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AI-enabled synthetic biology has tremendous potential but also significantly increases biorisks and brings about a new set of dual use concerns. The picture is complicated given the vast innovations envisioned to emerge by combining emerging technologies, as AI-enabled synthetic biology potentially scales up bioengineering into industrial biomanufacturing. However, the literature review indicates that goals such as maintaining a reasonable scope for innovation, or more ambitiously to foster a huge bioeconomy don't necessarily contrast with biosafety, but need to go hand in hand. This paper presents a literature review of the issues and describes emerging frameworks for policy and practice that transverse the options of command-and control, stewardship, bottom-up, and laissez-faire governance. How to achieve early warning systems that enable prevention and mitigation of future AI-enabled biohazards from the lab, from deliberate misuse, or from the public realm, will constantly need to evolve, and adaptive, interactive approaches should emerge. Although biorisk is subject to an established governance regime, and scientists generally adhere to biosafety protocols, even experimental, but legitimate use by scientists could lead to unexpected developments. Recent advances in chatbots enabled by generative AI have revived fears that advanced biological insight can more easily get into the hands of malignant individuals or organizations. Given these sets of issues, society needs to rethink how AI-enabled synthetic biology should be governed. The suggested way to visualize the challenge at hand is whack-a-mole governance, although the emerging solutions are perhaps not so different either.

SDRDPy is a desktop application that allows experts an intuitive graphic and tabular representation of the knowledge extracted by any supervised descriptive rule discovery algorithm. The application is able to provide an analysis of the data showing the relevant information of the data set and the relationship between the rules, data and the quality measures associated for each rule regardless of the tool where algorithm has been executed. All of the information is presented in a user-friendly application in order to facilitate expert analysis and also the exportation of reports in different formats.

In statistical inference, retrodiction is the act of inferring potential causes in the past based on knowledge of the effects in the present and the dynamics leading to the present. Retrodiction is applicable even when the dynamics is not reversible, and it agrees with the reverse dynamics when it exists, so that retrodiction may be viewed as an extension of inversion, i.e., time-reversal. Recently, an axiomatic definition of retrodiction has been made in a way that is applicable to both classical and quantum probability using ideas from category theory. Almost simultaneously, a framework for information flow in in terms of semicartesian categories has been proposed in the setting of categorical probability theory. Here, we formulate a general definition of retrodiction to add to the information flow axioms in semicartesian categories, thus providing an abstract framework for retrodiction beyond classical and quantum probability theory. More precisely, we extend Bayesian inference, and more generally Jeffrey's probability kinematics, to arbitrary semicartesian categories.

This paper presents GRASP, a novel benchmark to evaluate the language grounding and physical understanding capabilities of video-based multimodal large language models (LLMs). This evaluation is accomplished via a two-tier approach leveraging Unity simulations. The first level tests for language grounding by assessing a model's ability to relate simple textual descriptions with visual information. The second level evaluates the model's understanding of "Intuitive Physics" principles, such as object permanence and continuity. In addition to releasing the benchmark, we use it to evaluate several state-of-the-art multimodal LLMs. Our evaluation reveals significant shortcomings in the language grounding and intuitive physics capabilities of these models. Although they exhibit at least some grounding capabilities, particularly for colors and shapes, these capabilities depend heavily on the prompting strategy. At the same time, all models perform below or at the chance level of 50% in the Intuitive Physics tests, while human subjects are on average 80% correct. These identified limitations underline the importance of using benchmarks like GRASP to monitor the progress of future models in developing these competencies.

Representations from transformer-based unidirectional language models are known to be effective at predicting brain responses to natural language. However, most studies comparing language models to brains have used GPT-2 or similarly sized language models. Here we tested whether larger open-source models such as those from the OPT and LLaMA families are better at predicting brain responses recorded using fMRI. Mirroring scaling results from other contexts, we found that brain prediction performance scales logarithmically with model size from 125M to 30B parameter models, with ~15% increased encoding performance as measured by correlation with a held-out test set across 3 subjects. Similar logarithmic behavior was observed when scaling the size of the fMRI training set. We also characterized scaling for acoustic encoding models that use HuBERT, WavLM, and Whisper, and we found comparable improvements with model size. A noise ceiling analysis of these large, high-performance encoding models showed that performance is nearing the theoretical maximum for brain areas such as the precuneus and higher auditory cortex. These results suggest that increasing scale in both models and data will yield incredibly effective models of language processing in the brain, enabling better scientific understanding as well as applications such as decoding.

Lattices are architected metamaterials whose properties strongly depend on their geometrical design. The analogy between lattices and graphs enables the use of graph neural networks (GNNs) as a faster surrogate model compared to traditional methods such as finite element modelling. In this work we present a higher-order GNN model trained to predict the fourth-order stiffness tensor of periodic strut-based lattices. The key features of the model are (i) SE(3) equivariance, and (ii) consistency with the thermodynamic law of conservation of energy. We compare the model to non-equivariant models based on a number of error metrics and demonstrate the benefits of the encoded equivariance and energy conservation in terms of predictive performance and reduced training requirements.

We demonstrate that large language models can produce reasonable numerical ratings of the logical consistency of claims. We also outline a mathematical approach based on sheaf theory for lifting such ratings to hypertexts such as laws, jurisprudence, and social media and evaluating their consistency globally. This approach is a promising avenue to increasing consistency in and of government, as well as to combating mis- and disinformation and related ills.

The detection of toxic language in the Arabic language has emerged as an active area of research in recent years, and reviewing the existing datasets employed for training the developed solutions has become a pressing need. This paper offers a comprehensive survey of Arabic datasets focused on online toxic language. We systematically gathered a total of 54 available datasets and their corresponding papers and conducted a thorough analysis, considering 18 criteria across four primary dimensions: availability details, content, annotation process, and reusability. This analysis enabled us to identify existing gaps and make recommendations for future research works. For the convenience of the research community, the list of the analysed datasets is maintained in a GitHub repository (//github.com/Imene1/Arabic-toxic-language).

The remarkable practical success of deep learning has revealed some major surprises from a theoretical perspective. In particular, simple gradient methods easily find near-optimal solutions to non-convex optimization problems, and despite giving a near-perfect fit to training data without any explicit effort to control model complexity, these methods exhibit excellent predictive accuracy. We conjecture that specific principles underlie these phenomena: that overparametrization allows gradient methods to find interpolating solutions, that these methods implicitly impose regularization, and that overparametrization leads to benign overfitting. We survey recent theoretical progress that provides examples illustrating these principles in simpler settings. We first review classical uniform convergence results and why they fall short of explaining aspects of the behavior of deep learning methods. We give examples of implicit regularization in simple settings, where gradient methods lead to minimal norm functions that perfectly fit the training data. Then we review prediction methods that exhibit benign overfitting, focusing on regression problems with quadratic loss. For these methods, we can decompose the prediction rule into a simple component that is useful for prediction and a spiky component that is useful for overfitting but, in a favorable setting, does not harm prediction accuracy. We focus specifically on the linear regime for neural networks, where the network can be approximated by a linear model. In this regime, we demonstrate the success of gradient flow, and we consider benign overfitting with two-layer networks, giving an exact asymptotic analysis that precisely demonstrates the impact of overparametrization. We conclude by highlighting the key challenges that arise in extending these insights to realistic deep learning settings.

Graph representation learning for hypergraphs can be used to extract patterns among higher-order interactions that are critically important in many real world problems. Current approaches designed for hypergraphs, however, are unable to handle different types of hypergraphs and are typically not generic for various learning tasks. Indeed, models that can predict variable-sized heterogeneous hyperedges have not been available. Here we develop a new self-attention based graph neural network called Hyper-SAGNN applicable to homogeneous and heterogeneous hypergraphs with variable hyperedge sizes. We perform extensive evaluations on multiple datasets, including four benchmark network datasets and two single-cell Hi-C datasets in genomics. We demonstrate that Hyper-SAGNN significantly outperforms the state-of-the-art methods on traditional tasks while also achieving great performance on a new task called outsider identification. Hyper-SAGNN will be useful for graph representation learning to uncover complex higher-order interactions in different applications.