Jesper Tegnér

Srijith Radhakrishnan, Chao-Han Huck Yang, Sumeer Ahmad Khan et al.

We introduce a new cross-modal fusion technique designed for generative error correction in automatic speech recognition (ASR). Our methodology leverages both acoustic information and external linguistic representations to generate accurate speech transcription contexts. This marks a step towards a fresh paradigm in generative error correction within the realm of n-best hypotheses. Unlike the existing ranking-based rescoring methods, our approach adeptly uses distinct initialization techniques and parameter-efficient algorithms to boost ASR performance derived from pre-trained speech and text models. Through evaluation across diverse ASR datasets, we evaluate the stability and reproducibility of our fusion technique, demonstrating its improved word error rate relative (WERR) performance in comparison to n-best hypotheses by relatively 37.66%. To encourage future research, we have made our code and pre-trained models open source at https://github.com/Srijith-rkr/Whispering-LLaMA.

Hector Zenil, Jesper Tegnér, Felipe S. Abrahão et al. · cambridge

Recent advances in machine learning and AI, including Generative AI and LLMs, are disrupting technological innovation, product development, and society as a whole. AI's contribution to technology can come from multiple approaches that require access to large training data sets and clear performance evaluation criteria, ranging from pattern recognition and classification to generative models. Yet, AI has contributed less to fundamental science in part because large data sets of high-quality data for scientific practice and model discovery are more difficult to access. Generative AI, in general, and Large Language Models in particular, may represent an opportunity to augment and accelerate the scientific discovery of fundamental deep science with quantitative models. Here we explore and investigate aspects of an AI-driven, automated, closed-loop approach to scientific discovery, including self-driven hypothesis generation and open-ended autonomous exploration of the hypothesis space. Integrating AI-driven automation into the practice of science would mitigate current problems, including the replication of findings, systematic production of data, and ultimately democratisation of the scientific process. Realising these possibilities requires a vision for augmented AI coupled with a diversity of AI approaches able to deal with fundamental aspects of causality analysis and model discovery while enabling unbiased search across the space of putative explanations. These advances hold the promise to unleash AI's potential for searching and discovering the fundamental structure of our world beyond what human scientists have been able to achieve. Such a vision would push the boundaries of new fundamental science rather than automatize current workflows and instead open doors for technological innovation to tackle some of the greatest challenges facing humanity today.

Srijith Radhakrishnan, Chao-Han Huck Yang, Sumeer Ahmad Khan et al.

In this work, we explore Parameter-Efficient-Learning (PEL) techniques to repurpose a General-Purpose-Speech (GSM) model for Arabic dialect identification (ADI). Specifically, we investigate different setups to incorporate trainable features into a multi-layer encoder-decoder GSM formulation under frozen pre-trained settings. Our architecture includes residual adapter and model reprogramming (input-prompting). We design a token-level label mapping to condition the GSM for Arabic Dialect Identification (ADI). This is challenging due to the high variation in vocabulary and pronunciation among the numerous regional dialects. We achieve new state-of-the-art accuracy on the ADI-17 dataset by vanilla fine-tuning. We further reduce the training budgets with the PEL method, which performs within 1.86% accuracy to fine-tuning using only 2.5% of (extra) network trainable parameters. Our study demonstrates how to identify Arabic dialects using a small dataset and limited computation with open source code and pre-trained models.

Haoling Zhang, Chao-Han Huck Yang, Hector Zenil et al.

NeuroEvolution is one of the most competitive evolutionary learning frameworks for designing novel neural networks for use in specific tasks, such as logic circuit design and digital gaming. However, the application of benchmark methods such as the NeuroEvolution of Augmenting Topologies (NEAT) remains a challenge, in terms of their computational cost and search time inefficiency. This paper advances a method which incorporates a type of topological edge coding, named Reverse Encoding Tree (RET), for evolving scalable neural networks efficiently. Using RET, two types of approaches -- NEAT with Binary search encoding (Bi-NEAT) and NEAT with Golden-Section search encoding (GS-NEAT) -- have been designed to solve problems in benchmark continuous learning environments such as logic gates, Cartpole, and Lunar Lander, and tested against classical NEAT and FS-NEAT as baselines. Additionally, we conduct a robustness test to evaluate the resilience of the proposed NEAT algorithms. The results show that the two proposed strategies deliver improved performance, characterized by (1) a higher accumulated reward within a finite number of time steps; (2) using fewer episodes to solve problems in targeted environments, and (3) maintaining adaptive robustness under noisy perturbations, which outperform the baselines in all tested cases. Our analysis also demonstrates that RET expends potential future research directions in dynamic environments. Code is available from https://github.com/HaolingZHANG/ReverseEncodingTree.

Yanbo Zhang, Sumeer A. Khan, Adnan Mahmud et al.

With recent Nobel Prizes recognising AI contributions to science, Large Language Models (LLMs) are transforming scientific research by enhancing productivity and reshaping the scientific method. LLMs are now involved in experimental design, data analysis, and workflows, particularly in chemistry and biology. However, challenges such as hallucinations and reliability persist. In this contribution, we review how Large Language Models (LLMs) are redefining the scientific method and explore their potential applications across different stages of the scientific cycle, from hypothesis testing to discovery. We conclude that, for LLMs to serve as relevant and effective creative engines and productivity enhancers, their deep integration into all steps of the scientific process should be pursued in collaboration and alignment with human scientific goals, with clear evaluation metrics. The transition to AI-driven science raises ethical questions about creativity, oversight, and responsibility. With careful guidance, LLMs could evolve into creative engines, driving transformative breakthroughs across scientific disciplines responsibly and effectively. However, the scientific community must also decide how much it leaves to LLMs to drive science, even when associations with 'reasoning', mostly currently undeserved, are made in exchange for the potential to explore hypothesis and solution regions that might otherwise remain unexplored by human exploration alone.

Jun Qi, Chao-Han Yang, Samuel Yen-Chi Chen et al.

Quantum Machine Learning (QML) offers tremendous potential but is currently limited by the availability of qubits. We introduce an innovative approach that utilizes pre-trained neural networks to enhance Variational Quantum Circuits (VQC). This technique effectively separates approximation error from qubit count and removes the need for restrictive conditions, making QML more viable for real-world applications. Our method significantly improves parameter optimization for VQC while delivering notable gains in representation and generalization capabilities, as evidenced by rigorous theoretical analysis and extensive empirical testing on quantum dot classification tasks. Moreover, our results extend to applications such as human genome analysis, demonstrating the broad applicability of our approach. By addressing the constraints of current quantum hardware, our work paves the way for a new era of advanced QML applications, unlocking the full potential of quantum computing in fields such as machine learning, materials science, medicine, mimetics, and various interdisciplinary areas.

Jesus de la Fuente, Robert Lehmann, Carlos Ruiz-Arenas et al.

Predicting the impact of genomic and drug perturbations in cellular function is crucial for understanding gene functions and drug effects, ultimately leading to improved therapies. To this end, Causal Representation Learning (CRL) constitutes one of the most promising approaches, as it aims to identify the latent factors that causally govern biological systems, thus facilitating the prediction of the effect of unseen perturbations. Yet, current CRL methods fail in reconciling their principled latent representations with known biological processes, leading to models that are not interpretable. To address this major issue, we present SENA-discrepancy-VAE, a model based on the recently proposed CRL method discrepancy-VAE, that produces representations where each latent factor can be interpreted as the (linear) combination of the activity of a (learned) set of biological processes. To this extent, we present an encoder, SENA-δ, that efficiently compute and map biological processes' activity levels to the latent causal factors. We show that SENA-discrepancy-VAE achieves predictive performances on unseen combinations of interventions that are comparable with its original, non-interpretable counterpart, while inferring causal latent factors that are biologically meaningful.

Abdulrahman Ibraheem, Narsis Kiani, Jesper Tegner

This paper studies the usefulness of incorporating path information in predicting chemical properties from molecular graphs, in the domain of QSAR (Quantitative Structure-Activity Relationship). Towards this, we developed a GNN-style model which can be toggled to operate in one of two modes: a non-degenerate mode which incorporates path information, and a degenerate mode which leaves out path information. Thus, by comparing the performance of the non-degenerate mode versus the degenerate mode on relevant QSAR datasets, we were able to directly assess the significance of path information on those datasets. Our results corroborate previous works, by suggesting that the usefulness of path information is datasetdependent. Unlike previous studies however, we took the very first steps towards building a model that could predict upfront whether or not path information would be useful for a given dataset at hand. Moreover, we also found that, albeit its simplicity, the degenerate mode of our model yielded rather surprising results, which outperformed more sophisticated SOTA models in certain cases.

Mattia Soldan, Mengmeng Xu, Sisi Qu et al.

Grounding language queries in videos aims at identifying the time interval (or moment) semantically relevant to a language query. The solution to this challenging task demands understanding videos' and queries' semantic content and the fine-grained reasoning about their multi-modal interactions. Our key idea is to recast this challenge into an algorithmic graph matching problem. Fueled by recent advances in Graph Neural Networks, we propose to leverage Graph Convolutional Networks to model video and textual information as well as their semantic alignment. To enable the mutual exchange of information across the modalities, we design a novel Video-Language Graph Matching Network (VLG-Net) to match video and query graphs. Core ingredients include representation graphs built atop video snippets and query tokens separately and used to model intra-modality relationships. A Graph Matching layer is adopted for cross-modal context modeling and multi-modal fusion. Finally, moment candidates are created using masked moment attention pooling by fusing the moment's enriched snippet features. We demonstrate superior performance over state-of-the-art grounding methods on three widely used datasets for temporal localization of moments in videos with language queries: ActivityNet-Captions, TACoS, and DiDeMo.

Jia-Hong Huang, Chao-Han Huck Yang, Fangyu Liu et al.

In this work, we propose an AI-based method that intends to improve the conventional retinal disease treatment procedure and help ophthalmologists increase diagnosis efficiency and accuracy. The proposed method is composed of a deep neural networks-based (DNN-based) module, including a retinal disease identifier and clinical description generator, and a DNN visual explanation module. To train and validate the effectiveness of our DNN-based module, we propose a large-scale retinal disease image dataset. Also, as ground truth, we provide a retinal image dataset manually labeled by ophthalmologists to qualitatively show, the proposed AI-based method is effective. With our experimental results, we show that the proposed method is quantitatively and qualitatively effective. Our method is capable of creating meaningful retinal image descriptions and visual explanations that are clinically relevant.

Yi-Chieh Liu, Yung-An Hsieh, Min-Hung Chen et al.

Performing driving behaviors based on causal reasoning is essential to ensure driving safety. In this work, we investigated how state-of-the-art 3D Convolutional Neural Networks (CNNs) perform on classifying driving behaviors based on causal reasoning. We proposed a perturbation-based visual explanation method to inspect the models' performance visually. By examining the video attention saliency, we found that existing models could not precisely capture the causes (e.g., traffic light) of the specific action (e.g., stopping). Therefore, the Temporal Reasoning Block (TRB) was proposed and introduced to the models. With the TRB models, we achieved the accuracy of $\mathbf{86.3\%}$, which outperform the state-of-the-art 3D CNNs from previous works. The attention saliency also demonstrated that TRB helped models focus on the causes more precisely. With both numerical and visual evaluations, we concluded that our proposed TRB models were able to provide accurate driving behavior prediction by learning the causal reasoning of the behaviors.

Santiago Hernández-Orozco, Hector Zenil, Jürgen Riedel et al.

We show how complexity theory can be introduced in machine learning to help bring together apparently disparate areas of current research. We show that this new approach requires less training data and is more generalizable as it shows greater resilience to random attacks. We investigate the shape of the discrete algorithmic space when performing regression or classification using a loss function parametrized by algorithmic complexity, demonstrating that the property of differentiation is not necessary to achieve results similar to those obtained using differentiable programming approaches such as deep learning. In doing so we use examples which enable the two approaches to be compared (small, given the computational power required for estimations of algorithmic complexity). We find and report that (i) machine learning can successfully be performed on a non-smooth surface using algorithmic complexity; (ii) that parameter solutions can be found using an algorithmic-probability classifier, establishing a bridge between a fundamentally discrete theory of computability and a fundamentally continuous mathematical theory of optimization methods; (iii) a formulation of an algorithmically directed search technique in non-smooth manifolds can be defined and conducted; (iv) exploitation techniques and numerical methods for algorithmic search to navigate these discrete non-differentiable spaces can be performed; in application of the (a) identification of generative rules from data observations; (b) solutions to image classification problems more resilient against pixel attacks compared to neural networks; (c) identification of equation parameters from a small data-set in the presence of noise in continuous ODE system problem, (d) classification of Boolean NK networks by (1) network topology, (2) underlying Boolean function, and (3) number of incoming edges.

Yi-Chieh Liu, Hao-Hsiang Yang, Chao-Han Huck Yang et al.

Age-Related Macular Degeneration (AMD) is an asymptomatic retinal disease which may result in loss of vision. There is limited access to high-quality relevant retinal images and poor understanding of the features defining sub-classes of this disease. Motivated by recent advances in machine learning we specifically explore the potential of generative modeling, using Generative Adversarial Networks (GANs) and style transferring, to facilitate clinical diagnosis and disease understanding by feature extraction. We design an analytic pipeline which first generates synthetic retinal images from clinical images; a subsequent verification step is applied. In the synthesizing step we merge GANs (DCGANs and WGANs architectures) and style transferring for the image generation, whereas the verified step controls the accuracy of the generated images. We find that the generated images contain sufficient pathological details to facilitate ophthalmologists' task of disease classification and in discovery of disease relevant features. In particular, our system predicts the drusen and geographic atrophy sub-classes of AMD. Furthermore, the performance using CFP images for GANs outperforms the classification based on using only the original clinical dataset. Our results are evaluated using existing classifier of retinal diseases and class activated maps, supporting the predictive power of the synthetic images and their utility for feature extraction. Our code examples are available online.

Rise Ooi, Chao-Han Huck Yang, Pin-Yu Chen et al.

Networks are fundamental building blocks for representing data, and computations. Remarkable progress in learning in structurally defined (shallow or deep) networks has recently been achieved. Here we introduce evolutionary exploratory search and learning method of topologically flexible networks under the constraint of producing elementary computational steady-state input-output operations. Our results include; (1) the identification of networks, over four orders of magnitude, implementing computation of steady-state input-output functions, such as a band-pass filter, a threshold function, and an inverse band-pass function. Next, (2) the learned networks are technically controllable as only a small number of driver nodes are required to move the system to a new state. Furthermore, we find that the fraction of required driver nodes is constant during evolutionary learning, suggesting a stable system design. (3), our framework allows multiplexing of different computations using the same network. For example, using a binary representation of the inputs, the network can readily compute three different input-output functions. Finally, (4) the proposed evolutionary learning demonstrates transfer learning. If the system learns one function A, then learning B requires on average less number of steps as compared to learning B from tabula rasa. We conclude that the constrained evolutionary learning produces large robust controllable circuits, capable of multiplexing and transfer learning. Our study suggests that network-based computations of steady-state functions, representing either cellular modules of cell-to-cell communication networks or internal molecular circuits communicating within a cell, could be a powerful model for biologically inspired computing. This complements conceptualizations such as attractor based models, or reservoir computing.

C. -H. Huck Yang, Fangyu Liu, Jia-Hong Huang et al.

Automatic clinical diagnosis of retinal diseases has emerged as a promising approach to facilitate discovery in areas with limited access to specialists. Based on the fact that fundus structure and vascular disorders are the main characteristics of retinal diseases, we propose a novel visual-assisted diagnosis hybrid model mixing the support vector machine (SVM) and deep neural networks (DNNs). Furthermore, we present a new clinical retina dataset, called EyeNet2, for ophthalmology incorporating 52 retina diseases classes. Using EyeNet2, our model achieves 90.43\% diagnosis accuracy, and the model performance is comparable to the professional ophthalmologists.

C. H. Huck Yang, Rise Ooi, Tom Hiscock et al.

Networks are abundant in biological systems. Small sized over-represented network motifs have been discovered, and it has been suggested that these constitute functional building blocks. We ask whether larger dynamical network motifs exist in biological networks, thus contributing to the higher-order organization of a network. To end this, we introduce a gradient descent machine learning (ML) approach and genetic algorithms to learn larger functional motifs in contrast to an (unfeasible) exhaustive search. We use the French Flag (FF) and Switch functional motif as case studies motivated from biology. While our algorithm successfully learns large functional motifs, we identify a threshold size of approximately 20 nodes beyond which learning breaks down. Therefore we investigate the stability of the motifs. We find that the size of the real negative eigenvalues of the Jacobian decreases with increasing system size, thus conferring instability. Finally, without imposing learning an input-output for all the components of the network, we observe that unconstrained middle components of the network still learn the desired function, a form of homogeneous team learning. We conclude that the size limitation of learnability, most likely due to stability constraints, impose a definite requirement for modularity in networked systems while enabling team learning within unconstrained parts of the module. Thus, the observation that community structures and modularity are abundant in biological networks could be accounted for by a computational compositional network structure.

C. -H. Huck Yang, Jia-Hong Huang, Fangyu Liu et al.

Automatic clinical diagnosis of retinal diseases has emerged as a promising approach to facilitate discovery in areas with limited access to specialists. We propose a novel visual-assisted diagnosis hybrid model based on the support vector machine (SVM) and deep neural networks (DNNs). The model incorporates complementary strengths of DNNs and SVM. Furthermore, we present a new clinical retina label collection for ophthalmology incorporating 32 retina diseases classes. Using EyeNet, our model achieves 89.73% diagnosis accuracy and the model performance is comparable to the professional ophthalmologists.

Hector Zenil, Narsis A. Kiani, Allan A. Zea et al.

Complex data usually results from the interaction of objects produced by different generating mechanisms. Here we introduce a universal, unsupervised and parameter-free model-oriented approach, based upon the seminal concept of algorithmic probability, that decomposes an observation into its most likely algorithmic generative sources. Our approach uses a causal calculus to infer model representations. We demonstrate its ability to deconvolve interacting mechanisms regardless of whether the resultant objects are strings, space-time evolution diagrams, images or networks. While this is mostly a conceptual contribution and a novel framework, we provide numerical evidence evaluating the ability of our methods to separate data from observations produced by discrete dynamical systems such as cellular automata and complex networks. We think that these separating techniques can contribute to tackling the challenge of causation, thus complementing other statistically oriented approaches.

Hector Zenil, Angelika Schmidt, Jesper Tegnér

Biology has taken strong steps towards becoming a computer science aiming at reprogramming nature after the realisation that nature herself has reprogrammed organisms by harnessing the power of natural selection and the digital prescriptive nature of replicating DNA. Here we further unpack ideas related to computability, algorithmic information theory and software engineering, in the context of the extent to which biology can be (re)programmed, and with how we may go about doing so in a more systematic way with all the tools and concepts offered by theoretical computer science in a translation exercise from computing to molecular biology and back. These concepts provide a means to a hierarchical organization thereby blurring previously clear-cut lines between concepts like matter and life, or between tumour types that are otherwise taken as different and may not have however a different cause. This does not diminish the properties of life or make its components and functions less interesting. On the contrary, this approach makes for a more encompassing and integrated view of nature, one that subsumes observer and observed within the same system, and can generate new perspectives and tools with which to view complex diseases like cancer, approaching them afresh from a software-engineering viewpoint that casts evolution in the role of programmer, cells as computing machines, DNA and genes as instructions and computer programs, viruses as hacking devices, the immune system as a software debugging tool, and diseases as an information-theoretic battlefield where all these forces deploy. We show how information theory and algorithmic programming may explain fundamental mechanisms of life and death.

Nicolas Gauvrit, Hector Zenil, Jesper Tegnér

We survey concepts at the frontier of research connecting artificial, animal and human cognition to computation and information processing---from the Turing test to Searle's Chinese Room argument, from Integrated Information Theory to computational and algorithmic complexity. We start by arguing that passing the Turing test is a trivial computational problem and that its pragmatic difficulty sheds light on the computational nature of the human mind more than it does on the challenge of artificial intelligence. We then review our proposed algorithmic information-theoretic measures for quantifying and characterizing cognition in various forms. These are capable of accounting for known biases in human behavior, thus vindicating a computational algorithmic view of cognition as first suggested by Turing, but this time rooted in the concept of algorithmic probability, which in turn is based on computational universality while being independent of computational model, and which has the virtue of being predictive and testable as a model theory of cognitive behavior.

Jose M. Pena, Roland Nilsson, Johan Björkegren et al.

We propose a method to identify all the nodes that are relevant to compute all the conditional probability distributions for a given set of nodes. Our method is simple, effcient, consistent, and does not require learning a Bayesian network first. Therefore, our method can be applied to high-dimensional databases, e.g. gene expression databases.