fine-tuned models and (2) extremely large language models on the task of check-worthy claim detection. For the purpose of the comparison we composed a multilingual and multi-topical dataset comprising texts of various sources and styles. Building on this, we performed a benchmark analysis to determine the most general multilingual and multi-topical claim detector. We chose three state-of-the-art models in the check-worthy claim detection task and fine-tuned them. Furthermore, we selected three state-of-the-art extremely large language models without any fine-tuning. We made modifications to the models to adapt them for multilingual settings and through extensive experimentation and evaluation. We assessed the performance of all the models in terms of accuracy, recall, and F1-score in in-domain and cross-domain scenarios. Our results demonstrate that despite the technological progress in the area of natural language processing, the models fine-tuned for the task of check-worthy claim detection still outperform the zero-shot approaches in a cross-domain settings.
Our knowledge of the organisation of the human brain at the population-level is yet to translate into power to predict functional differences at the individual-level, limiting clinical applications, and casting doubt on the generalisability of inferred mechanisms. It remains unknown whether the difficulty arises from the absence of individuating biological patterns within the brain, or from limited power to access them with the models and compute at our disposal. Here we comprehensively investigate the resolvability of such patterns with data and compute at unprecedented scale. Across 23810 unique participants from UK Biobank, we systematically evaluate the predictability of 25 individual biological characteristics, from all available combinations of structural and functional neuroimaging data. Over 4526 GPU*hours of computation, we train, optimize, and evaluate out-of-sample 700 individual predictive models, including multilayer perceptrons of demographic, psychological, serological, chronic morbidity, and functional connectivity characteristics, and both uni- and multi-modal 3D convolutional neural network models of macro- and micro-structural brain imaging. We find a marked discrepancy between the high predictability of sex (balanced accuracy 99.7%), age (mean absolute error 2.048 years, R2 0.859), and weight (mean absolute error 2.609Kg, R2 0.625), for which we set new state-of-the-art performance, and the surprisingly low predictability of other characteristics. Neither structural nor functional imaging predicted individual psychology better than the coincidence of common chronic morbidity (p<0.05). Serology predicted common morbidity (p<0.05) and was best predicted by it (p<0.001), followed by structural neuroimaging (p<0.05). Our findings suggest either more informative imaging or more powerful models will be needed to decipher individual level characteristics from the brain.
With large language models (LLMs) appearing to behave increasingly human-like in text-based interactions, it has become popular to attempt to evaluate various properties of these models using tests originally designed for humans. While re-using existing tests is a resource-efficient way to evaluate LLMs, careful adjustments are usually required to ensure that test results are even valid across human sub-populations. Thus, it is not clear to what extent different tests' validity generalizes to LLMs. In this work, we provide evidence that LLMs' responses to personality tests systematically deviate from typical human responses, implying that these results cannot be interpreted in the same way as human test results. Concretely, reverse-coded items (e.g. "I am introverted" vs "I am extraverted") are often both answered affirmatively by LLMs. In addition, variation across different prompts designed to "steer" LLMs to simulate particular personality types does not follow the clear separation into five independent personality factors from human samples. In light of these results, we believe it is important to pay more attention to tests' validity for LLMs before drawing strong conclusions about potentially ill-defined concepts like LLMs' "personality".
As the IT industry advances, system log data becomes increasingly crucial. Many computer systems rely on log texts for management due to restricted access to source code. The need for log anomaly detection is growing, especially in real-world applications, but identifying anomalies in rapidly accumulating logs remains a challenging task. Traditional deep learning-based anomaly detection models require dataset-specific training, leading to corresponding delays. Notably, most methods only focus on sequence-level log information, which makes the detection of subtle anomalies harder, and often involve inference processes that are difficult to utilize in real-time. We introduce RAPID, a model that capitalizes on the inherent features of log data to enable anomaly detection without training delays, ensuring real-time capability. RAPID treats logs as natural language, extracting representations using pre-trained language models. Given that logs can be categorized based on system context, we implement a retrieval-based technique to contrast test logs with the most similar normal logs. This strategy not only obviates the need for log-specific training but also adeptly incorporates token-level information, ensuring refined and robust detection, particularly for unseen logs. We also propose the core set technique, which can reduce the computational cost needed for comparison. Experimental results show that even without training on log data, RAPID demonstrates competitive performance compared to prior models and achieves the best performance on certain datasets. Through various research questions, we verified its capability for real-time detection without delay.
Graph-centric artificial intelligence (graph AI) has achieved remarkable success in modeling interacting systems prevalent in nature, from dynamical systems in biology to particle physics. The increasing heterogeneity of data calls for graph neural architectures that can combine multiple inductive biases. However, combining data from various sources is challenging because appropriate inductive bias may vary by data modality. Multimodal learning methods fuse multiple data modalities while leveraging cross-modal dependencies to address this challenge. Here, we survey 140 studies in graph-centric AI and realize that diverse data types are increasingly brought together using graphs and fed into sophisticated multimodal models. These models stratify into image-, language-, and knowledge-grounded multimodal learning. We put forward an algorithmic blueprint for multimodal graph learning based on this categorization. The blueprint serves as a way to group state-of-the-art architectures that treat multimodal data by choosing appropriately four different components. This effort can pave the way for standardizing the design of sophisticated multimodal architectures for highly complex real-world problems.
Although measuring held-out accuracy has been the primary approach to evaluate generalization, it often overestimates the performance of NLP models, while alternative approaches for evaluating models either focus on individual tasks or on specific behaviors. Inspired by principles of behavioral testing in software engineering, we introduce CheckList, a task-agnostic methodology for testing NLP models. CheckList includes a matrix of general linguistic capabilities and test types that facilitate comprehensive test ideation, as well as a software tool to generate a large and diverse number of test cases quickly. We illustrate the utility of CheckList with tests for three tasks, identifying critical failures in both commercial and state-of-art models. In a user study, a team responsible for a commercial sentiment analysis model found new and actionable bugs in an extensively tested model. In another user study, NLP practitioners with CheckList created twice as many tests, and found almost three times as many bugs as users without it.
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