Motivation: Curation of literature in life sciences is a growing challenge. The continued increase in the rate of publication, coupled with the relatively fixed number of curators worldwide presents a major challenge to developers of biomedical knowledgebases. Very few knowledgebases have resources to scale to the whole relevant literature and all have to prioritise their efforts. Results: In this work, we take a first step to alleviating the lack of curator time in RNA science by generating summaries of literature for non-coding RNAs using large language models (LLMs). We demonstrate that high-quality, factually accurate summaries with accurate references can be automatically generated from the literature using a commercial LLM and a chain of prompts and checks. Manual assessment was carried out for a subset of summaries, with the majority being rated extremely high quality. We also applied the most commonly used automated evaluation approaches, finding that they do not correlate with human assessment. Finally, we apply our tool to a selection of over 4,600 ncRNAs and make the generated summaries available via the RNAcentral resource. We conclude that automated literature summarization is feasible with the current generation of LLMs, provided careful prompting and automated checking are applied. Availability: Code used to produce these summaries can be found here: //github.com/RNAcentral/litscan-summarization and the dataset of contexts and summaries can be found here: //huggingface.co/datasets/RNAcentral/litsumm-v1. Summaries are also displayed on the RNA report pages in RNAcentral (//rnacentral.org/)
Preference modelling lies at the intersection of economics, decision theory, machine learning and statistics. By understanding individuals' preferences and how they make choices, we can build products that closely match their expectations, paving the way for more efficient and personalised applications across a wide range of domains. The objective of this tutorial is to present a cohesive and comprehensive framework for preference learning with Gaussian Processes (GPs), demonstrating how to seamlessly incorporate rationality principles (from economics and decision theory) into the learning process. By suitably tailoring the likelihood function, this framework enables the construction of preference learning models that encompass random utility models, limits of discernment, and scenarios with multiple conflicting utilities for both object- and label-preference. This tutorial builds upon established research while simultaneously introducing some novel GP-based models to address specific gaps in the existing literature.
This paper presents a novel FPGA-based neuromorphic cochlea, leveraging the general-purpose spike-coding algorithm, Spiketrum. The focus of this study is on the development and characterization of this cochlea model, which excels in transforming audio vibrations into biologically realistic auditory spike trains. These spike trains are designed to withstand neural fluctuations and spike losses while accurately encapsulating the spatial and precise temporal characteristics of audio, along with the intensity of incoming vibrations. Noteworthy features include the ability to generate real-time spike trains with minimal information loss and the capacity to reconstruct original signals. This fine-tuning capability allows users to optimize spike rates, achieving an optimal balance between output quality and power consumption. Furthermore, the integration of a feedback system into Spiketrum enables selective amplification of specific features while attenuating others, facilitating adaptive power consumption based on application requirements. The hardware implementation supports both spike-based and non-spike-based processors, making it versatile for various computing systems. The cochlea's ability to encode diverse sensory information, extending beyond sound waveforms, positions it as a promising sensory input for current and future spike-based intelligent computing systems, offering compact and real-time spike train generation.
Accurate prediction of antibody structure is a central task in the design and development of monoclonal antibodies, notably to understand both their developability and their binding properties. In this article, we introduce ABodyBuilder3, an improved and scalable antibody structure prediction model based on ImmuneBuilder. We achieve a new state-of-the-art accuracy in the modelling of CDR loops by leveraging language model embeddings, and show how predicted structures can be further improved through careful relaxation strategies. Finally, we incorporate a predicted Local Distance Difference Test into the model output to allow for a more accurate estimation of uncertainties.
Legged locomotion has recently achieved remarkable success with the progress of machine learning techniques, especially deep reinforcement learning (RL). Controllers employing neural networks have demonstrated empirical and qualitative robustness against real-world uncertainties, including sensor noise and external perturbations. However, formally investigating the vulnerabilities of these locomotion controllers remains a challenge. This difficulty arises from the requirement to pinpoint vulnerabilities across a long-tailed distribution within a high-dimensional, temporally sequential space. As a first step towards quantitative verification, we propose a computational method that leverages sequential adversarial attacks to identify weaknesses in learned locomotion controllers. Our research demonstrates that, even state-of-the-art robust controllers can fail significantly under well-designed, low-magnitude adversarial sequence. Through experiments in simulation and on the real robot, we validate our approach's effectiveness, and we illustrate how the results it generates can be used to robustify the original policy and offer valuable insights into the safety of these black-box policies. Project page: //fanshi14.github.io/me/rss24.html
This paper presents a novel approach for constructing graph neural networks equivariant to 2D rotations and translations and leveraging them as PDE surrogates on non-gridded domains. We show that aligning the representations with the principal axis allows us to sidestep many constraints while preserving SE(2) equivariance. By applying our model as a surrogate for fluid flow simulations and conducting thorough benchmarks against non-equivariant models, we demonstrate significant gains in terms of both data efficiency and accuracy.
The rapid development of large language models (LLMs) in recent years has largely focused on English, resulting in models that respond exclusively in English. To adapt these models to other languages, continual pre-training (CP) is often employed, followed by supervised fine-tuning (SFT) to maintain conversational abilities. However, CP and SFT can reduce a model's ability to filter harmful content. We propose Instruction Continual Pre-training (InsCP), which integrates instruction tags into the CP process to prevent loss of conversational proficiency while acquiring new languages. Our experiments demonstrate that InsCP retains conversational and Reinforcement Learning from Human Feedback (RLHF) abilities. Empirical evaluations on language alignment, reliability, and knowledge benchmarks confirm the efficacy of InsCP. Notably, this approach requires only 0.1 billion tokens of high-quality instruction-following data, thereby reducing resource consumption.
We present Tachis, a higher-order separation logic to reason about the expected cost of probabilistic programs. Inspired by the uses of time credits for reasoning about the running time of deterministic programs, we introduce a novel notion of probabilistic cost credit. Probabilistic cost credits are a separation logic resource that can be used to pay for the cost of operations in programs, and that can be distributed across all possible branches of sampling instructions according to their weight, thus enabling us to reason about expected cost. The representation of cost credits as separation logic resources gives Tachis a great deal of flexibility and expressivity. In particular, it permits reasoning about amortized expected cost by storing excess credits as potential into data structures to pay for future operations. Tachis further supports a range of cost models, including running time and entropy usage. We showcase the versatility of this approach by applying our techniques to prove upper bounds on the expected cost of a variety of probabilistic algorithms and data structures, including randomized quicksort, hash tables, and meldable heaps. All of our results have been mechanized using Coq, Iris, and the Coquelicot real analysis library.
Temporal reasoning with conditionals is more complex than both classical temporal reasoning and reasoning with timeless conditionals, and can lead to some rather counter-intuitive conclusions. For instance, Aristotle's famous "Sea Battle Tomorrow" puzzle leads to a fatalistic conclusion: whether there will be a sea battle tomorrow or not, but that is necessarily the case now. We propose a branching-time logic LTC to formalise reasoning about temporal conditionals and provide that logic with adequate formal semantics. The logic LTC extends the Nexttime fragment of CTL*, with operators for model updates, restricting the domain to only future moments where antecedent is still possible to satisfy. We provide formal semantics for these operators that implements the restrictor interpretation of antecedents of temporalized conditionals, by suitably restricting the domain of discourse. As a motivating example, we demonstrate that a naturally formalised in our logic version of the `Sea Battle' argument renders it unsound, thereby providing a solution to the problem with fatalist conclusion that it entails, because its underlying reasoning per cases argument no longer applies when these cases are treated not as material implications but as temporal conditionals. On the technical side, we analyze the semantics of LTC and provide a series of reductions of LTC-formulae, first recursively eliminating the dynamic update operators and then the path quantifiers in such formulae. Using these reductions we obtain a sound and complete axiomatization for LTC, and reduce its decision problem to that of the modal logic KD.
This article presents the affordances that Generative Artificial Intelligence can have in disinformation context, one of the major threats to our digitalized society. We present a research framework to generate customized agent-based social networks for disinformation simulations that would enable understanding and evaluation of the phenomena whilst discussing open challenges.
Link prediction on knowledge graphs (KGs) is a key research topic. Previous work mainly focused on binary relations, paying less attention to higher-arity relations although they are ubiquitous in real-world KGs. This paper considers link prediction upon n-ary relational facts and proposes a graph-based approach to this task. The key to our approach is to represent the n-ary structure of a fact as a small heterogeneous graph, and model this graph with edge-biased fully-connected attention. The fully-connected attention captures universal inter-vertex interactions, while with edge-aware attentive biases to particularly encode the graph structure and its heterogeneity. In this fashion, our approach fully models global and local dependencies in each n-ary fact, and hence can more effectively capture associations therein. Extensive evaluation verifies the effectiveness and superiority of our approach. It performs substantially and consistently better than current state-of-the-art across a variety of n-ary relational benchmarks. Our code is publicly available.