Molecular graph representation learning is widely used in chemical and biomedical research. While pre-trained 2D graph encoders have demonstrated strong performance, they overlook the rich molecular domain knowledge associated with submolecular instances (atoms and bonds). While molecular pre-training approaches incorporate such knowledge into their pre-training objectives, they typically employ designs tailored to a specific type of knowledge, lacking the flexibility to integrate diverse knowledge present in molecules. Hence, reusing widely available and well-validated pre-trained 2D encoders, while incorporating molecular domain knowledge during downstream adaptation, offers a more practical alternative. In this work, we propose MolGA, which adapts pre-trained 2D graph encoders to downstream molecular applications by flexibly incorporating diverse molecular domain knowledge. First, we propose a molecular alignment strategy that bridge the gap between pre-trained topological representations with domain-knowledge representations. Second, we introduce a conditional adaptation mechanism that generates instance-specific tokens to enable fine-grained integration of molecular domain knowledge for downstream tasks. Finally, we conduct extensive experiments on eleven public datasets, demonstrating the effectiveness of MolGA.

Many empirical studies have demonstrated the performance benefits of conditional computation in neural networks, including reduced inference time and power consumption. We study the fundamental limits of neural conditional computation from the perspective of memorization capacity. For Rectified Linear Unit (ReLU) networks without conditional computation, it is known that memorizing a collection of $n$ input-output relationships can be accomplished via a neural network with $O(\sqrt{n})$ neurons. Calculating the output of this neural network can be accomplished using $O(\sqrt{n})$ elementary arithmetic operations of additions, multiplications and comparisons for each input. Using a conditional ReLU network, we show that the same task can be accomplished using only $O(\log n)$ operations per input. This represents an almost exponential improvement as compared to networks without conditional computation. We also show that the $\Theta(\log n)$ rate is the best possible. Our achievability result utilizes a general methodology to synthesize a conditional network out of an unconditional network in a computationally-efficient manner, bridging the gap between unconditional and conditional architectures.

We applied Generative Adversarial Networks (GANs) to learn a model of DOOM levels from human-designed content. Initially, we analysed the levels and extracted several topological features. Then, for each level, we extracted a set of images identifying the occupied area, the height map, the walls, and the position of game objects. We trained two GANs: one using plain level images, one using both the images and some of the features extracted during the preliminary analysis. We used the two networks to generate new levels and compared the results to assess whether the network trained using also the topological features could generate levels more similar to human-designed ones. Our results show that GANs can capture intrinsic structure of DOOM levels and appears to be a promising approach to level generation in first person shooter games.