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Moving beyond simulation: data-driven quantitative photoacoustic imaging using tissue-mimicking phantoms

arXiv.org Artificial Intelligence

Accurate measurement of optical absorption coefficients from photoacoustic imaging (PAI) data would enable direct mapping of molecular concentrations, providing vital clinical insight. The ill-posed nature of the problem of absorption coefficient recovery has prohibited PAI from achieving this goal in living systems due to the domain gap between simulation and experiment. To bridge this gap, we introduce a collection of experimentally well-characterised imaging phantoms and their digital twins. This first-of-a-kind phantom data set enables supervised training of a U-Net on experimental data for pixel-wise estimation of absorption coefficients. We show that training on simulated data results in artefacts and biases in the estimates, reinforcing the existence of a domain gap between simulation and experiment. Training on experimentally acquired data, however, yielded more accurate and robust estimates of optical absorption coefficients. We compare the results to fluence correction with a Monte Carlo model from reference optical properties of the materials, which yields a quantification error of approximately 20%. Application of the trained U-Nets to a blood flow phantom demonstrated spectral biases when training on simulated data, while application to a mouse model highlighted the ability of both learning-based approaches to recover the depth-dependent loss of signal intensity. We demonstrate that training on experimental phantoms can restore the correlation of signal amplitudes measured in depth. While the absolute quantification error remains high and further improvements are needed, our results highlight the promise of deep learning to advance quantitative PAI.


CrysMMNet: Multimodal Representation for Crystal Property Prediction

arXiv.org Artificial Intelligence

Machine Learning models have emerged as a powerful tool for fast and accurate prediction of different crystalline properties. Exiting state-of-the-art models rely on a single modality of crystal data i.e. crystal graph structure, where they construct multi-graph by establishing edges between nearby atoms in 3D space and apply GNN to learn materials representation. Thereby, they encode local chemical semantics around the atoms successfully but fail to capture important global periodic structural information like space group number, crystal symmetry, rotational information, etc, which influence different crystal properties. In this work, we leverage textual descriptions of materials to model global structural information into graph structure and learn a more robust and enriched representation of crystalline materials. To this effect, we first curate a textual dataset for crystalline material databases containing descriptions of each material. Further, we propose CrysMMNet, a simple multi-modal framework, which fuses both structural and textual representation together to generate a joint multimodal representation of crystalline materials. We conduct extensive experiments on two benchmark datasets across ten different properties to show that CrysMMNet outperforms existing state-of-the-art baseline methods with a good margin. We also observe that fusing the textual representation with crystal graph structure provides consistent improvement for all the SOTA GNN models compared to their own vanilla versions. We have shared the textual dataset, that we have curated for both the benchmark material databases, with the community for future use.


GPT Self-Supervision for a Better Data Annotator

arXiv.org Artificial Intelligence

The task of annotating data into concise summaries poses a significant challenge across various domains, frequently requiring the allocation of significant time and specialized knowledge by human experts. Despite existing efforts to use large language models for annotation tasks, significant problems such as limited applicability to unlabeled data, the absence of self-supervised methods, and the lack of focus on complex structured data still persist. In this work, we propose a GPT self-supervision annotation method, which embodies a generating-recovering paradigm that leverages the one-shot learning capabilities of the Generative Pretrained Transformer (GPT). The proposed approach comprises a one-shot tuning phase followed by a generation phase. In the one-shot tuning phase, we sample a data from the support set as part of the prompt for GPT to generate a textual summary, which is then used to recover the original data. The alignment score between the recovered and original data serves as a self-supervision navigator to refine the process. In the generation stage, the optimally selected one-shot sample serves as a template in the prompt and is applied to generating summaries from challenging datasets. The annotation performance is evaluated by tuning several human feedback reward networks and by calculating alignment scores between original and recovered data at both sentence and structure levels. Our self-supervised annotation method consistently achieves competitive scores, convincingly demonstrating its robust strength in various data-to-summary annotation tasks.


Perching by hugging: an initial feasibility study

arXiv.org Artificial Intelligence

Current UAVs capable of perching require added structure and mechanisms to accomplish this. These take the form of hooks, claws, needles, etc which add weight and usually drag. We propose in this paper the dual use of structures already on the vehicle to enable perching, thus reducing the weight and drag cost associated with perching UAVs. We propose a wing design capable of passively wrapping around a vertical pole to perch. We experimentally investigate the feasibility of the design, presenting results on minimum required perching speeds as well as the effect of weight distribution on the success rate of the wing wrapping. Finally, we comment on design requirements for holding onto the pole based on our findings.


Explainable Predictive Maintenance

arXiv.org Artificial Intelligence

Explainable Artificial Intelligence (XAI) fills the role of a critical interface fostering interactions between sophisticated intelligent systems and diverse individuals, including data scientists, domain experts, end-users, and more. It aids in deciphering the intricate internal mechanisms of ``black box'' Machine Learning (ML), rendering the reasons behind their decisions more understandable. However, current research in XAI primarily focuses on two aspects; ways to facilitate user trust, or to debug and refine the ML model. The majority of it falls short of recognising the diverse types of explanations needed in broader contexts, as different users and varied application areas necessitate solutions tailored to their specific needs. One such domain is Predictive Maintenance (PdM), an exploding area of research under the Industry 4.0 \& 5.0 umbrella. This position paper highlights the gap between existing XAI methodologies and the specific requirements for explanations within industrial applications, particularly the Predictive Maintenance field. Despite explainability's crucial role, this subject remains a relatively under-explored area, making this paper a pioneering attempt to bring relevant challenges to the research community's attention. We provide an overview of predictive maintenance tasks and accentuate the need and varying purposes for corresponding explanations. We then list and describe XAI techniques commonly employed in the literature, discussing their suitability for PdM tasks. Finally, to make the ideas and claims more concrete, we demonstrate XAI applied in four specific industrial use cases: commercial vehicles, metro trains, steel plants, and wind farms, spotlighting areas requiring further research.


Exploring the effects of robotic design on learning and neural control

arXiv.org Artificial Intelligence

The ongoing deep learning revolution has allowed computers to outclass humans in various games and perceive features imperceptible to humans during classification tasks. Current machine learning techniques have clearly distinguished themselves in specialized tasks. However, we have yet to see robots capable of performing multiple tasks at an expert level. Most work in this field is focused on the development of more sophisticated learning algorithms for a robot's controller given a largely static and presupposed robotic design. By focusing on the development of robotic bodies, rather than neural controllers, I have discovered that robots can be designed such that they overcome many of the current pitfalls encountered by neural controllers in multitask settings. Through this discovery, I also present novel metrics to explicitly measure the learning ability of a robotic design and its resistance to common problems such as catastrophic interference. Traditionally, the physical robot design requires human engineers to plan every aspect of the system, which is expensive and often relies on human intuition. In contrast, within the field of evolutionary robotics, evolutionary algorithms are used to automatically create optimized designs, however, such designs are often still limited in their ability to perform in a multitask setting. The metrics created and presented here give a novel path to automated design that allow evolved robots to synergize with their controller to improve the computational efficiency of their learning while overcoming catastrophic interference. Overall, this dissertation intimates the ability to automatically design robots that are more general purpose than current robots and that can perform various tasks while requiring less computation.


Scientists develop self-healing skin for 'Terminator robots' that realigns to restore function

Daily Mail - Science & tech

A new Terminator-like skin that self-heals could give rise to killer robots. Scientists at Stanford University have developed synthetic skin made of silicone and polypropylene glycol materials that stretch like human skin without tearing, while magnetic properties allow the skin to self-align. When warmed, both polymers soften and flow, solidifying as they cool. When heated to just 158 degrees Fahrenheit, the self-alignment and healing happen in about 24 hours. The team said the skin could lead to'reconfigurable soft robots that can change shape and sense their deformation on demand,' ultimately transforming warfare.


$\mathsf{G^2Retro}$ as a Two-Step Graph Generative Models for Retrosynthesis Prediction

arXiv.org Artificial Intelligence

Retrosynthesis is a procedure where a target molecule is transformed into potential reactants and thus the synthesis routes can be identified. Recently, computational approaches have been developed to accelerate the design of synthesis routes. In this paper, we develop a generative framework $\mathsf{G^2Retro}$ for one-step retrosynthesis prediction. $\mathsf{G^2Retro}$ imitates the reversed logic of synthetic reactions. It first predicts the reaction centers in the target molecules (products), identifies the synthons needed to assemble the products, and transforms these synthons into reactants. $\mathsf{G^2Retro}$ defines a comprehensive set of reaction center types, and learns from the molecular graphs of the products to predict potential reaction centers. To complete synthons into reactants, $\mathsf{G^2Retro}$ considers all the involved synthon structures and the product structures to identify the optimal completion paths, and accordingly attaches small substructures sequentially to the synthons. Here we show that $\mathsf{G^2Retro}$ is able to better predict the reactants for given products in the benchmark dataset than the state-of-the-art methods.


Machine Learning Force Fields with Data Cost Aware Training

arXiv.org Artificial Intelligence

Machine learning force fields (MLFF) have been proposed to accelerate molecular dynamics (MD) simulation, which finds widespread applications in chemistry and biomedical research. Even for the most data-efficient MLFFs, reaching chemical accuracy can require hundreds of frames of force and energy labels generated by expensive quantum mechanical algorithms, which may scale as $O(n^3)$ to $O(n^7)$, with $n$ proportional to the number of basis functions. To address this issue, we propose a multi-stage computational framework -- ASTEROID, which lowers the data cost of MLFFs by leveraging a combination of cheap inaccurate data and expensive accurate data. The motivation behind ASTEROID is that inaccurate data, though incurring large bias, can help capture the sophisticated structures of the underlying force field. Therefore, we first train a MLFF model on a large amount of inaccurate training data, employing a bias-aware loss function to prevent the model from overfitting tahe potential bias of this data. We then fine-tune the obtained model using a small amount of accurate training data, which preserves the knowledge learned from the inaccurate training data while significantly improving the model's accuracy. Moreover, we propose a variant of ASTEROID based on score matching for the setting where the inaccurate training data are unlabeled. Extensive experiments on MD datasets and downstream tasks validate the efficacy of ASTEROID. Our code and data are available at https://github.com/abukharin3/asteroid.


Exploring and Verbalizing Academic Ideas by Concept Co-occurrence

arXiv.org Artificial Intelligence

Researchers usually come up with new ideas only after thoroughly comprehending vast quantities of literature. The difficulty of this procedure is exacerbated by the fact that the number of academic publications is growing exponentially. In this study, we devise a framework based on concept co-occurrence for academic idea inspiration, which has been integrated into a research assistant system. From our perspective, the fusion of two concepts that co-occur in an academic paper can be regarded as an important way of the emergence of a new idea. We construct evolving concept graphs according to the co-occurrence relationship of concepts from 20 disciplines or topics. Then we design a temporal link prediction method based on masked language model to explore potential connections between different concepts. To verbalize the newly discovered connections, we also utilize the pretrained language model to generate a description of an idea based on a new data structure called co-occurrence citation quintuple. We evaluate our proposed system using both automatic metrics and human assessment. The results demonstrate that our system has broad prospects and can assist researchers in expediting the process of discovering new ideas.