Large-scale literature mining to assess the relation between anti-cancer drugs and cancer types.

BACKGROUND: There is a huge body of scientific literature describing the relation between tumor types and anti-cancer drugs. The vast amount of scientific literature makes it impossible for researchers and physicians to extract all relevant information manually. METHODS: In order to cope with the large amount of literature we applied an automated text mining approach to assess the relations between 30 most frequent cancer types and 270 anti-cancer drugs. We applied two different approaches, a classical text mining based on named entity recognition and an AI-based approach employing word embeddings. The consistency of literature mining results was validated with 3 independent methods: first, using data from FDA approvals, second, using experimentally measured IC-50 cell line data and third, using clinical patient survival data. RESULTS: We demonstrated that the automated text mining was able to successfully assess the relation between cancer types and anti-cancer drugs. All validation methods showed a good correspondence between the results from literature mining and independent confirmatory approaches. The relation between most frequent cancer types and drugs employed for their treatment were visualized in a large heatmap. All results are accessible in an interactive web-based knowledge base using the following link: https://knowledgebase.microdiscovery.de/heatmap . CONCLUSIONS: Our approach is able to assess the relations between compounds and cancer types in an automated manner. Both, cancer types and compounds could be grouped into different clusters. Researchers can use the interactive knowledge base to inspect the presented results and follow their own research questions, for example the identification of novel indication areas for known drugs.

Transportation model for acute aortic dissection: implications for reduced treatment centres.

OBJECTIVES: The objective of the present study was to model the effects of a reduced number of treatment centres for acute type A aortic dissection on preclinical transportation distance and time. We examined whether treatment in selected centres in Germany would be implementable with respect to time to treatment. METHODS: For our transportation model, the number of aortic dissections and respective mean annual volume were collected from the annual quality reports (2015-2017) of all German cardiac surgery centres (n = 76). For each German postal code, the fastest and shortest routes to the nearest centre were calculated using Google Maps. Furthermore, we analysed data from the German Federal Statistical Office from January 2005 to December 2015 to identify all surgically treated patients with acute type A aortic dissection (n = 14 102) and examined the relationship between in-hospital mortality and mean annual volume of medical centres. RESULTS: Our simulation showed a median transportation distance of 27.13 km and transportation time of 35.78 min for 76 centres. Doubling the transportation time (70 min) would allow providing appropriate care with only 12 medical centres. Therefore, a mean annual volume of >25 should be obtained. High mean annual volume was associated with significantly lower in-hospital mortality rates (P < 0.001). A significantly lower mortality rate of 14% was observed (P < 0.001) if a mean annual volume of 30 was achieved. CONCLUSIONS: Operationalizing the volume-outcome relationship with fewer but larger medical centres results in lower mortality, which outweighs the disadvantage of longer transportation time.

Cancer drug sensitivity estimation using modular deep Graph Neural Networks.

Computational drug sensitivity models have the potential to improve therapeutic outcomes by identifying targeted drugs components that are tailored to the transcriptomic profile of a given primary tumor. The SMILES representation of molecules that is used by state-of-the-art drug-sensitivity models is not conducive for neural networks to generalize to new drugs, in part because the distance between atoms does not generally correspond to the distance between their representation in the SMILES strings. Graph-attention networks, on the other hand, are high-capacity models that require large training-data volumes which are not available for drug-sensitivity estimation. We develop a modular drug-sensitivity graph-attentional neural network. The modular architecture allows us to separately pre-train the graph encoder and graph-attentional pooling layer on related tasks for which more data are available. We observe that this model outperforms reference models for the use cases of precision oncology and drug discovery; in particular, it is better able to predict the specific interaction between drug and cell line that is not explained by the general cytotoxicity of the drug and the overall survivability of the cell line. The complete source code is available at https://zenodo.org/doi/10.5281/zenodo.8020945. All experiments are based on the publicly available GDSC data.

Patterns in acute aortic dissection and a connection to meteorological conditions in Germany.

Acute type A aortic dissection (ATAAD) is a dramatic emergency exhibiting a mortality of 50% within the first 48 hours if not operated. This study found an absolute value of cosine-like seasonal variation pattern for Germany with significantly fewer ATAAD events (Wilcoxon test) for the warm months of June, July, and August from 2005 to 2015. Many studies suspect a connection between ATAAD events and weather conditions. Using ERA5 reanalysis data and an objective weather type classification in a contingency table approach showed that for Germany, significantly more ATAAD events occurred during lower temperatures (by about 4.8 K), lower water vapor pressure (by about 2.6 hPa), and prevailing wind patterns from the northeast. In addition, we used data from a classification scheme for human-biometeorological weather conditions which was not used before in ATAAD studies. For the German region of Berlin and Brandenburg, for 2006 to 2019, the proportion of days with ATAAD events during weather conditions favoring hypertension (cold air advection, in the center of a cyclone, conditions with cold stress or thermal comfort) was significantly increased by 13% (Chi-squared test for difference of proportions). In contrast, the proportion was decreased by 19% for conditions associated with a higher risk for patients with hypotension and therefore a lower risk for patients with hypertension (warm air advection ahead of warm fronts, conditions with no thermal stress or heat stress, in the center of a cyclone with thermal stress). As many studies have shown that hypertension is a risk factor for ATAAD, our findings support the hypothesized relation between ATAAD and hypertension-favoring weather conditions.

Matching anticancer compounds and tumor cell lines by neural networks with ranking loss.

Computational drug sensitivity models have the potential to improve therapeutic outcomes by identifying targeted drug components that are likely to achieve the highest efficacy for a cancer cell line at hand at a therapeutic dose. State of the art drug sensitivity models use regression techniques to predict the inhibitory concentration of a drug for a tumor cell line. This regression objective is not directly aligned with either of these principal goals of drug sensitivity models: We argue that drug sensitivity modeling should be seen as a ranking problem with an optimization criterion that quantifies a drug's inhibitory capacity for the cancer cell line at hand relative to its toxicity for healthy cells. We derive an extension to the well-established drug sensitivity regression model PaccMann that employs a ranking loss and focuses on the ratio of inhibitory concentration and therapeutic dosage range. We find that the ranking extension significantly enhances the model's capability to identify the most effective anticancer drugs for unseen tumor cell profiles based in on in-vitro data.

Pre-Training on In Vitro and Fine-Tuning on Patient-Derived Data Improves Deep Neural Networks for Anti-Cancer Drug-Sensitivity Prediction.

Large-scale databases that report the inhibitory capacities of many combinations of candidate drug compounds and cultivated cancer cell lines have driven the development of preclinical drug-sensitivity models based on machine learning. However, cultivated cell lines have devolved from human cancer cells over years or even decades under selective pressure in culture conditions. Moreover, models that have been trained on in vitro data cannot account for interactions with other types of cells. Drug-response data that are based on patient-derived cell cultures, xenografts, and organoids, on the other hand, are not available in the quantities that are needed to train high-capacity machine-learning models. We found that pre-training deep neural network models of drug sensitivity on in vitro drug-sensitivity databases before fine-tuning the model parameters on patient-derived data improves the models' accuracy and improves the biological plausibility of the features, compared to training only on patient-derived data. From our experiments, we can conclude that pre-trained models outperform models that have been trained on the target domains in the vast majority of cases.