Machine unlearning (MU) aims to remove the influence of specific data from trained models, addressing privacy concerns and ensuring compliance with regulations such as the "right to be forgotten." Evaluating strong unlearning, where the unlearned model is indistinguishable from one retrained without the forgetting data, remains a significant challenge in deep neural networks (DNNs). Common black-box metrics, such as variants of membership inference attacks and accuracy comparisons, primarily assess model outputs but often fail to capture residual information in intermediate layers. To bridge this gap, we introduce the Information Difference Index (IDI), a novel white-box metric inspired by information theory. IDI quantifies retained information in intermediate features by measuring mutual information between those features and the labels to be forgotten, offering a more comprehensive assessment of unlearning efficacy. Our experiments demonstrate that IDI effectively measures the degree of unlearning across various datasets and architectures, providing a reliable tool for evaluating strong unlearning in DNNs.

Machine unlearning aims to selectively remove targeted knowledge from Large Language Models (LLMs), ensuring they forget specified content while retaining essential information.Existing unlearning metrics assess whether a model correctly answers retain queries and rejects forget queries, but they fail to capture real-world scenarios where forget queries rarely appear in isolation.In fact, forget and retain queries often coexist within the same prompt, making mixed-query evaluation crucial.We introduce SEPS, an evaluation framework that explicitly measures a model's ability to both forget and retain information within a single prompt.Through extensive experiments across three benchmarks, we identify two key failure modes in existing unlearning methods: (1) untargeted unlearning indiscriminately erases both forget and retain content once a forget query appears, and (2) targeted unlearning overfits to single-query scenarios, leading to catastrophic failures when handling multiple queries.To address these issues, we propose Mixed Prompt (MP) unlearning, a strategy that integrates both forget and retain queries into a unified training objective.Our approach significantly improves unlearning effectiveness, demonstrating robustness even in complex settings with up to eight mixed forget and retain queries in a single prompt.

Large Reasoning Models (LRMs) embed private or copyrighted information not only in their final answers but also throughout multistep chain-of-thought (CoT) traces, making reliable unlearning far more demanding than in standard LLMs.We introduce Reasoning-TOFU (R-TOFU), the first benchmark tailored to this setting.R-TOFU augments existing unlearning tasks with realistic CoT annotations and provides step-wise metrics that expose residual knowledge invisible to answer-level checks.Using R-TOFU, we carry out a comprehensive comparison of gradient-based and preference-optimization baselines and show that conventional answer-only objectives leave substantial forget traces in reasoning.We further propose Reasoned IDK, a preferenceoptimization variant that preserves coherent yet inconclusive reasoning, achieving a stronger balance between forgetting efficacy and model utility than earlier refusal styles.Finally, we identify a failure mode: decoding variants such as ZeroThink and LessThink can still reveal forgotten content despite seemingly successful unlearning, emphasizing the need to evaluate models under diverse decoding settings.Together, the benchmark, analysis, and new baseline establish a systematic foundation for studying and improving unlearning in LRMs while preserving their reasoning capabilities.We release R-TOFU and code at https://ai-isl.github.io/r-tofu.

In this paper, we introduce a geometric framework to analyze memorization in diffusion models through the sharpness of the log probability density. We mathematically justify a previously proposed score-difference-based memorization metric by demonstrating its effectiveness in quantifying sharpness. Additionally, we propose a novel memorization metric that captures sharpness at the initial stage of image generation in latent diffusion models, offering early insights into potential memorization. Leveraging this metric, we develop a mitigation strategy that optimizes the initial noise of the generation process using a sharpness-aware regularization term. The code is publicly available at https://github.com/Dongjae0324/sharpness_memorization_diffusion.

We present an information-theoretic framework for discrete diffusion models that yields principled estimators of log-likelihood using score-matching losses. Inspired by the I-MMSE identity for the Gaussian setup, we derive analogous results for the discrete setting. Specifically, we introduce the Information–Minimum Denoising Score Entropy (I-MDSE) relation, which links mutual information between data and its diffused version to the minimum denoising score entropy (DSE) loss. We extend this theory to masked diffusion and establish the Information–Minimum Denoising Cross-Entropy (I-MDCE) relation, connecting cross-entropy losses to mutual information in discrete masked processes. These results provide a time-integral decomposition of the log-likelihood of the data in terms of optimal score-based losses, showing that commonly used losses such as DSE and DCE are not merely variational bounds but tight and principled estimators of log-likelihood. The I-MDCE decomposition further enables practical extensions, including time-free formula, conditional likelihood estimation in prompt–response tasks, and coupled Monte Carlo estimation of likelihood ratios. Experiments on synthetic and real-world data confirm the accuracy, variance stability, and utility of our estimators. The code is publicly available at https://github.com/Dongjae0324/infodis.

Large Reasoning Models (LRMs) have become powerful tools for complex problem solving, but their structured reasoning pathways can lead to unsafe outputs when exposed to harmful prompts. Existing safety alignment methods reduce harmful outputs but can degrade reasoning depth, leading to significant trade-offs in complex, multi-step tasks, and remain vulnerable to sophisticated jailbreak attacks. To address this, we introduce SAFEPATH, a lightweight alignment method that fine-tunes LRMs to emit a short, 8-token Safety Primer at the start of their reasoning, in response to harmful prompts, while leaving the rest of the reasoning process unsupervised. Empirical results across multiple benchmarks indicate that SAFEPATH effectively reduces harmful outputs while maintaining reasoning performance. Specifically, SAFEPATH reduces harmful responses by up to 90.0\% and blocks 83.3\% of jailbreak attempts in the DeepSeek-R1-Distill-Llama-8B model, while requiring 295.9x less compute than Direct Refusal and 314.1x less than SafeChain. We further introduce a zero-shot variant that requires no fine-tuning. In addition, we provide a comprehensive analysis of how existing methods in LLMs generalize, or fail, when applied to reasoning-centric models, revealing critical gaps and new directions for safer AI.

We study $L_2$ mean estimation under central differential privacy and communication constraints, and address two key challenges: firstly, existing mean estimation schemes that simultaneously handle both constraints are usually optimized for $L_\infty$ geometry and rely on random rotation or Kashin’s representation to adapt to $L_2$ geometry, resulting in suboptimal leading constants in mean square errors (MSEs); secondly, schemes achieving order-optimal communication-privacy trade-offs do not extend seamlessly to streaming differential privacy (DP) settings (e.g., tree aggregation or matrix factorization), rendering them incompatible with DP-FTRL type optimizers. In this work, we tackle these issues by introducing a novel privacy accounting method for the sparsified Gaussian mechanism that incorporates the randomness inherent in sparsification into the DP noise. Unlike previous approaches, our accounting algorithm directly operates in $L_2$ geometry, yielding MSEs that fast converge to those of the uncompressed Gaussian mechanism. Additionally, we extend the sparsification scheme to the matrix factorization framework under streaming DP and provide a precise accountant tailored for DP-FTRL type optimizers. Empirically, our method demonstrates at least a 100x improvement of compression for DP-SGD across various FL tasks.

Efficient DNA-based storage systems offer substantial capacity and longevity at reduced costs, addressing anticipated data growth. However, encoding data into DNA sequences is limited by two key constraints: 1) a maximum of h consecutive identical bases (homopolymer constraint h), and 2) a GC ratio between $$ [0.5 - c_{{GC}}, 0.5 + c_{{GC}} ] $$ (GC content constraint $$c_{GC}$$ ). Sequencing or synthesis errors tend to increase when these constraints are violated. In this research, we address a pure source coding problem in the context of DNA storage, considering both homopolymer and GC content constraints. We introduce a novel coding technique that adheres to these constraints while maintaining linear complexity for increased block lengths and achieving near-optimal rates. We demonstrate the effectiveness of the proposed method through experiments on both randomly generated data and existing files. For example, when $$h = 4$$ and $$c_{GC} = 0.05$$ , the rate reached 1.988, close to the theoretical limit of 1.990. The associated code can be accessed at GitHub. We propose a variable-to-variable-length encoding method that does not rely on concatenating short predefined sequences, which achieves near-optimal rates.

We study the mean estimation problem under communication and local differential privacy constraints. While previous work has proposed order-optimal algorithms for the same problem (i.e., asymptotically optimal as we spend more bits), exact optimality (in the non-asymptotic setting) still has not been achieved. In this work, we take a step towards characterizing the exact-optimal approach in the presence of shared randomness (a random variable shared between the server and the user) and identify several conditions for exact optimality. We prove that one of the conditions is to utilize a rotationally symmetric shared random codebook. Based on this, we propose a randomization mechanism where the codebook is a randomly rotated simplex -- satisfying the properties of the exact-optimal codebook. The proposed mechanism is based on a $k$-closest encoding which we prove to be exact-optimal for the randomly rotated simplex codebook.

Diffusion models have recently shown remarkable success in high-quality image generation. Sometimes, however, a pre-trained diffusion model exhibits partial misalignment in the sense that the model can generate good images, but it sometimes outputs undesirable images. If so, we simply need to prevent the generation of the bad images, and we call this task censoring. In this work, we present censored generation with a pre-trained diffusion model using a reward model trained on minimal human feedback. We show that censoring can be accomplished with extreme human feedback efficiency and that labels generated with a mere few minutes of human feedback are sufficient.

MOTIVATION: DNA-based data storage is one of the most attractive research areas for future archival storage. However, it faces the problems of high writing and reading costs for practical use. There have been many efforts to resolve this problem, but existing schemes are not fully suitable for DNA-based data storage, and more cost reduction is needed. RESULTS: We propose whole encoding and decoding procedures for DNA storage. The encoding procedure consists of a carefully designed single low-density parity-check code as an inter-oligo code, which corrects errors and dropouts efficiently. We apply new clustering and alignment methods that operate on variable-length reads to aid the decoding performance. We use edit distance and quality scores during the sequence analysis-aided decoding procedure, which can discard abnormal reads and utilize high-quality soft information. We store 548.83 KB of an image file in DNA oligos and achieve a writing cost reduction of 7.46% and a significant reading cost reduction of 26.57% and 19.41% compared with the two previous works. AVAILABILITY AND IMPLEMENTATION: Data and codes for all the algorithms proposed in this study are available at: https://github.com/sjpark0905/DNA-LDPC-codes.

We study the neural network (NN) compression problem, viewing the tension between the compression ratio and NN performance through the lens of rate-distortion theory. We choose a distortion metric that reflects the effect of NN compression on the model output and then derive the tradeoff between rate (compression ratio) and distortion. In addition to characterizing theoretical limits of NN compression, this formulation shows that pruning, implicitly or explicitly, must be a part of a good compression algorithm. This observation bridges a gap between parts of the literature pertaining to NN and data compression, respectively, providing insight into the empirical success of pruning for NN compression. Finally, we propose a novel pruning strategy derived from our information-theoretic formulation and show that it outperforms the relevant baselines on CIFAR-10 and ImageNet datasets.

The tremendous recent progress in analyzing the training dynamics of overparameterized neural networks has primarily focused on wide networks and therefore does not sufficiently address the role of depth in deep learning. In this work, we present the first trainability guarantee of infinitely deep but narrow neural networks. We study the infinite-depth limit of a multilayer perceptron (MLP) with a specific initialization and establish a trainability guarantee using the NTK theory. We then extend the analysis to an infinitely deep convolutional neural network (CNN) and perform brief experiments.

Generative adversarial networks (GAN) are a widely used class of deep generative models, but their minimax training dynamics are not understood very well. In this work, we show that GANs with a 2-layer infinite-width generator and a 2-layer finite-width discriminator trained with stochastic gradient ascent-descent have no spurious stationary points. We then show that when the width of the generator is finite but wide, there are no spurious stationary points within a ball whose radius becomes arbitrarily large (to cover the entire parameter space) as the width goes to infinity.

MOTIVATION: In DNA storage systems, there are tradeoffs between writing and reading costs. Increasing the code rate of error-correcting codes may save writing cost, but it will need more sequence reads for data retrieval. There is potentially a way to improve sequencing and decoding processes in such a way that the reading cost induced by this tradeoff is reduced without increasing the writing cost. In past researches, clustering, alignment and decoding processes were considered as separate stages but we believe that using the information from all these processes together may improve decoding performance. Actual experiments of DNA synthesis and sequencing should be performed because simulations cannot be relied on to cover all error possibilities in practical circumstances. RESULTS: For DNA storage systems using fountain code and Reed-Solomon (RS) code, we introduce several techniques to improve the decoding performance. We designed the decoding process focusing on the cooperation of key components: Hamming-distance based clustering, discarding of abnormal sequence reads, RS error correction as well as detection and quality score-based ordering of sequences. We synthesized 513.6 KB data into DNA oligo pools and sequenced this data successfully with Illumina MiSeq instrument. Compared to Erlich's research, the proposed decoding method additionally incorporates sequence reads with minor errors which had been discarded before, and thus was able to make use of 10.6-11.9% more sequence reads from the same sequencing environment, this resulted in 6.5-8.9% reduction in the reading cost. Channel characteristics including sequence coverage and read-length distributions are provided as well. AVAILABILITY AND IMPLEMENTATION: The raw data files and the source codes of our experiments are available at: https://github.com/jhjeong0702/dna-storage.

BACKGROUND: Advances in sequencing technology have drastically reduced sequencing costs. As a result, the amount of sequencing data increases explosively. Since FASTQ files (standard sequencing data formats) are huge, there is a need for efficient compression of FASTQ files, especially quality scores. Several quality scores compression algorithms are recently proposed, mainly focused on lossy compression to boost the compression rate further. However, for clinical applications and archiving purposes, lossy compression cannot replace lossless compression. One of the main challenges for lossless compression is time complexity, where it takes thousands of seconds to compress a 1 GB file. Also, there are desired features for compression algorithms, such as random access. Therefore, there is a need for a fast lossless compressor with a reasonable compression rate and random access functionality. RESULTS: This paper proposes a Fast and Concurrent Lossless Quality scores Compressor (FCLQC) that supports random access and achieves a lower running time based on concurrent programming. Experimental results reveal that FCLQC is significantly faster than the baseline compressors on compression and decompression at the expense of compression ratio. Compared to LCQS (baseline quality score compression algorithm), FCLQC shows at least 31x compression speed improvement in all settings, where a performance degradation in compression ratio is up to 13.58% (8.26% on average). Compared to general-purpose compressors (such as 7-zip), FCLQC shows 3x faster compression speed while having better compression ratios, at least 2.08% (4.69% on average). Moreover, the speed of random access decompression also outperforms the others. The concurrency of FCLQC is implemented using Rust; the performance gain increases near-linearly with the number of threads. CONCLUSION: The superiority of compression and decompression speed makes FCLQC a practical lossless quality score compressor candidate for speed-sensitive applications of DNA sequencing data. FCLQC is available at https://github.com/Minhyeok01/FCLQC and is freely available for non-commercial usage.

Over a decade, as a specialized workshop in the field of text mining applied to biomedical informatics, DTMBIO (ACM international workshop on Data and Text Mining in Biomedical Informatics) has been held annually in conjunction with one of the largest data management conferences, CIKM. The purpose of DTMBIO is to foster discussions regarding the state-of-the-art applications of data and text mining on biomedical research problems. To address our purpose, we bring together researchers working on computer science and bio/medical informatics area including text mining and high throughput genomic data analysis, such as the next generation Sequencing (NGS) data. DTMBIO 2020 will help scientists navigate emerging trends and opportunities in the evolving area of informatics related techniques and problems in the context of biomedical research.

This paper proposes a video delivery strategy for dynamic streaming services which maximizes time-average streaming quality under a playback delay constraint in wireless caching networks. The network where popular videos encoded by scalable video coding are already stored in randomly distributed caching nodes is considered under adaptive video streaming concepts, and distance-based interference management is investigated in this paper. In this network model, a streaming user makes delay-constrained decisions depending on stochastic network states: 1) caching node for video delivery, 2) video quality, and 3) the quantity of video chunks to receive. Since wireless link activation for video delivery may introduce delays, different timescales for updating caching node association, video quality adaptation, and chunk amounts are considered. After associating with a caching node for video delivery, the streaming user chooses combinations of quality and chunk amounts in the small timescale. The dynamic decision making process for video quality and chunk amounts at each slot is modeled using Markov decision process, and the caching node decision is made based on the framework of Lyapunov optimization. Our intensive simulations verify that the proposed video delivery algorithm works reliably and also can control the tradeoff between video quality and playback latency.

In mobile multimedia devices, the frame memory compression (FMC) technique by embedded compression (EC) is becoming an increasingly important video-processing method for reducing the external data bandwidth requirement, which, in turn, results in power savings. Among various EC schemes, the combination of discrete wavelet transform (DWT) and set partitioning in hierarchical trees (SPIHT) is widely used for FMC because it achieves high compression efficiency with low computational complexity. However, there is room for improvement in the conventional DWT and SPIHT algorithm because it compresses all blocks with the same compression ratio without taking into account the correlation between DWT coefficients and the SPIHT algorithm. This study proposes a novel one-dimensional (1-D) DWT and SPIHT algorithm, which enhances the quality of the compressed video by internally applying an adaptive compression ratio for the SPIHT algorithm based on DWT coefficients while keeping the same bit-stream size. The block complexity is predicted from the distribution of DWT coefficients. Then, simple blocks are aggressively compressed with a low compression ratio, while the complex blocks are compressed with a high ratio. Furthermore, to achieve the best video quality, each compression ratio is decided by an optimization technique based on mathematical formulation. Precisely, the logarithm of mean squared error by the SPIHT algorithm is assumed to be linearly correlated with the logarithm of processed DWT coefficients. Experimental results are provided that support the aforementioned model. Compared to the conventional 1-D DWT and SPIHT algorithm, the proposed scheme remarkably improves the video quality by an average of 2.23 dB in peak signal-to-noise ratio when the target compression ratio for the SPIHT algorithm is 5/16.

Massive amounts of sequencing data are being generated thanks to advances in sequencing technology and a dramatic drop in the sequencing cost. Much of the data are comprised of nucleotides and the corresponding quality scores that indicate their reliability. The latter are more difficult to compress and are themselves noisy. As a result, lossy compression of the quality scores has recently been proposed to alleviate the storage costs. Further, it has been shown that lossy compression, at some specific rates, can achieve a performance on variant calling similar to that achieved with the lossless compressed data. We propose CROMqs, a new lossy compressor for the quality scores with the property of "infinitesimal successive refinability". This property allows the decoder to decompress the data iteratively without the need of agreeing with the encoder on a specific rate prior to compression. This characteristic is particularly amenable in practice, as in most cases the appropriate rate at which the lossy compressor should operate can not be established prior to compression. Further, this property can be of interest in scenarios involving streaming of genomic data. CROMqs is the first infinitesimal successive refinement lossy compressor for the quality scores in the literature, and we show that it obtains a comparable rate-distortion performance to previously proposed algorithms. Moreover, we also show that CROMqs achieves a comparable performance on variant calling to that of the lossless compressed data.

We investigate the second order asymptotics (source dispersion) of the successive refinement problem. Similar to the classical definition of a successively refinable source, we say that a source is strongly successively refinable if successive refinement coding can achieve the second order optimum rate (including the dispersion terms) at both decoders. We establish a sufficient condition for strong successive refinability. We show that any discrete source under Hamming distortion and the Gaussian source under quadratic distortion are strongly successively refinable. We also demonstrate how successive refinement ideas can be used in point-to-point lossy compression problems in order to reduce complexity. We give two examples, the binary-Hamming and Gaussian-quadratic cases, in which a layered code construction results in a low complexity scheme that attains optimal performance. For example, when the number of layers grows with the block length n, we show how to design an O(nlog(n)) algorithm that asymptotically achieves the rate-distortion bound.

We begin by presenting a simple lossy compressor operating at near-zero rate: The encoder merely describes the indices of the few maximal source components, while the decoder's reconstruction is a natural estimate of the source components based on this information. This scheme turns out to be near optimal for the memoryless Gaussian source in the sense of achieving the zero-rate slope of its distortion-rate function. Motivated by this finding, we then propose a scheme comprised of iterating the above lossy compressor on an appropriately transformed version of the difference between the source and its reconstruction from the previous iteration. The proposed scheme achieves the rate distortion function of the Gaussian memoryless source (under squared error distortion) when employed on any finite-variance ergodic source. It further possesses desirable properties, and we, respectively, refer to as infinitesimal successive refinability, ratelessness, and complete separability. Its storage and computation requirements are of order no more than (n2)/(logβn) per source symbol for β > 0 at both the encoder and the decoder. Though the details of its derivation, construction, and analysis differ considerably, we discuss similarities between the proposed scheme and the recently introduced Sparse Regression Codes of Venkataramanan et al.

We establish two strong senses of universality of logarithmic loss as a distortion criterion in lossy compression: For any fixed length lossy compression problem under an arbitrary distortion criterion, we show that there is an equivalent lossy compression problem under logarithmic loss. In the successive refinement problem, if the first decoder operates under logarithmic loss, we show that any discrete memoryless source is successively refinable under an arbitrary distortion criterion for the second decoder.

Four problems related to information divergence measures defined on finite alphabets are considered. In three of the cases we consider, we illustrate a contrast which arises between the binary-alphabet and larger-alphabet settings. This is surprising in some instances, since characterizations for the larger-alphabet settings do not generalize their binary-alphabet counterparts. For example, we show that f-divergences are not the unique decomposable divergences on binary alphabets that satisfy the data processing inequality, despite contrary claims in the literature.

We investigate the second order asymptotics (source dispersion) of the successive refinement problem. Similarly to the classical definition of a successively refinable source, we say that a source is strongly successively refinable if successive refinement coding can achieve the second order optimum rate (including the dispersion terms) at both receivers. We propose a sufficient condition for strong successive refinability. As a corollary, we show that any discrete source with Hamming distortion is strongly successively refinable. For a Gaussian source with quadratic distortion, we show directly that the source is strongly successively refinable.

Four problems related to information divergence measures defined on finite alphabets are considered. In three of the cases we consider, we illustrate a contrast that arises between the binary-alphabet and larger alphabet settings. This is surprising in some instances, since characterizations for the larger alphabet settings do not generalize their binary-alphabet counterparts. In particular, we show that f-divergences are not the unique decomposable divergences on binary alphabets that satisfy the data processing inequality, thereby clarifying claims that have previously appeared in the literature. We also show that Kullback-Leibler (KL) divergence is the unique Bregman divergence, which is also an f-divergence for any alphabet size. We show that KL divergence is the unique Bregman divergence, which is invariant to statistically sufficient transformations of the data, even when nondecomposable divergences are considered. Like some of the problems we consider, this result holds only when the alphabet size is at least three.

We investigate the problem of continuous-time causal estimation under a minimax criterion. Let XT= (Xt,0 ≤ t ≤ T) be governed by the probability law Pθfrom a class of possible laws indexed by θ ∈ A, and YTbe the noise corrupted observations of XTavailable to the estimator. We characterize the estimator minimizing the worst case regret, where regret is the difference between the causal estimation loss of the estimator and that of the optimum estimator. One of the main contributions of this paper is characterizing the minimax estimator, showing that it is in fact a Bayesian estimator. We then relate minimax regret to the channel capacity when the channel is either Gaussian or Poisson. In this case, we characterize the minimax regret and the minimax estimator more explicitly. If we further assume that the uncertainty set consists of deterministic signals, the worst case regret is exactly equal to the corresponding channel capacity, namely the maximal mutual information attainable across the channel among all possible distributions on the uncertainty set of signals. The corresponding minimax estimator is the Bayesian estimator assuming the capacity-achieving prior. Using this relation, we also show that the capacity achieving prior coincides with the least favorable input. In addition, we show that this minimax estimator is not only minimizing the worst case regret, but also essentially minimizing regret for most of the other sources in the uncertainty set. We present a couple of examples for the construction of a minimax filter via an approximation of the associated capacity achieving distribution.

We investigate the problem of continuous-time causal estimation under a minimax criterion. Let XT= {Xt, 0 ≤ t ≤ T} be governed by probability law Pθfrom some class of possible laws indexed by θ ∈ S, and YTbe the noise corrupted observations of XTavailable to the estimator. We characterize the estimator minimizing the worst case regret, where regret is the difference between the expected loss of the estimator and that optimized for the true law of XT. We then relate this minimax regret to the channel capacity when the channel is either Gaussian or Poisson. In this case, we characterize the minimax regret and the minimax estimator more explicitly. If we assume that the uncertainty set consists of deterministic signals, the worst case regret is exactly equal to the corresponding channel capacity, namely the maximal mutual information attainable across the channel among all possible distributions on the uncertainty set of signals. Also, the optimum minimax estimator is the Bayesian estimator assuming the capacity-achieving prior. Moreover, we show that this minimax estimator is not only minimizing the worst case regret but also essentially minimizing the regret for “most” of the other sources in the uncertainty set. We present a couple of examples for the construction of an approximately minimax filter via an approximation of the associated capacity achieving distribution.

We study the transmission of a single random variable across the Poisson channel, which takes a continuous-time waveform {λt: 0 ≤ λt≤ T} as an input, where 0 ≤ λt≤ A, for all 0 ≤ t ≤ T. The output of the channel is a non-homogeneous Poisson arrival process with rate λT. We explore the class of schemes that are optimal in the distortion exponent sense under mean squared loss. We determine a family of optimal encoders for this channel which achieves the minimum mean squared error. In addition, we characterize the distortion exponent for `separation' based schemes, and also provide an upper bound for the maximal distortion exponent across all joint source channel strategies under this setting.

DNA sequencing technology has advanced to a point where storage is becoming the central bottleneck in the acquisition and mining of more data. Large amounts of data are vital for genomics research, and generic compression tools, while viable, cannot offer the same savings as approaches tuned to inherent biological properties. We propose an algorithm to compress a target genome given a known reference genome. The proposed algorithm first generates a mapping from the reference to the target genome, and then compresses this mapping with an entropy coder. As an illustration of the performance: applying our algorithm to James Watson's genome with hg18 as a reference, we are able to reduce the 2991 megabyte (MB) genome down to 6.99 MB, while Gzip compresses it to 834.8 MB.