We propose a novel and flexible DNA-storage architecture, which divides the storage space into fixed-size units (blocks) that can be independently and efficiently accessed at random for both read and write operations, and further allows efficient sequential access to consecutive data blocks. In contrast to prior work, in our architecture a pair of random-access PCR primers of length 20 does not define a single object, but an independent storage partition, which is internally blocked and managed independently of other partitions. We expose the flexibility and constraints with which the internal address space of each partition can be managed, and incorporate them into our design to provide rich and functional storage semantics, such as block-storage organization, efficient implementation of data updates, and sequential access. To leverage the full power of the prefix-based nature of PCR addressing, we define a methodology for transforming the internal addressing scheme of a partition into an equivalent that is PCR-compatible. This allows us to run PCR with primers that can be variably elongated to include a desired part of the internal address, and thus narrow down the scope of the reaction to retrieve a specific block or a range of blocks within the partition with sufficiently high accuracy. Our wetlab evaluation demonstrates the practicality of the proposed ideas and a 140x reduction in sequencing cost and latency for retrieval of individual blocks within the partition.
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We consider a system model with two sources, a reliable source and an unreliable source, who are responsible for disseminating updates regarding a process to an age-based gossip network of $n$ nodes. Nodes wish to have fresh information, however, they have preference for packets that originated at the reliable source and are willing to sacrifice their version age of information by up to $G$ versions to switch from an unreliable packet to a reliable packet. We study how this protocol impacts the prevalence of unreliable packets at nodes in the network and their version age. Using a stochastic hybrid system (SHS) framework, we formulate analytical equations to characterize two quantities: expected fraction of nodes with unreliable packets and expected version age of information at network nodes. We show that as $G$ increases, fewer nodes have unreliable packet, however, their version age increases as well, thereby inducing a freshness-reliability trade-off in the network. We present numerical results to support our findings.
Sequence models based on linear state spaces (SSMs) have recently emerged as a promising choice of architecture for modeling long range dependencies across various modalities. However, they invariably rely on discretization of a continuous state space, which complicates their presentation and understanding. In this work, we dispose of the discretization step, and propose a model based on vanilla Diagonal Linear RNNs ($\mathrm{DLR}$). We empirically show that, despite being conceptually much simpler, $\mathrm{DLR}$ is as performant as previously-proposed SSMs on a variety of tasks and benchmarks including Long Range Arena and raw speech classification. Moreover, we characterize the expressivity of SSMs (including $\mathrm{DLR}$) and attention-based models via a suite of $13$ synthetic sequence-to-sequence tasks involving interactions over tens of thousands of tokens, ranging from simple operations, such as shifting an input sequence, to detecting co-dependent visual features over long spatial ranges in flattened images. We find that while SSMs report near-perfect performance on tasks that can be modeled via $\textit{few}$ convolutional kernels, they struggle on tasks requiring $\textit{many}$ such kernels and especially when the desired sequence manipulation is $\textit{context-dependent}$. Despite these limitations, $\mathrm{DLR}$ reaches high performance on two higher-order reasoning tasks $\mathrm{ListOpsSubTrees}$ and $\mathrm{PathfinderSegmentation}\text{-}\mathrm{256}$ with input lengths $8K$ and $65K$ respectively, and gives encouraging performance on $\mathrm{PathfinderSegmentation}\text{-}\mathrm{512}$ with input length $262K$ for which attention is not a viable choice.
Data uncertainties, such as sensor noise or occlusions, can introduce irreducible ambiguities in images, which result in varying, yet plausible, semantic hypotheses. In Machine Learning, this ambiguity is commonly referred to as aleatoric uncertainty. Latent density models can be utilized to address this problem in image segmentation. The most popular approach is the Probabilistic U-Net (PU-Net), which uses latent Normal densities to optimize the conditional data log-likelihood Evidence Lower Bound. In this work, we demonstrate that the PU- Net latent space is severely inhomogenous. As a result, the effectiveness of gradient descent is inhibited and the model becomes extremely sensitive to the localization of the latent space samples, resulting in defective predictions. To address this, we present the Sinkhorn PU-Net (SPU-Net), which uses the Sinkhorn Divergence to promote homogeneity across all latent dimensions, effectively improving gradient-descent updates and model robustness. Our results show that by applying this on public datasets of various clinical segmentation problems, the SPU-Net receives up to 11% performance gains compared against preceding latent variable models for probabilistic segmentation on the Hungarian-Matched metric. The results indicate that by encouraging a homogeneous latent space, one can significantly improve latent density modeling for medical image segmentation.
Quantum copy protection, introduced by Aaronson, enables giving out a quantum program-description that cannot be meaningfully duplicated. Despite over a decade of study, copy protection is only known to be possible for a very limited class of programs. As our first contribution, we show how to achieve "best-possible" copy protection for all programs. We do this by introducing quantum state indistinguishability obfuscation (qsiO), a notion of obfuscation for quantum descriptions of classical programs. We show that applying qsiO to a program immediately achieves best-possible copy protection. Our second contribution is to show that, assuming injective one-way functions exist, qsiO is concrete copy protection for a large family of puncturable programs -- significantly expanding the class of copy-protectable programs. A key tool in our proof is a new variant of unclonable encryption (UE) that we call coupled unclonable encryption (cUE). While constructing UE in the standard model remains an important open problem, we are able to build cUE from one-way functions. If we additionally assume the existence of UE, then we can further expand the class of puncturable programs for which qsiO is copy protection. Finally, we construct qsiO relative to an efficient quantum oracle.
Integrating different functionalities, conventionally implemented as dedicated systems, into a single platform allows utilising the available resources more efficiently. We consider an integrated sensing and power transfer (ISAPT) system and propose the joint optimisation of the rectangular pulse-shaped transmit signal and the beamforming vector to combine sensing and wireless power transfer (WPT) functionalities efficiently. In contrast to prior works, we adopt an accurate non-linear circuit-based energy harvesting (EH) model. We formulate and solve a non-convex optimisation problem for a general number of EH receivers to maximise a weighted sum of the average harvested powers at the EH receivers while ensuring the received echo signal reflected by a sensing target (ST) has sufficient power for estimating the range to the ST with a prescribed accuracy within the considered coverage region. The average harvested power is shown to monotonically increase with the pulse duration when the average transmit power budget is sufficiently large. We discuss the trade-off between sensing performance and power transfer for the considered ISAPT system. The proposed approach significantly outperforms a heuristic baseline scheme based on a linear EH model, which linearly combines energy beamforming with the beamsteering vector in the direction to the ST as its transmit strategy.
The first part of this thesis focuses on maximizing the overall recommendation accuracy. This accuracy is usually evaluated with some user-oriented metric tailored to the recommendation scenario, but because recommendation is usually treated as a machine learning problem, recommendation models are trained to maximize some other generic criteria that does not necessarily align with the criteria ultimately captured by the user-oriented evaluation metric. Recent research aims at bridging this gap between training and evaluation via direct ranking optimization, but still assumes that the metric used for evaluation should also be the metric used for training. We challenge this assumption, mainly because some metrics are more informative than others. Indeed, we show that models trained via the optimization of a loss inspired by Rank-Biased Precision (RBP) tend to yield higher accuracy, even when accuracy is measured with metrics other than RBP. However, the superiority of this RBP-inspired loss stems from further benefiting users who are already well-served, rather than helping those who are not. This observation inspires the second part of this thesis, where our focus turns to helping non-mainstream users. These are users who are difficult to recommend to either because there is not enough data to model them, or because they have niche taste and thus few similar users to look at when recommending in a collaborative way. These differences in mainstreamness introduce a bias reflected in an accuracy gap between users or user groups, which we try to narrow.
We propose a general method to break down a main complex task into a set of intermediary easier sub-tasks, which are formulated in natural language as binary questions related to the final target task. Our method allows for representing each example by a vector consisting of the answers to these questions. We call this representation Natural Language Learned Features (NLLF). NLLF is generated by a small transformer language model (e.g., BERT) that has been trained in a Natural Language Inference (NLI) fashion, using weak labels automatically obtained from a Large Language Model (LLM). We show that the LLM normally struggles for the main task using in-context learning, but can handle these easiest subtasks and produce useful weak labels to train a BERT. The NLI-like training of the BERT allows for tackling zero-shot inference with any binary question, and not necessarily the ones seen during the training. We show that this NLLF vector not only helps to reach better performances by enhancing any classifier, but that it can be used as input of an easy-to-interpret machine learning model like a decision tree. This decision tree is interpretable but also reaches high performances, surpassing those of a pre-trained transformer in some cases.We have successfully applied this method to two completely different tasks: detecting incoherence in students' answers to open-ended mathematics exam questions, and screening abstracts for a systematic literature review of scientific papers on climate change and agroecology.
Deep neural network architectures have traditionally been designed and explored with human expertise in a long-lasting trial-and-error process. This process requires huge amount of time, expertise, and resources. To address this tedious problem, we propose a novel algorithm to optimally find hyperparameters of a deep network architecture automatically. We specifically focus on designing neural architectures for medical image segmentation task. Our proposed method is based on a policy gradient reinforcement learning for which the reward function is assigned a segmentation evaluation utility (i.e., dice index). We show the efficacy of the proposed method with its low computational cost in comparison with the state-of-the-art medical image segmentation networks. We also present a new architecture design, a densely connected encoder-decoder CNN, as a strong baseline architecture to apply the proposed hyperparameter search algorithm. We apply the proposed algorithm to each layer of the baseline architectures. As an application, we train the proposed system on cine cardiac MR images from Automated Cardiac Diagnosis Challenge (ACDC) MICCAI 2017. Starting from a baseline segmentation architecture, the resulting network architecture obtains the state-of-the-art results in accuracy without performing any trial-and-error based architecture design approaches or close supervision of the hyperparameters changes.
Object detection typically assumes that training and test data are drawn from an identical distribution, which, however, does not always hold in practice. Such a distribution mismatch will lead to a significant performance drop. In this work, we aim to improve the cross-domain robustness of object detection. We tackle the domain shift on two levels: 1) the image-level shift, such as image style, illumination, etc, and 2) the instance-level shift, such as object appearance, size, etc. We build our approach based on the recent state-of-the-art Faster R-CNN model, and design two domain adaptation components, on image level and instance level, to reduce the domain discrepancy. The two domain adaptation components are based on H-divergence theory, and are implemented by learning a domain classifier in adversarial training manner. The domain classifiers on different levels are further reinforced with a consistency regularization to learn a domain-invariant region proposal network (RPN) in the Faster R-CNN model. We evaluate our newly proposed approach using multiple datasets including Cityscapes, KITTI, SIM10K, etc. The results demonstrate the effectiveness of our proposed approach for robust object detection in various domain shift scenarios.
Dynamic programming (DP) solves a variety of structured combinatorial problems by iteratively breaking them down into smaller subproblems. In spite of their versatility, DP algorithms are usually non-differentiable, which hampers their use as a layer in neural networks trained by backpropagation. To address this issue, we propose to smooth the max operator in the dynamic programming recursion, using a strongly convex regularizer. This allows to relax both the optimal value and solution of the original combinatorial problem, and turns a broad class of DP algorithms into differentiable operators. Theoretically, we provide a new probabilistic perspective on backpropagating through these DP operators, and relate them to inference in graphical models. We derive two particular instantiations of our framework, a smoothed Viterbi algorithm for sequence prediction and a smoothed DTW algorithm for time-series alignment. We showcase these instantiations on two structured prediction tasks and on structured and sparse attention for neural machine translation.
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