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Publications
SynFlowNet: Design of Diverse and Novel Molecules with Synthesis Constraints
Generative models see increasing use in computer-aided drug design. However, while performing well at capturing distributions of molecular m… (see more)otifs, they often produce synthetically inaccessible molecules. To address this, we introduce SynFlowNet, a GFlowNet model whose action space uses chemical reactions and buyable reactants to sequentially build new molecules. By incorporating forward synthesis as an explicit constraint of the generative mechanism, we aim at bridging the gap between in silico molecular generation and real world synthesis capabilities. We evaluate our approach using synthetic accessibility scores and an independent retrosynthesis tool to assess the synthesizability of our compounds, and motivate the choice of GFlowNets through considerable improvement in sample diversity compared to baselines. Additionally, we identify challenges with reaction encodings that can complicate traversal of the MDP in the backward direction. To address this, we introduce various strategies for learning the GFlowNet backward policy and thus demonstrate how additional constraints can be integrated into the GFlowNet MDP framework. This approach enables our model to successfully identify synthesis pathways for previously unseen molecules.
This paper tackles the challenge of detecting unreliable behavior in regression algorithms, which may arise from intrinsic variability (e.g.… (see more), aleatoric uncertainty) or modeling errors (e.g., model uncertainty). First, we formally introduce the notion of unreliability in regression, i.e., when the output of the regressor exceeds a specified discrepancy (or error). Then, using powerful tools for probabilistic modeling, we estimate the discrepancy density, and we measure its statistical diversity using our proposed metric for statistical dissimilarity. In turn, this allows us to derive a data-driven score that expresses the uncertainty of the regression outcome. We show empirical improvements in error detection for multiple regression tasks, consistently outperforming popular baseline approaches, and contributing to the broader field of uncertainty quantification and safe machine learning systems.
Clinical research emphasizes the implementation of rigorous and reproducible study designs that rely on between-group matching or controllin… (see more)g for sources of biological variation such as subject’s sex and age. However, corrections for body size (i.e. height and weight) are mostly lacking in clinical neuroimaging designs. This study investigates the importance of body size parameters in their relationship with spinal cord (SC) and brain magnetic resonance imaging (MRI) metrics. Data were derived from a cosmopolitan population of 267 healthy human adults (age 30.1±6.6 years old, 125 females). We show that body height correlated strongly or moderately with brain gray matter (GM) volume, cortical GM volume, total cerebellar volume, brainstem volume, and cross-sectional area (CSA) of cervical SC white matter (CSA-WM; 0.44≤r≤0.62). In comparison, age correlated weakly with cortical GM volume, precentral GM volume, and cortical thickness (-0.21≥r≥-0.27). Body weight correlated weakly with magnetization transfer ratio in the SC WM, dorsal columns, and lateral corticospinal tracts (-0.20≥r≥-0.23). Body weight further correlated weakly with the mean diffusivity derived from diffusion tensor imaging (DTI) in SC WM (r=-0.20) and dorsal columns (-0.21), but only in males. CSA-WM correlated strongly or moderately with brain volumes (0.39≤r≤0.64), and weakly with precentral gyrus thickness and DTI-based fractional anisotropy in SC dorsal columns and SC lateral corticospinal tracts (-0.22≥r≥-0.25). Linear mixture of sex and age explained 26±10% of data variance in brain volumetry and SC CSA. The amount of explained variance increased at 33±11% when body height was added into the mixture model. Age itself explained only 2±2% of such variance. In conclusion, body size is a significant biological variable. Along with sex and age, body size should therefore be included as a mandatory variable in the design of clinical neuroimaging studies examining SC and brain structure.
Clinical research emphasizes the implementation of rigorous and reproducible study designs that rely on between-group matching or controllin… (see more)g for sources of biological variation such as subject’s sex and age. However, corrections for body size (i.e. height and weight) are mostly lacking in clinical neuroimaging designs. This study investigates the importance of body size parameters in their relationship with spinal cord (SC) and brain magnetic resonance imaging (MRI) metrics. Data were derived from a cosmopolitan population of 267 healthy human adults (age 30.1±6.6 years old, 125 females). We show that body height correlated strongly or moderately with brain gray matter (GM) volume, cortical GM volume, total cerebellar volume, brainstem volume, and cross-sectional area (CSA) of cervical SC white matter (CSA-WM; 0.44≤r≤0.62). In comparison, age correlated weakly with cortical GM volume, precentral GM volume, and cortical thickness (-0.21≥r≥-0.27). Body weight correlated weakly with magnetization transfer ratio in the SC WM, dorsal columns, and lateral corticospinal tracts (-0.20≥r≥-0.23). Body weight further correlated weakly with the mean diffusivity derived from diffusion tensor imaging (DTI) in SC WM (r=-0.20) and dorsal columns (-0.21), but only in males. CSA-WM correlated strongly or moderately with brain volumes (0.39≤r≤0.64), and weakly with precentral gyrus thickness and DTI-based fractional anisotropy in SC dorsal columns and SC lateral corticospinal tracts (-0.22≥r≥-0.25). Linear mixture of sex and age explained 26±10% of data variance in brain volumetry and SC CSA. The amount of explained variance increased at 33±11% when body height was added into the mixture model. Age itself explained only 2±2% of such variance. In conclusion, body size is a significant biological variable. Along with sex and age, body size should therefore be included as a mandatory variable in the design of clinical neuroimaging studies examining SC and brain structure.
The existing definitions of graph convolution, either from spatial or spectral perspectives, are inflexible and not unified. Defining a gene… (see more)ral convolution operator in the graph domain is challenging due to the lack of canonical coordinates, the presence of irregular structures, and the properties of graph symmetries. In this work, we propose a novel graph convolution framework by parameterizing the kernels as continuous functions of pseudo-coordinates derived via graph positional encoding. We name this Continuous Kernel Graph Convolution (CKGConv). Theoretically, we demonstrate that CKGConv is flexible and expressive. CKGConv encompasses many existing graph convolutions, and exhibits the same expressiveness as graph transformers in terms of distinguishing non-isomorphic graphs. Empirically, we show that CKGConv-based Networks outperform existing graph convolutional networks and perform comparably to the best graph transformers across a variety of graph datasets.
This paper contributes a new approach for distributional reinforcement learning which elucidates
a clean separation of transition structure … (see more)and reward in the learning process. Analogous to how
the successor representation (SR) describes the expected consequences of behaving according to a
given policy, our distributional successor measure
(SM) describes the distributional consequences of
this behaviour. We formulate the distributional
SM as a distribution over distributions and provide theory connecting it with distributional and
model-based reinforcement learning. Moreover,
we propose an algorithm that learns the distributional SM from data by minimizing a two-level
maximum mean discrepancy. Key to our method
are a number of algorithmic techniques that are
independently valuable for learning generative
models of state. As an illustration of the usefulness of the distributional SM, we show that it
enables zero-shot risk-sensitive policy evaluation
in a way that was not previously possible.
Establishing an accurate model of dynamic systems poses a challenge for complex industrial processes. Due to the ability to handle complex t… (see more)asks, modular neural networks (MNN) have been widely applied to industrial process modeling. However, the phenomenon of domain drift caused by operating conditions may lead to a cold start of the model, which affects the performance of MNN. For this reason, a multisource transfer learning-based MNN (MSTL-MNN) is proposed in this study. First, the knowledge-driven transfer learning process is performed with domain similarity evaluation, knowledge extraction, and fusion, aiming to form an initial subnetwork in the target domain. Then, the positive transfer process of effective knowledge can avoid the cold start problem of MNN. Second, during the data-driven fine-tuning process, a regularized self-organizing long short-term memory algorithm is designed to fine-tune the structure and parameters of the initial subnetwork, which can improve the prediction performance of MNN. Meanwhile, relevant theoretical analysis is given to ensure the feasibility of MSTL-MNN. Finally, the effectiveness of the proposed method is confirmed by two benchmark simulations and a real industrial dataset of a municipal solid waste incineration process. Experimental results demonstrate the merits of MSTL-MNN for industrial applications.
2024-05-01
IEEE Transactions on Industrial Informatics (published)
