Penalizing the nuclear norm of a function's Jacobian encourages it to locally behave like a low-rank linear map. Such functions vary locally along only a handful of directions, making the Jacobian nuclear norm a natural regularizer for machine learning problems. However, this regularizer is intractable for high-dimensional problems, as it requires computing a large Jacobian matrix and taking its SVD. We show how to efficiently penalize the Jacobian nuclear norm using techniques tailor-made for deep learning. We prove that for functions parametrized as compositions $f = g \circ h$, one may equivalently penalize the average squared Frobenius norm of $Jg$ and $Jh$. We then propose a denoising-style approximation that avoids the Jacobian computations altogether. Our method is simple, efficient, and accurate, enabling Jacobian nuclear norm regularization to scale to high-dimensional deep learning problems. We complement our theory with an empirical study of our regularizer's performance and investigate applications to denoising and representation learning.

However, its efficacy is heavily dependent on the availability of labeled data, and annotating biochemical data is extremely laborious. To surmount this data sparsity challenge, we present an instructive learning algorithm named InstructMol to measure pseudo-labels' reliability and help the target model leverage large-scale unlabeled data. InstructMol does not require transferring knowledge between multiple domains, which avoids the potential gap between the pretraining and fine-tuning stages. We demonstrated the high accuracy of InstructMol on several real-world molecular datasets and out-of-distribution (OOD) benchmarks.

Exploring the loss landscape offers insights into the inherent principles of deep neural networks (DNNs). Recent work suggests an additional asymmetry of the valley beyond the flat and sharp ones, yet without thoroughly examining its causes or implications. Our study methodically explores the factors affecting the symmetry of DNN valleys, encompassing (1) the dataset, network architecture, initialization, and hyperparameters that influence the convergence point; and (2) the magnitude and direction of the noise for 1D visualization. Our major observation shows that the {\it degree of sign consistency} between the noise and the convergence point is a critical indicator of valley symmetry. Theoretical insights from the aspects of ReLU activation and softmax function could explain the interesting phenomenon. Our discovery propels novel understanding and applications in the scenario of Model Fusion: (1) the efficacy of interpolating separate models significantly correlates with their sign consistency ratio, and (2) imposing sign alignment during federated learning emerges as an innovative approach for model parameter alignment.

Antibodies are crucial proteins produced by the immune system to eliminate harmful foreign substances and have become pivotal therapeutic agents for treating human diseases.To accelerate the discovery of antibody therapeutics, there is growing interest in constructing language models using antibody sequences.However, the applicability of pre-trained language models for antibody discovery has not been thoroughly evaluated due to the scarcity of labeled datasets.To overcome these limitations, we introduce AVIDa-SARS-CoV-2, a dataset featuring the antigen-variable domain of heavy chain of heavy chain antibody (VHH) interactions obtained from two alpacas immunized with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike proteins.AVIDa-SARS-CoV-2 includes binary labels indicating the binding or non-binding of diverse VHH sequences to 12 SARS-CoV-2 mutants, such as the Delta and Omicron variants.Furthermore, we release VHHCorpus-2M, a pre-training dataset for antibody language models, containing over two million VHH sequences.We report benchmark results for predicting SARS-CoV-2-VHH binding using VHHBERT pre-trained on VHHCorpus-2M and existing general protein and antibody-specific pre-trained language models.These results confirm that AVIDa-SARS-CoV-2 provides valuable benchmarks for evaluating the representation capabilities of antibody language models for binding prediction, thereby facilitating the development of AI-driven antibody discovery.The datasets are available at https://datasets.cognanous.com.

The proliferation of large language models (LLMs) has led to the adoption of Mixture-of-Experts (MoE) architectures that dynamically leverage specialized subnetworks for improved efficiency and performance. Despite their benefits, MoE models face significant challenges during inference, including inefficient memory management and suboptimal batching, due to misaligned design choices between the model architecture and the system policies. Furthermore, the conventional approach of training MoEs from scratch is increasingly prohibitive in terms of cost. In this paper, we propose a novel framework $\textit{Read-ME}$ that transforms pre-trained dense LLMs into smaller MoE models (in contrast to ``upcycling generalist MoEs), avoiding the high costs of ground-up training. Our approach employs activation sparsity to extract experts. To compose experts, we examine the widely-adopted layer-wise router design and show its redundancy, and thus we introduce the pre-gating router decoupled from the MoE backbone that facilitates system-friendly pre-computing and lookahead scheduling, enhancing expert-aware batching and caching.Our codesign therefore addresses critical gaps on both the algorithmic and system fronts, establishing a scalable and efficient alternative for LLM inference in resource-constrained settings.$\textit{Read-ME}$

Self-Supervised learning (SSL) with Joint-Embedding Architectures (JEA) has led to outstanding performances. All instantiations of this paradigm were trained using strong and well-established hand-crafted data augmentations, leading to the general belief that they are required for the proper training and performance of such models. On the other hand, generative reconstruction-based models such as BEIT and MAE or Joint-Embedding Predictive Architectures such as I-JEPA have shown strong performance without using data augmentations except masking. In this work, we challenge the importance of invariance and data-augmentation in JEAs at scale. By running a case-study on a recent SSL foundation model -- DINOv2 -- we show that strong image representations can be obtained with JEAs and only cropping without resizing provided the training data is large enough, reaching state-of-the-art results and using the least amount of augmentation in the literature. Through this study, we also discuss the impact of compute constraints on the outcomes of experimental deep learning research, showing that they can lead to very different conclusions.

While 3D object bounding box (bbox) representation has been widely used in autonomous driving perception, it lacks the ability to capture the precise details of an object's intrinsic geometry. Recently, occupancy has emerged as a promising alternative for 3D scene perception. However, constructing a high-resolution occupancy map remains infeasible for large scenes due to computational constraints. Recognizing that foreground objects only occupy a small portion of the scene, we introduce object-centric occupancy as a supplement to object bboxes. This representation not only provides intricate details for detected objects but also enables higher voxel resolution in practical applications.

In the recent literature on machine learning and decision making, calibration has emerged as a desirable and widely-studied statistical property of the outputs of binary prediction models. However, the algorithmic aspects of measuring model calibration have remained relatively less well-explored. Motivated by Blasiok et al '23, which proposed a rigorous framework for measuring distances to calibration, we initiate the algorithmic study of calibration through the lens of property testing. We define the problem of calibration testing from samples where given $n$ draws from a distribution $\mathcal{D}$ on $(\text{predictions}, \text{binary outcomes})$, our goal is to distinguish between the cases where $\mathcal{D}$ is perfectly calibrated or $\epsilon$-far from calibration. We make the simple observation that the empirical smooth calibration linear program can be reformulated as an instance of minimum-cost flow on a highly-structured graph, and design an exact dynamic programming-based solver for it which runs in time $O(n\log^2(n))$, and solves the calibration testing problem information-theoretically optimally in the same time. This improves upon state-of-the-art black-box linear program solvers requiring $\Omega(n^\omega)$ time, where $\omega > 2$ is the exponent of matrix multiplication. We also develop algorithms for tolerant variants of our testing problem improving upon black-box linear program solvers, and give sample complexity lower bounds for alternative calibration measures to the one considered in this work. Finally, we present experiments showing the testing problem we define faithfully captures standard notions of calibration, and that our algorithms scale efficiently to accommodate large sample sizes.

Existing ML benchmarks lack the depth and diversity of annotations needed for evaluating models on business process management (BPM) tasks. BPM is the practice of documenting, measuring, improving, and automating enterprise workflows. However, research has focused almost exclusively on one task -- full end-to-end automation using agents based on multimodal foundation models (FMs) like GPT-4. This focus on automation ignores the reality of how most BPM tools are applied today -- simply documenting the relevant workflow takes 60% of the time of the typical process optimization project. To address this gap we present WONDERBREAD, the first benchmark for evaluating multimodal FMs on BPM tasks beyond automation. Our contributions are: (1) a dataset containing 2928 documented workflow demonstrations; (2) 6 novel BPM tasks sourced from real-world applications ranging from workflow documentation to knowledge transfer to process improvement; and (3) an automated evaluation harness. Our benchmark shows that while state-of-the-art FMs can automatically generate documentation (e.g.

In recent years, there has been a proliferation of ready-to-use large language models (LLMs) designed for various applications, both general-purpose and domain-specific. Instead of advocating for the development of a new model or continuous pretraining of an existing one, this paper introduces a pragmatic teacher-teacher framework to facilitate mutual learning between two pre-existing models.By leveraging two teacher models possessing complementary knowledge, we introduce a LIghtweight kNowledge alignmEnt (LINE) module aimed at harmonizing their knowledge within a unified representation space. This framework is particularly valuable in clinical settings, where stringent regulations and privacy considerations dictate the handling of detailed clinical notes. Our trained LINE module excels in capturing critical information from clinical notes, leveraging highly de-identified data. Validation and downstream tasks further demonstrate the effectiveness of the proposed framework.