VN-EGNN: E(3)-Equivariant Graph Neural Networks with Virtual Nodes Enhance Protein Binding Site Identification

Being able to identify regions within or around proteins, to which ligands can potentially bind, is an essential step to develop new drugs. Binding site identification methods can now profit from the availability of large amounts of 3D structures in protein structure databases or from AlphaFold predictions. Current binding site identification methods heavily rely on graph neural networks (GNNs), usually designed to output E(3)-equivariant predictions. Such methods turned out to be very beneficial for physics-related tasks like binding energy or motion trajectory prediction. However, the performance of GNNs at binding site identification is still limited potentially due to the lack of dedicated nodes that model hidden geometric entities, such as binding pockets. In this work, we extend E(n)-Equivariant Graph Neural Networks (EGNNs) by adding virtual nodes and applying an extended message passing scheme. The virtual nodes in these graphs are dedicated quantities to learn representations of binding sites, which leads to improved predictive performance. In our experiments, we show that our proposed method VN-EGNN sets a new state-of-the-art at locating binding site centers on COACH420, HOLO4K and PDBbind2020.

Geometry-Informed Neural Networks

We introduce the concept of geometry-informed neural networks (GINNs), which encompass (i) learning under geometric constraints, (ii) neural fields as a suitable representation, and (iii) generating diverse solutions to under-determined systems often encountered in geometric tasks. Notably, the GINN formulation does not require training data, and as such can be considered generative modeling driven purely by constraints. We add an explicit diversity loss to mitigate mode collapse. We consider several constraints, in particular, the connectedness of components which we convert to a differentiable loss through Morse theory. Experimentally, we demonstrate the efficacy of the GINN learning paradigm across a range of two and three-dimensional scenarios with increasing levels of complexity.

Overcoming Saturation in Density Ratio Estimation by Iterated Regularization

Estimating the ratio of two probability densities from finitely many samples, is a central task in machine learning and statistics. In this work, we show that a large class of kernel methods for density ratio estimation suffers from error saturation, which prevents algorithms from achieving fast error convergence rates on highly regular learning problems. To resolve saturation, we introduce iterated regularization in density ratio estimation to achieve fast error rates. Our methods outperform its non-iteratively regularized versions on benchmarks for density ratio estimation as well as on large-scale evaluations for importance-weighted ensembling of deep unsupervised domain adaptation models.

MIM-Refiner: A Contrastive Learning Boost from Intermediate Pre-Trained Representations

We introduce MIM (Masked Image Modeling)-Refiner, a contrastive learning boost for pre-trained MIM models. The motivation behind MIM-Refiner is rooted in the insight that optimal representations within MIM models generally reside in intermediate layers. Accordingly, MIM-Refiner leverages multiple contrastive heads that are connected to diverse intermediate layers. In each head, a modified nearest neighbor objective helps to construct respective semantic clusters. The refinement process is short but effective. Within a few epochs, we refine the features of MIM models from subpar to state-of-the-art, off-the-shelf features. Refining a ViT-H, pre-trained with data2vec 2.0 on ImageNet-1K, achieves new state-of-the-art results in linear probing (84.7%) and low-shot classification among models that are pre-trained on ImageNet-1K. In ImageNet-1K 1-shot classification, MIM-Refiner sets a new state-of-the-art of 64.2%, outperforming larger models that were trained on up to 2000x more data such as DINOv2-g, OpenCLIP-G and MAWS-6.5B. Project page: https://ml-jku.github.io/MIM-Refiner

SymbolicAI: A framework for logic-based approaches combining generative models and solvers

We introduce SymbolicAI, a versatile and modular framework employing a logic-based approach to concept learning and flow management in generative processes. SymbolicAI enables the seamless integration of generative models with a diverse range of solvers by treating large language models (LLMs) as semantic parsers that execute tasks based on both natural and formal language instructions, thus bridging the gap between symbolic reasoning and generative AI. We leverage probabilistic programming principles to tackle complex tasks, and utilize differentiable and classical programming paradigms with their respective strengths. The framework introduces a set of polymorphic, compositional, and self-referential operations for data stream manipulation, aligning LLM outputs with user objectives. As a result, we can transition between the capabilities of various foundation models endowed with zero- and few-shot learning capabilities and specialized, fine-tuned models or solvers proficient in addressing specific problems. In turn, the framework facilitates the creation and evaluation of explainable computational graphs. We conclude by introducing a quality measure and its empirical score for evaluating these computational graphs, and propose a benchmark that compares various state-of-the-art LLMs across a set of complex workflows. We refer to the empirical score as the "Vector Embedding for Relational Trajectory Evaluation through Cross-similarity", or VERTEX score for short. The framework codebase and benchmark are linked below.

Variational Annealing on Graphs for Combinatorial Optimization

Several recent unsupervised learning methods use probabilistic approaches to solve combinatorial optimization (CO) problems based on the assumption of statistically independent solution variables. We demonstrate that this assumption imposes performance limitations in particular on difficult problem instances. Our results corroborate that an autoregressive approach which captures statistical dependencies among solution variables yields superior performance on many popular CO problems. We introduce subgraph tokenization in which the configuration of a set of solution variables is represented by a single token. This tokenization technique alleviates the drawback of the long sequential sampling procedure which is inherent to autoregressive methods without sacrificing expressivity. Importantly, we theoretically motivate an annealed entropy regularization and show empirically that it is essential for efficient and stable learning.

Introducing an Improved Information-Theoretic Measure of Predictive Uncertainty

Applying a machine learning model for decision-making in the real world requires to distinguish what the model knows from what it does not. A critical factor in assessing the knowledge of a model is to quantify its predictive uncertainty. Predictive uncertainty is commonly measured by the entropy of the Bayesian model average (BMA) predictive distribution. Yet, the properness of this current measure of predictive uncertainty was recently questioned. We provide new insights regarding those limitations. Our analyses show that the current measure erroneously assumes that the BMA predictive distribution is equivalent to the predictive distribution of the true model that generated the dataset. Consequently, we introduce a theoretically grounded measure to overcome these limitations. We experimentally verify the benefits of our introduced measure of predictive uncertainty. We find that our introduced measure behaves more reasonably in controlled synthetic tasks. Moreover, our evaluations on ImageNet demonstrate that our introduced measure is advantageous in real-world applications utilizing predictive uncertainty.

Functional trustworthiness of AI systems by statistically valid testing

The authors are concerned about the safety, health, and rights of the European citizens due to inadequate measures and procedures required by the current draft of the EU Artificial Intelligence (AI) Act for the conformity assessment of AI systems. We observe that not only the current draft of the EU AI Act, but also the accompanying standardization efforts in CEN/CENELEC, have resorted to the position that real functional guarantees of AI systems supposedly would be unrealistic and too complex anyways. Yet enacting a conformity assessment procedure that creates the false illusion of trust in insufficiently assessed AI systems is at best naive and at worst grossly negligent. The EU AI Act thus misses the point of ensuring quality by functional trustworthiness and correctly attributing responsibilities. The trustworthiness of an AI decision system lies first and foremost in the correct statistical testing on randomly selected samples and in the precision of the definition of the application domain, which enables drawing samples in the first place. We will subsequently call this testable quality functional trustworthiness. It includes a design, development, and deployment that enables correct statistical testing of all relevant functions. We are firmly convinced and advocate that a reliable assessment of the statistical functional properties of an AI system has to be the indispensable, mandatory nucleus of the conformity assessment. In this paper, we describe the three necessary elements to establish a reliable functional trustworthiness, i.e., (1) the definition of the technical distribution of the application, (2) the risk-based minimum performance requirements, and (3) the statistically valid testing based on independent random samples.

SITTA: A Semantic Image-Text Alignment for Image Captioning

Textual and semantic comprehension of images is essential for generating proper captions. The comprehension requires detection of objects, modeling of relations between them, an assessment of the semantics of the scene and, finally, representing the extracted knowledge in a language space. To achieve rich language capabilities while ensuring good image-language mappings, pretrained language models (LMs) were conditioned on pretrained multi-modal (image-text) models that allow for image inputs. This requires an alignment of the image representation of the multi-modal model with the language representations of a generative LM. However, it is not clear how to best transfer semantics detected by the vision encoder of the multi-modal model to the LM. We introduce two novel ways of constructing a linear mapping that successfully transfers semantics between the embedding spaces of the two pretrained models. The first aligns the embedding space of the multi-modal language encoder with the embedding space of the pretrained LM via token correspondences. The latter leverages additional data that consists of image-text pairs to construct the mapping directly from vision to language space. Using our semantic mappings, we unlock image captioning for LMs without access to gradient information. By using different sources of data we achieve strong captioning performance on MS-COCO and Flickr30k datasets. Even in the face of limited data, our method partly exceeds the performance of other zero-shot and even finetuned competitors. Our ablation studies show that even LMs at a scale of merely 250M parameters can generate decent captions employing our semantic mappings. Our approach makes image captioning more accessible for institutions with restricted computational resources.