Daily Papers

In this article, we introduce a new parameterized family of topological invariants, taking the form of candidate decompositions, for multi-parameter persistence modules. We prove that our candidate decompositions are controllable approximations: when restricting to modules that can be decomposed into interval summands, we establish theoretical results about the approximation error between our candidate decompositions and the true underlying module in terms of the standard interleaving and bottleneck distances. Moreover, even when the underlying module does not admit such a decomposition, our candidate decompositions are nonetheless stable invariants; small perturbations in the underlying module lead to small perturbations in the candidate decomposition. Then, we introduce MMA (Multipersistence Module Approximation): an algorithm for computing stable instances of such invariants, which is based on fibered barcodes and exact matchings, two constructions that stem from the theory of single-parameter persistence. By design, MMA can handle an arbitrary number of filtrations, and has bounded complexity and running time. Finally, we present empirical evidence validating the generalization capabilities and running time speed-ups of MMA on several data sets.

Understanding biodiversity is a global challenge, in which DNA barcodes - short snippets of DNA that cluster by species - play a pivotal role. In particular, invertebrates, a highly diverse and under-explored group, pose unique taxonomic complexities. We explore machine learning approaches, comparing supervised CNNs, fine-tuned foundation models, and a DNA barcode-specific masking strategy across datasets of varying complexity. While simpler datasets and tasks favor supervised CNNs or fine-tuned transformers, challenging species-level identification demands a paradigm shift towards self-supervised pretraining. We propose BarcodeBERT, the first self-supervised method for general biodiversity analysis, leveraging a 1.5 M invertebrate DNA barcode reference library. This work highlights how dataset specifics and coverage impact model selection, and underscores the role of self-supervised pretraining in achieving high-accuracy DNA barcode-based identification at the species and genus level. Indeed, without the fine-tuning step, BarcodeBERT pretrained on a large DNA barcode dataset outperforms DNABERT and DNABERT-2 on multiple downstream classification tasks. The code repository is available at https://github.com/Kari-Genomics-Lab/BarcodeBERT

Vision-language (VL) pre-training has recently received considerable attention. However, most existing end-to-end pre-training approaches either only aim to tackle VL tasks such as image-text retrieval, visual question answering (VQA) and image captioning that test high-level understanding of images, or only target region-level understanding for tasks such as phrase grounding and object detection. We present FIBER (Fusion-In-the-Backbone-based transformER), a new VL model architecture that can seamlessly handle both these types of tasks. Instead of having dedicated transformer layers for fusion after the uni-modal backbones, FIBER pushes multimodal fusion deep into the model by inserting cross-attention into the image and text backbones, bringing gains in terms of memory and performance. In addition, unlike previous work that is either only pre-trained on image-text data or on fine-grained data with box-level annotations, we present a two-stage pre-training strategy that uses both these kinds of data efficiently: (i) coarse-grained pre-training based on image-text data; followed by (ii) fine-grained pre-training based on image-text-box data. We conduct comprehensive experiments on a wide range of VL tasks, ranging from VQA, image captioning, and retrieval, to phrase grounding, referring expression comprehension, and object detection. Using deep multimodal fusion coupled with the two-stage pre-training, FIBER provides consistent performance improvements over strong baselines across all tasks, often outperforming methods using magnitudes more data. Code is available at https://github.com/microsoft/FIBER.

With the success of Diffusion Models for image generation, the technologies also have revolutionized the aesthetic Quick Response (QR) code generation. Despite significant improvements in visual attractiveness for the beautified codes, their scannabilities are usually sacrificed and thus hinder their practical uses in real-world scenarios. To address this issue, we propose a novel training-free Diffusion-based QR Code generator (DiffQRCoder) to effectively craft both scannable and visually pleasing QR codes. The proposed approach introduces Scanning-Robust Perceptual Guidance (SRPG), a new diffusion guidance for Diffusion Models to guarantee the generated aesthetic codes to obey the ground-truth QR codes while maintaining their attractiveness during the denoising process. Additionally, we present another post-processing technique, Scanning Robust Manifold Projected Gradient Descent (SR-MPGD), to further enhance their scanning robustness through iterative latent space optimization. With extensive experiments, the results demonstrate that our approach not only outperforms other compared methods in Scanning Success Rate (SSR) with better or comparable CLIP aesthetic score (CLIP-aes.) but also significantly improves the SSR of the ControlNet-only approach from 60% to 99%. The subjective evaluation indicates that our approach achieves promising visual attractiveness to users as well. Finally, even with different scanning angles and the most rigorous error tolerance settings, our approach robustly achieves over 95% SSR, demonstrating its capability for real-world applications. Our project page is available at https://jwliao1209.github.io/DiffQRCoder.

As part of an ongoing worldwide effort to comprehend and monitor insect biodiversity, this paper presents the BIOSCAN-5M Insect dataset to the machine learning community and establish several benchmark tasks. BIOSCAN-5M is a comprehensive dataset containing multi-modal information for over 5 million insect specimens, and it significantly expands existing image-based biological datasets by including taxonomic labels, raw nucleotide barcode sequences, assigned barcode index numbers, and geographical information. We propose three benchmark experiments to demonstrate the impact of the multi-modal data types on the classification and clustering accuracy. First, we pretrain a masked language model on the DNA barcode sequences of the BIOSCAN-5M dataset, and demonstrate the impact of using this large reference library on species- and genus-level classification performance. Second, we propose a zero-shot transfer learning task applied to images and DNA barcodes to cluster feature embeddings obtained from self-supervised learning, to investigate whether meaningful clusters can be derived from these representation embeddings. Third, we benchmark multi-modality by performing contrastive learning on DNA barcodes, image data, and taxonomic information. This yields a general shared embedding space enabling taxonomic classification using multiple types of information and modalities. The code repository of the BIOSCAN-5M Insect dataset is available at {https://github.com/zahrag/BIOSCAN-5M}

Diffusion models excel in image generation, but controlling them remains a challenge. We focus on the problem of style-conditioned image generation. Although example images work, they are cumbersome: srefs (style-reference codes) from MidJourney solve this issue by expressing a specific image style in a short numeric code. These have seen widespread adoption throughout social media due to both their ease of sharing and the fact they allow using an image for style control, without having to post the source images themselves. However, users are not able to generate srefs from their own images, nor is the underlying training procedure public. We propose StyleCodes: an open-source and open-research style encoder architecture and training procedure to express image style as a 20-symbol base64 code. Our experiments show that our encoding results in minimal loss in quality compared to traditional image-to-style techniques.

Real-valued functions on geometric data -- such as node attributes on a graph -- can be optimized using descriptors from persistent homology, allowing the user to incorporate topological terms in the loss function. When optimizing a single real-valued function (the one-parameter setting), there is a canonical choice of descriptor for persistent homology: the barcode. The operation mapping a real-valued function to its barcode is differentiable almost everywhere, and the convergence of gradient descent for losses using barcodes is relatively well understood. When optimizing a vector-valued function (the multiparameter setting), there is no unique choice of descriptor for multiparameter persistent homology, and many distinct descriptors have been proposed. This calls for the development of a general framework for differentiability and optimization that applies to a wide range of multiparameter homological descriptors. In this article, we develop such a framework and show that it encompasses well-known descriptors of different flavors, such as signed barcodes and the multiparameter persistence landscape. We complement the theory with numerical experiments supporting the idea that optimizing multiparameter homological descriptors can lead to improved performances compared to optimizing one-parameter descriptors, even when using the simplest and most efficiently computable multiparameter descriptors.

Persistent homology (PH) provides topological descriptors for geometric data, such as weighted graphs, which are interpretable, stable to perturbations, and invariant under, e.g., relabeling. Most applications of PH focus on the one-parameter case -- where the descriptors summarize the changes in topology of data as it is filtered by a single quantity of interest -- and there is now a wide array of methods enabling the use of one-parameter PH descriptors in data science, which rely on the stable vectorization of these descriptors as elements of a Hilbert space. Although the multiparameter PH (MPH) of data that is filtered by several quantities of interest encodes much richer information than its one-parameter counterpart, the scarceness of stability results for MPH descriptors has so far limited the available options for the stable vectorization of MPH. In this paper, we aim to bring together the best of both worlds by showing how the interpretation of signed barcodes -- a recent family of MPH descriptors -- as signed measures leads to natural extensions of vectorization strategies from one parameter to multiple parameters. The resulting feature vectors are easy to define and to compute, and provably stable. While, as a proof of concept, we focus on simple choices of signed barcodes and vectorizations, we already see notable performance improvements when comparing our feature vectors to state-of-the-art topology-based methods on various types of data.

We address the task of generating 3D hair geometry from a single image, which is challenging due to the diversity of hairstyles and the lack of paired image-to-3D hair data. Previous methods are primarily trained on synthetic data and cope with the limited amount of such data by using low-dimensional intermediate representations, such as guide strands and scalp-level embeddings, that require post-processing to decode, upsample, and add realism. These approaches fail to reconstruct detailed hair, struggle with curly hair, or are limited to handling only a few hairstyles. To overcome these limitations, we propose DiffLocks, a novel framework that enables detailed reconstruction of a wide variety of hairstyles directly from a single image. First, we address the lack of 3D hair data by automating the creation of the largest synthetic hair dataset to date, containing 40K hairstyles. Second, we leverage the synthetic hair dataset to learn an image-conditioned diffusion-transfomer model that generates accurate 3D strands from a single frontal image. By using a pretrained image backbone, our method generalizes to in-the-wild images despite being trained only on synthetic data. Our diffusion model predicts a scalp texture map in which any point in the map contains the latent code for an individual hair strand. These codes are directly decoded to 3D strands without post-processing techniques. Representing individual strands, instead of guide strands, enables the transformer to model the detailed spatial structure of complex hairstyles. With this, DiffLocks can recover highly curled hair, like afro hairstyles, from a single image for the first time. Data and code is available at https://radualexandru.github.io/difflocks/