Thomas Heinis

Jasmine Quah, Omer Sella, Thomas Heinis

DNA is a leading candidate as the next archival storage media due to its density, durability and sustainability. To read (and write) data DNA storage exploits technology that has been developed over decades to sequence naturally occurring DNA in the life sciences. To achieve higher accuracy for previously unseen, biological DNA, sequencing relies on extending and training deep machine learning models known as basecallers. This growth in model complexity requires substantial resources, both computational and data sets. It also eliminates the possibility of a compact read head for DNA as a storage medium. We argue that we need to depart from blindly using sequencing models from the life sciences for DNA data storage. The difference is striking: for life science applications we have no control over the DNA, however, in the case of DNA data storage, we control how it is written, as well as the particular write head. More specifically, data-carrying DNA can be modulated and embedded with alignment markers and error correcting codes to guarantee higher fidelity and to carry out some of the work that the machine learning models perform. In this paper, we study accuracy trade-offs between deep model size and error correcting codes. We show that, starting with a model size of 107MB, the reduced accuracy from model compression can be compensated by using simple error correcting codes in the DNA sequences. In our experiments, we show that a substantial reduction in the size of the model does not incur an undue penalty for the error correcting codes used, therefore paving the way for portable data-carrying DNA read head. Crucially, we show that through the joint use of model compression and error correcting codes, we achieve a higher read accuracy than without compression and error correction codes.

Gabriel della Maggiora, Luis Alberto Croquevielle, Nikita Deshpande et al.

Inverse problems aim to determine parameters from observations, a crucial task in engineering and science. Lately, generative models, especially diffusion models, have gained popularity in this area for their ability to produce realistic solutions and their good mathematical properties. Despite their success, an important drawback of diffusion models is their sensitivity to the choice of variance schedule, which controls the dynamics of the diffusion process. Fine-tuning this schedule for specific applications is crucial but time-costly and does not guarantee an optimal result. We propose a novel approach for learning the schedule as part of the training process. Our method supports probabilistic conditioning on data, provides high-quality solutions, and is flexible, proving able to adapt to different applications with minimum overhead. This approach is tested in two unrelated inverse problems: super-resolution microscopy and quantitative phase imaging, yielding comparable or superior results to previous methods and fine-tuned diffusion models. We conclude that fine-tuning the schedule by experimentation should be avoided because it can be learned during training in a stable way that yields better results.

Taiyi Wang, Liang Liang, Guang Yang et al.

Learned Index Structures (LIS) have significantly advanced data management by leveraging machine learning models to optimize data indexing. However, designing these structures often involves critical trade-offs, making it challenging for both designers and end-users to find an optimal balance tailored to specific workloads and scenarios. While some indexes offer adjustable parameters that demand intensive manual tuning, others rely on fixed configurations based on heuristic auto-tuners or expert knowledge, which may not consistently deliver optimal performance. This paper introduces LITune, a novel framework for end-to-end automatic tuning of Learned Index Structures. LITune employs an adaptive training pipeline equipped with a tailor-made Deep Reinforcement Learning (DRL) approach to ensure stable and efficient tuning. To accommodate long-term dynamics arising from online tuning, we further enhance LITune with an on-the-fly updating mechanism termed the O2 system. These innovations allow LITune to effectively capture state transitions in online tuning scenarios and dynamically adjust to changing data distributions and workloads, marking a significant improvement over other tuning methods. Our experimental results demonstrate that LITune achieves up to a 98% reduction in runtime and a 17-fold increase in throughput compared to default parameter settings given a selected Learned Index instance. These findings highlight LITune's effectiveness and its potential to facilitate broader adoption of LIS in real-world applications.

Anisha Banerjee, Roman Sokolovskii, Thomas Heinis et al.

Nanopore sequencing technology remains highly error-prone, making efficient error correction essential in DNA-based data storage. Prior work addressed high error rates using convolutional codes with their decoder coupled with the basecaller, but such approaches only accommodate a limited number of code classes and incur significant decoding complexity. To overcome these limitations, we propose two algorithms: PrimerSeeker, which efficiently detects primer sequences in raw nanopore sequencing reads, and SynDe, a decoder that operates on the same raw reads and supports any linear error correction code with a low-complexity graphical representation. PrimerSeeker provides primer location estimates close to those of existing approaches while being better suited for real-time primer detection during sequencing. SynDe performs well with convolutional codes augmented with periodic markers, often approaching or exceeding the performance of existing algorithms with a lower time complexity. Remarkably, the confidence scores produced by SynDe reliably identify which of its outputs should be discarded.

Shunjie Wen, Thomas Heinis, Dong-Wan Choi

Online class-incremental learning (OCIL) focuses on gradually learning new classes (called plasticity) from a stream of data in a single-pass, while concurrently preserving knowledge of previously learned classes (called stability). The primary challenge in OCIL lies in maintaining a good balance between the knowledge of old and new classes within the continually updated model. Most existing methods rely on explicit knowledge interaction through experience replay, and often employ exclusive training separation to address bias problems. Nevertheless, it still remains a big challenge to achieve a well-balanced learner, as these methods often exhibit either reduced plasticity or limited stability due to difficulties in continually integrating knowledge in the OCIL setting. In this paper, we propose a novel replay-based method, called Balanced Online Incremental Learning (BOIL), which can achieve both high plasticity and stability, thus ensuring more balanced performance in OCIL. Our BOIL method proposes an inclusive training separation strategy using dual classifiers so that knowledge from both old and new classes can effectively be integrated into the model, while introducing implicit approaches for transferring knowledge across the two classifiers. Extensive experimental evaluations over three widely-used OCIL benchmark datasets demonstrate the superiority of BOIL, showing more balanced yet better performance compared to state-of-the-art replay-based OCIL methods.

Gabriel della Maggiora, Luis Alberto Croquevielle, Harry Horsley et al.

Phase imaging is gaining importance due to its applications in fields like biomedical imaging and material characterization. In biomedical applications, it can provide quantitative information missing in label-free microscopy modalities. One of the most prominent methods in phase quantification is the Transport-of-Intensity Equation (TIE). TIE often requires multiple acquisitions at different defocus distances, which is not always feasible in a clinical setting. To address this issue, we propose to use chromatic aberrations to induce the required through-focus images with a single exposure, effectively generating a through-focus stack. Since the defocus distance induced by the aberrations is small, conventional TIE solvers are insufficient to address the resulting artifacts. We propose Zero-Mean Diffusion, a modified version of diffusion models designed for quantitative image prediction, and train it with synthetic data to ensure robust phase retrieval. Our contributions offer an alternative TIE approach that leverages chromatic aberrations, achieving accurate single-exposure phase measurement with white light and thus improving the efficiency of phase imaging. Moreover, we present a new class of diffusion models that are well-suited for quantitative data and have a sound theoretical basis. To validate our approach, we employ a widespread brightfield microscope equipped with a commercially available color camera. We apply our model to clinical microscopy of patients' urine, obtaining accurate phase measurements.

Ali Hadian, Ankit Kumar, Thomas Heinis

Spatial indexes are crucial for the analysis of the increasing amounts of spatial data, for example generated through IoT applications. The plethora of indexes that has been developed in recent decades has primarily been optimised for disk. With increasing amounts of memory even on commodity machines, however, moving them to main memory is an option. Doing so opens up the opportunity to use additional optimizations that are only amenable to main memory. In this paper we thus explore the opportunity to use light-weight machine learning models to accelerate queries on spatial indexes. We do so by exploring the potential of using interpolation and similar techniques on the R-tree, arguably the most broadly used spatial index. As we show in our experimental analysis, the query execution time can be reduced by up to 60% while simultaneously shrinking the index's memory footprint by over 90%

Ali Hadian, Behzad Ghaffari, Taiyi Wang et al.

Recent work proposed learned index structures, which learn the distribution of the underlying dataset to improve performance. The initial work on learned indexes has shown that by learning the cumulative distribution function of the data, index structures such as the B-Tree can improve their performance by one order of magnitude while having a smaller memory footprint. In this paper, we present COAX, a learned index for multidimensional data that, instead of learning the distribution of keys, learns the correlations between attributes of the dataset. Our approach is driven by the observation that in many datasets, values of two (or multiple) attributes are correlated. COAX exploits these correlations to reduce the dimensionality of the datasets. More precisely, we learn how to infer one (or multiple) attribute $C_d$ from the remaining attributes and hence no longer need to index attribute $C_d$. This reduces the dimensionality and hence makes the index smaller and more efficient. We theoretically investigate the effectiveness of the proposed technique based on the predictability of the FD attributes. We further show experimentally that by predicting correlated attributes in the data, we can improve the query execution time and reduce the memory overhead of the index. In our experiments, we reduce the execution time by 25% while reducing the memory footprint of the index by four orders of magnitude.