...

.env.prod.example

@@ -16,5 +16,3 @@ POSTGRES_PORT=
 # MAIL
 EMAIL_HOST_USER=
 EMAIL_HOST_PASSWORD=
-# MATOMO
-MATOMO_SITE_ID

envipath/settings.py

@@ -357,6 +357,3 @@ if MS_ENTRA_ENABLED:
     MS_ENTRA_AUTHORITY = f"https://login.microsoftonline.com/{MS_ENTRA_TENANT_ID}"
     MS_ENTRA_REDIRECT_URI = os.environ["MS_REDIRECT_URI"]
     MS_ENTRA_SCOPES = os.environ.get("MS_SCOPES", "").split(",")
-
-# Site ID 10 -> beta.envipath.org
-MATOMO_SITE_ID = os.environ.get("MATOMO_SITE_ID", "10")

epdb/logic.py

@@ -1542,7 +1542,9 @@ class SPathway(object):
                 if sub.app_domain_assessment is None:
                     if self.prediction_setting.model:
                         if self.prediction_setting.model.app_domain:
-                            app_domain_assessment = self.prediction_setting.model.app_domain.assess(sub.smiles)
+                            app_domain_assessment = self.prediction_setting.model.app_domain.assess(
+                                sub.smiles
+                            )[0]
 
                             if self.persist is not None:
                                 n = self.snode_persist_lookup[sub]
@@ -1574,7 +1576,11 @@ class SPathway(object):
                                     app_domain_assessment = None
                                     if self.prediction_setting.model:
                                         if self.prediction_setting.model.app_domain:
-                                            app_domain_assessment = (self.prediction_setting.model.app_domain.assess(c))
+                                            app_domain_assessment = (
+                                                self.prediction_setting.model.app_domain.assess(c)[
+                                                    0
+                                                ]
+                                            )
 
                                     self.smiles_to_node[c] = SNode(
                                         c, sub.depth + 1, app_domain_assessment

epdb/models.py

@@ -28,8 +28,7 @@ from sklearn.metrics import precision_score, recall_score, jaccard_score
 from sklearn.model_selection import ShuffleSplit
 
 from utilities.chem import FormatConverter, ProductSet, PredictionResult, IndigoUtils
-from utilities.ml import RuleBasedDataset, ApplicabilityDomainPCA, EnsembleClassifierChain, RelativeReasoning, \
-    EnviFormerDataset, Dataset
+from utilities.ml import Dataset, ApplicabilityDomainPCA, EnsembleClassifierChain, RelativeReasoning
 
 logger = logging.getLogger(__name__)
 
@@ -1574,14 +1573,12 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
         while len(queue):
             current = queue.pop()
             processed.add(current)
-
             nodes.append(current.d3_json())
 
-            for e in self.edges:
-                if current in e.start_nodes.all():
-                    for prod in e.end_nodes.all():
-                        if prod not in queue and prod not in processed:
-                            queue.append(prod)
+            for e in self.edges.filter(start_nodes=current).distinct():
+                for prod in e.end_nodes.all():
+                    if prod not in queue and prod not in processed:
+                        queue.append(prod)
 
         # We shouldn't lose or make up nodes...
         assert len(nodes) == len(self.nodes)
@@ -2176,7 +2173,7 @@ class PackageBasedModel(EPModel):
 
         applicable_rules = self.applicable_rules
         reactions = list(self._get_reactions())
-        ds = RuleBasedDataset.generate_dataset(reactions, applicable_rules, educts_only=True)
+        ds = Dataset.generate_dataset(reactions, applicable_rules, educts_only=True)
 
         end = datetime.now()
         logger.debug(f"build_dataset took {(end - start).total_seconds()} seconds")
@@ -2185,7 +2182,7 @@ class PackageBasedModel(EPModel):
         ds.save(f)
         return ds
 
-    def load_dataset(self) -> "Dataset | RuleBasedDataset | EnviFormerDataset":
+    def load_dataset(self) -> "Dataset":
         ds_path = os.path.join(s.MODEL_DIR, f"{self.uuid}_ds.pkl")
         return Dataset.load(ds_path)
 
@@ -2226,7 +2223,7 @@ class PackageBasedModel(EPModel):
         self.model_status = self.BUILT_NOT_EVALUATED
         self.save()
 
-    def evaluate_model(self, multigen: bool, eval_packages: List["Package"] = None, **kwargs):
+    def evaluate_model(self, multigen: bool, eval_packages: List["Package"] = None):
         if self.model_status != self.BUILT_NOT_EVALUATED:
             raise ValueError(f"Can't evaluate a model in state {self.model_status}!")
 
@@ -2344,37 +2341,37 @@ class PackageBasedModel(EPModel):
             eval_reactions = list(
                 Reaction.objects.filter(package__in=self.eval_packages.all()).distinct()
             )
-            ds = RuleBasedDataset.generate_dataset(eval_reactions, self.applicable_rules, educts_only=True)
+            ds = Dataset.generate_dataset(eval_reactions, self.applicable_rules, educts_only=True)
             if isinstance(self, RuleBasedRelativeReasoning):
-                X = ds.X(exclude_id_col=False, na_replacement=None).to_numpy()
-                y = ds.y(na_replacement=np.nan).to_numpy()
+                X = np.array(ds.X(exclude_id_col=False, na_replacement=None))
+                y = np.array(ds.y(na_replacement=np.nan))
             else:
-                X = ds.X(na_replacement=np.nan).to_numpy()
-                y = ds.y(na_replacement=np.nan).to_numpy()
+                X = np.array(ds.X(na_replacement=np.nan))
+                y = np.array(ds.y(na_replacement=np.nan))
             single_gen_result = evaluate_sg(self.model, X, y, np.arange(len(X)), self.threshold)
             self.eval_results = self.compute_averages([single_gen_result])
         else:
             ds = self.load_dataset()
 
             if isinstance(self, RuleBasedRelativeReasoning):
-                X = ds.X(exclude_id_col=False, na_replacement=None).to_numpy()
-                y = ds.y(na_replacement=np.nan).to_numpy()
+                X = np.array(ds.X(exclude_id_col=False, na_replacement=None))
+                y = np.array(ds.y(na_replacement=np.nan))
             else:
-                X = ds.X(na_replacement=np.nan).to_numpy()
-                y = ds.y(na_replacement=np.nan).to_numpy()
+                X = np.array(ds.X(na_replacement=np.nan))
+                y = np.array(ds.y(na_replacement=np.nan))
 
-            n_splits = kwargs.get("n_splits", 20)
+            n_splits = 20
 
             shuff = ShuffleSplit(n_splits=n_splits, test_size=0.25, random_state=42)
             splits = list(shuff.split(X))
 
             from joblib import Parallel, delayed
 
-            models = Parallel(n_jobs=min(10, len(splits)))(
+            models = Parallel(n_jobs=10)(
                 delayed(train_func)(X, y, train_index, self._model_args())
                 for train_index, _ in splits
             )
-            evaluations = Parallel(n_jobs=min(10, len(splits)))(
+            evaluations = Parallel(n_jobs=10)(
                 delayed(evaluate_sg)(model, X, y, test_index, self.threshold)
                 for model, (_, test_index) in zip(models, splits)
             )
@@ -2586,11 +2583,11 @@ class RuleBasedRelativeReasoning(PackageBasedModel):
 
         return rbrr
 
-    def _fit_model(self, ds: RuleBasedDataset):
+    def _fit_model(self, ds: Dataset):
         X, y = ds.X(exclude_id_col=False, na_replacement=None), ds.y(na_replacement=None)
         model = RelativeReasoning(
             start_index=ds.triggered()[0],
-            end_index=ds.triggered()[-1],
+            end_index=ds.triggered()[1],
         )
         model.fit(X, y)
         return model
@@ -2600,7 +2597,7 @@ class RuleBasedRelativeReasoning(PackageBasedModel):
         return {
             "clz": "RuleBaseRelativeReasoning",
             "start_index": ds.triggered()[0],
-            "end_index": ds.triggered()[-1],
+            "end_index": ds.triggered()[1],
         }
 
     def _save_model(self, model):
@@ -2688,11 +2685,11 @@ class MLRelativeReasoning(PackageBasedModel):
 
         return mlrr
 
-    def _fit_model(self, ds: RuleBasedDataset):
+    def _fit_model(self, ds: Dataset):
         X, y = ds.X(na_replacement=np.nan), ds.y(na_replacement=np.nan)
 
         model = EnsembleClassifierChain(**s.DEFAULT_MODEL_PARAMS)
-        model.fit(X.to_numpy(), y.to_numpy())
+        model.fit(X, y)
         return model
 
     def _model_args(self):
@@ -2715,7 +2712,7 @@ class MLRelativeReasoning(PackageBasedModel):
         start = datetime.now()
         ds = self.load_dataset()
         classify_ds, classify_prods = ds.classification_dataset([smiles], self.applicable_rules)
-        pred = self.model.predict_proba(classify_ds.X().to_numpy())
+        pred = self.model.predict_proba(classify_ds.X())
 
         res = MLRelativeReasoning.combine_products_and_probs(
             self.applicable_rules, pred[0], classify_prods[0]
@@ -2760,9 +2757,7 @@ class ApplicabilityDomain(EnviPathModel):
 
     @cached_property
     def training_set_probs(self):
-        ds = self.model.load_dataset()
-        col_ids = ds.block_indices("prob")
-        return ds[:, col_ids]
+        return joblib.load(os.path.join(s.MODEL_DIR, f"{self.model.uuid}_train_probs.pkl"))
 
     def build(self):
         ds = self.model.load_dataset()
@@ -2770,9 +2765,9 @@ class ApplicabilityDomain(EnviPathModel):
         start = datetime.now()
 
         # Get Trainingset probs and dump them as they're required when using the app domain
-        probs = self.model.model.predict_proba(ds.X().to_numpy())
-        ds.add_probs(probs)
-        ds.save(os.path.join(s.MODEL_DIR, f"{self.model.uuid}_ds.pkl"))
+        probs = self.model.model.predict_proba(ds.X())
+        f = os.path.join(s.MODEL_DIR, f"{self.model.uuid}_train_probs.pkl")
+        joblib.dump(probs, f)
 
         ad = ApplicabilityDomainPCA(num_neighbours=self.num_neighbours)
         ad.build(ds)
@@ -2795,19 +2790,16 @@ class ApplicabilityDomain(EnviPathModel):
         joblib.dump(ad, f)
 
     def assess(self, structure: Union[str, "CompoundStructure"]):
-        return self.assess_batch([structure])[0]
-
-    def assess_batch(self, structures: List["CompoundStructure | str"]):
         ds = self.model.load_dataset()
 
-        smiles = []
-        for struct in structures:
-            if isinstance(struct, CompoundStructure):
-                smiles.append(structures.smiles)
-            else:
-                smiles.append(structures)
+        if isinstance(structure, CompoundStructure):
+            smiles = structure.smiles
+        else:
+            smiles = structure
 
-        assessment_ds, assessment_prods = ds.classification_dataset(structures, self.model.applicable_rules)
+        assessment_ds, assessment_prods = ds.classification_dataset(
+            [structure], self.model.applicable_rules
+        )
 
         # qualified_neighbours_per_rule is a nested dictionary structured as:
         #   {
@@ -2820,46 +2812,82 @@ class ApplicabilityDomain(EnviPathModel):
         # it identifies all training structures that have the same trigger reaction activated (i.e., value 1).
         # This is used to find "qualified neighbours" — training examples that share the same triggered feature
         # with a given assessment structure under a particular rule.
-        qualified_neighbours_per_rule: Dict = {}
+        qualified_neighbours_per_rule: Dict[int, Dict[int, List[int]]] = defaultdict(
+            lambda: defaultdict(list)
+        )
 
-        import polars as pl
-        # Select only the triggered columns
-        for i, row in enumerate(assessment_ds[:, assessment_ds.triggered()].iter_rows(named=True)):
-            # Find the rules the structure triggers. For each rule, filter the training dataset to rows that also
-            # trigger that rule.
-            train_trig = {trig_uuid.split("_")[-1]: ds.filter(pl.col(trig_uuid).eq(1))
-                          for trig_uuid, value in row.items() if value == 1}
-            qualified_neighbours_per_rule[i] = train_trig
-        rule_to_i = {str(r.uuid): i for i, r in enumerate(self.model.applicable_rules)}
+        for rule_idx, feature_index in enumerate(range(*assessment_ds.triggered())):
+            feature = ds.columns[feature_index]
+            if feature.startswith("trig_"):
+                # TODO unroll loop
+                for i, cx in enumerate(assessment_ds.X(exclude_id_col=False)):
+                    if int(cx[feature_index]) == 1:
+                        for j, tx in enumerate(ds.X(exclude_id_col=False)):
+                            if int(tx[feature_index]) == 1:
+                                qualified_neighbours_per_rule[i][rule_idx].append(j)
+
+        probs = self.training_set_probs
+        # preds = self.model.model.predict_proba(assessment_ds.X())
         preds = self.model.combine_products_and_probs(
             self.model.applicable_rules,
-            self.model.model.predict_proba(assessment_ds.X().to_numpy())[0],
+            self.model.model.predict_proba(assessment_ds.X())[0],
             assessment_prods[0],
         )
 
         assessments = list()
+
         # loop through our assessment dataset
-        for i, instance in enumerate(assessment_ds[:, assessment_ds.struct_features()]):
+        for i, instance in enumerate(assessment_ds):
             rule_reliabilities = dict()
             local_compatibilities = dict()
             neighbours_per_rule = dict()
             neighbor_probs_per_rule = dict()
 
             # loop through rule indices together with the collected neighbours indices from train dataset
-            for rule_uuid, train_instances in qualified_neighbours_per_rule[i].items():
-                # compute tanimoto distance for all neighbours and add to dataset
-                dists = self._compute_distances(assessment_ds[i, assessment_ds.struct_features()].to_numpy()[0],
-                                                train_instances[:, train_instances.struct_features()].to_numpy())
-                train_instances = train_instances.with_columns(dist=pl.Series(dists))
+            for rule_idx, vals in qualified_neighbours_per_rule[i].items():
+                # collect the train dataset instances and store it along with the index (a.k.a. row number) of the
+                # train dataset
+                train_instances = []
+                for v in vals:
+                    train_instances.append((v, ds.at(v)))
+
+                # sf is a tuple with start/end index of the features
+                sf = ds.struct_features()
+
+                # compute tanimoto distance for all neighbours
+                # result ist a list of tuples with train index and computed distance
+                dists = self._compute_distances(
+                    instance.X()[0][sf[0] : sf[1]],
+                    [ti[1].X()[0][sf[0] : sf[1]] for ti in train_instances],
+                )
+
+                dists_with_index = list()
+                for ti, dist in zip(train_instances, dists):
+                    dists_with_index.append((ti[0], dist[1]))
 
                 #  sort them in a descending way and take at most `self.num_neighbours`
-                train_instances = train_instances.sort("dist", descending=True)[:self.num_neighbours]
+                dists_with_index = sorted(dists_with_index, key=lambda x: x[1], reverse=True)
+                dists_with_index = dists_with_index[: self.num_neighbours]
+
                 # compute average distance
-                rule_reliabilities[rule_uuid] = train_instances.select(pl.mean("dist")).fill_nan(0.0).item()
+                rule_reliabilities[rule_idx] = (
+                    sum([d[1] for d in dists_with_index]) / len(dists_with_index)
+                    if len(dists_with_index) > 0
+                    else 0.0
+                )
+
                 # for local_compatibility we'll need the datasets for the indices having the highest similarity
-                local_compatibilities[rule_uuid] = self._compute_compatibility(rule_uuid, train_instances)
-                neighbours_per_rule[rule_uuid] = list(CompoundStructure.objects.filter(uuid__in=train_instances["structure_id"]))
-                neighbor_probs_per_rule[rule_uuid] = train_instances[f"prob_{rule_uuid}"].to_list()
+                neighbour_datasets = [(d[0], ds.at(d[0])) for d in dists_with_index]
+                local_compatibilities[rule_idx] = self._compute_compatibility(
+                    rule_idx, probs, neighbour_datasets
+                )
+                neighbours_per_rule[rule_idx] = [
+                    CompoundStructure.objects.get(uuid=ds[1].structure_id())
+                    for ds in neighbour_datasets
+                ]
+                neighbor_probs_per_rule[rule_idx] = [
+                    probs[d[0]][rule_idx] for d in dists_with_index
+                ]
 
             ad_res = {
                 "ad_params": {
@@ -2870,21 +2898,23 @@ class ApplicabilityDomain(EnviPathModel):
                     "local_compatibility_threshold": self.local_compatibilty_threshold,
                 },
                 "assessment": {
-                    "smiles": smiles[i],
-                    "inside_app_domain": self.pca.is_applicable(assessment_ds[i])[0],
+                    "smiles": smiles,
+                    "inside_app_domain": self.pca.is_applicable(instance)[0],
                 },
             }
 
             transformations = list()
-            for rule_uuid in rule_reliabilities.keys():
-                rule = Rule.objects.get(uuid=rule_uuid)
+            for rule_idx in rule_reliabilities.keys():
+                rule = Rule.objects.get(
+                    uuid=instance.columns[instance.observed()[0] + rule_idx].replace("obs_", "")
+                )
 
                 rule_data = rule.simple_json()
                 rule_data["image"] = f"{rule.url}?image=svg"
 
                 neighbors = []
                 for n, n_prob in zip(
-                    neighbours_per_rule[rule_uuid], neighbor_probs_per_rule[rule_uuid]
+                    neighbours_per_rule[rule_idx], neighbor_probs_per_rule[rule_idx]
                 ):
                     neighbor = n.simple_json()
                     neighbor["image"] = f"{n.url}?image=svg"
@@ -2901,14 +2931,14 @@ class ApplicabilityDomain(EnviPathModel):
 
                 transformation = {
                     "rule": rule_data,
-                    "reliability": rule_reliabilities[rule_uuid],
+                    "reliability": rule_reliabilities[rule_idx],
                     # We're setting it here to False, as we don't know whether "assess" is called during pathway
                     # prediction or from Model Page. For persisted Nodes this field will be overwritten at runtime
                     "is_predicted": False,
-                    "local_compatibility": local_compatibilities[rule_uuid],
-                    "probability": preds[rule_to_i[rule_uuid]].probability,
+                    "local_compatibility": local_compatibilities[rule_idx],
+                    "probability": preds[rule_idx].probability,
                     "transformation_products": [
-                        x.product_set for x in preds[rule_to_i[rule_uuid]].product_sets
+                        x.product_set for x in preds[rule_idx].product_sets
                     ],
                     "times_triggered": ds.times_triggered(str(rule.uuid)),
                     "neighbors": neighbors,
@@ -2926,21 +2956,32 @@ class ApplicabilityDomain(EnviPathModel):
     def _compute_distances(classify_instance: List[int], train_instances: List[List[int]]):
         from utilities.ml import tanimoto_distance
 
-        distances = [tanimoto_distance(classify_instance, train) for train in train_instances]
+        distances = [
+            (i, tanimoto_distance(classify_instance, train))
+            for i, train in enumerate(train_instances)
+        ]
         return distances
 
-    def _compute_compatibility(self, rule_idx: int, neighbours: "RuleBasedDataset"):
+    @staticmethod
+    def _compute_compatibility(rule_idx: int, preds, neighbours: List[Tuple[int, "Dataset"]]):
+        tp, tn, fp, fn = 0.0, 0.0, 0.0, 0.0
         accuracy = 0.0
-        import polars as pl
-        obs_pred = neighbours.select(obs=pl.col(f"obs_{rule_idx}").cast(pl.Boolean),
-                                     pred=pl.col(f"prob_{rule_idx}") >= self.model.threshold)
-        # Compute tp, tn, fp, fn using polars expressions
-        tp = obs_pred.filter((pl.col("obs")) & (pl.col("pred"))).height
-        tn = obs_pred.filter((~pl.col("obs")) & (~pl.col("pred"))).height
-        fp = obs_pred.filter((~pl.col("obs")) & (pl.col("pred"))).height
-        fn = obs_pred.filter((pl.col("obs")) & (~pl.col("pred"))).height
-        if tp + tn > 0.0:
-            accuracy = (tp + tn) / (tp + tn + fp + fn)
+
+        for n in neighbours:
+            obs = n[1].y()[0][rule_idx]
+            pred = preds[n[0]][rule_idx]
+            if obs and pred:
+                tp += 1
+            elif not obs and pred:
+                fp += 1
+            elif obs and not pred:
+                fn += 1
+            else:
+                tn += 1
+            # Jaccard Index
+            if tp + tn > 0.0:
+                accuracy = (tp + tn) / (tp + tn + fp + fn)
+
         return accuracy
 
 
@@ -3041,24 +3082,44 @@ class EnviFormer(PackageBasedModel):
         self.save()
 
         start = datetime.now()
-        ds = EnviFormerDataset.generate_dataset(self._get_reactions())
+        # Standardise reactions for the training data, EnviFormer ignores stereochemistry currently
+        co2 = {"C(=O)=O", "O=C=O"}
+        ds = []
+        for reaction in self._get_reactions():
+            educts = ".".join(
+                [
+                    FormatConverter.standardize(smile.smiles, remove_stereo=True)
+                    for smile in reaction.educts.all()
+                ]
+            )
+            products = ".".join(
+                [
+                    FormatConverter.standardize(smile.smiles, remove_stereo=True)
+                    for smile in reaction.products.all()
+                ]
+            )
+            if products not in co2:
+                ds.append(f"{educts}>>{products}")
 
         end = datetime.now()
         logger.debug(f"build_dataset took {(end - start).total_seconds()} seconds")
         f = os.path.join(s.MODEL_DIR, f"{self.uuid}_ds.json")
-        ds.save(f)
+        with open(f, "w") as d_file:
+            json.dump(ds, d_file)
         return ds
 
-    def load_dataset(self):
+    def load_dataset(self) -> "Dataset":
         ds_path = os.path.join(s.MODEL_DIR, f"{self.uuid}_ds.json")
-        return EnviFormerDataset.load(ds_path)
+        with open(ds_path) as d_file:
+            ds = json.load(d_file)
+        return ds
 
     def _fit_model(self, ds):
         # Call to enviFormer's fine_tune function and return the model
         from enviformer.finetune import fine_tune
 
         start = datetime.now()
-        model = fine_tune(ds.X(), ds.y(), s.MODEL_DIR, str(self.uuid), device=s.ENVIFORMER_DEVICE)
+        model = fine_tune(ds, s.MODEL_DIR, str(self.uuid), device=s.ENVIFORMER_DEVICE)
         end = datetime.now()
         logger.debug(f"EnviFormer finetuning took {(end - start).total_seconds():.2f} seconds")
         return model
@@ -3074,7 +3135,7 @@ class EnviFormer(PackageBasedModel):
         args = {"clz": "EnviFormer"}
         return args
 
-    def evaluate_model(self, multigen: bool, eval_packages: List["Package"] = None, **kwargs):
+    def evaluate_model(self, multigen: bool, eval_packages: List["Package"] = None):
         if self.model_status != self.BUILT_NOT_EVALUATED:
             raise ValueError(f"Can't evaluate a model in state {self.model_status}!")
 
@@ -3089,20 +3150,21 @@ class EnviFormer(PackageBasedModel):
         self.model_status = self.EVALUATING
         self.save()
 
-        def evaluate_sg(test_ds, predictions, model_thresh):
+        def evaluate_sg(test_reactions, predictions, model_thresh):
             # Group the true products of reactions with the same reactant together
-            assert len(test_ds) == len(predictions)
             true_dict = {}
-            for r in test_ds:
-                reactant, true_product_set = r
+            for r in test_reactions:
+                reactant, true_product_set = r.split(">>")
                 true_product_set = {p for p in true_product_set.split(".")}
                 true_dict[reactant] = true_dict.setdefault(reactant, []) + [true_product_set]
+            assert len(test_reactions) == len(predictions)
+            assert sum(len(v) for v in true_dict.values()) == len(test_reactions)
 
             # Group the predicted products of reactions with the same reactant together
             pred_dict = {}
             for k, pred in enumerate(predictions):
                 pred_smiles, pred_proba = zip(*pred.items())
-                reactant, true_product = test_ds[k, "educts"], test_ds[k, "products"]
+                reactant, true_product = test_reactions[k].split(">>")
                 pred_dict.setdefault(reactant, {"predict": [], "scores": []})
                 for smiles, proba in zip(pred_smiles, pred_proba):
                     smiles = set(smiles.split("."))
@@ -3137,7 +3199,7 @@ class EnviFormer(PackageBasedModel):
                                 break
 
             # Recall is TP (correct) / TP + FN (len(test_reactions))
-            rec = {f"{k:.2f}": v / len(test_ds) for k, v in correct.items()}
+            rec = {f"{k:.2f}": v / len(test_reactions) for k, v in correct.items()}
             # Precision is TP (correct) / TP + FP (predicted)
             prec = {
                 f"{k:.2f}": v / predicted[k] if predicted[k] > 0 else 0 for k, v in correct.items()
@@ -3216,32 +3278,47 @@ class EnviFormer(PackageBasedModel):
 
         # If there are eval packages perform single generation evaluation on them instead of random splits
         if self.eval_packages.count() > 0:
-            ds = EnviFormerDataset.generate_dataset(Reaction.objects.filter(
-                package__in=self.eval_packages.all()).distinct())
-            test_result = self.model.predict_batch(ds.X())
+            ds = []
+            for reaction in Reaction.objects.filter(
+                package__in=self.eval_packages.all()
+            ).distinct():
+                educts = ".".join(
+                    [
+                        FormatConverter.standardize(smile.smiles, remove_stereo=True)
+                        for smile in reaction.educts.all()
+                    ]
+                )
+                products = ".".join(
+                    [
+                        FormatConverter.standardize(smile.smiles, remove_stereo=True)
+                        for smile in reaction.products.all()
+                    ]
+                )
+                ds.append(f"{educts}>>{products}")
+            test_result = self.model.predict_batch([smirk.split(">>")[0] for smirk in ds])
             single_gen_result = evaluate_sg(ds, test_result, self.threshold)
             self.eval_results = self.compute_averages([single_gen_result])
         else:
             from enviformer.finetune import fine_tune
 
             ds = self.load_dataset()
-            n_splits = kwargs.get("n_splits", 20)
+            n_splits = 20
             shuff = ShuffleSplit(n_splits=n_splits, test_size=0.1, random_state=42)
 
             # Single gen eval is done in one loop of train then evaluate rather than storing all n_splits trained models
             # this helps reduce the memory footprint.
             single_gen_results = []
             for split_id, (train_index, test_index) in enumerate(shuff.split(ds)):
-                train = ds[train_index]
-                test = ds[test_index]
+                train = [ds[i] for i in train_index]
+                test = [ds[i] for i in test_index]
                 start = datetime.now()
-                model = fine_tune(train.X(), train.y(), s.MODEL_DIR, str(split_id), device=s.ENVIFORMER_DEVICE)
+                model = fine_tune(train, s.MODEL_DIR, str(split_id), device=s.ENVIFORMER_DEVICE)
                 end = datetime.now()
                 logger.debug(
                     f"EnviFormer finetuning took {(end - start).total_seconds():.2f} seconds"
                 )
                 model.to(s.ENVIFORMER_DEVICE)
-                test_result = model.predict_batch(test.X())
+                test_result = model.predict_batch([smirk.split(">>")[0] for smirk in test])
                 single_gen_results.append(evaluate_sg(test, test_result, self.threshold))
 
             self.eval_results = self.compute_averages(single_gen_results)
@@ -3312,15 +3389,31 @@ class EnviFormer(PackageBasedModel):
                     for pathway in train_pathways:
                         for reaction in pathway.edges:
                             reaction = reaction.edge_label
-                            if any([educt in test_educts for educt in reaction_to_educts[str(reaction.uuid)]]):
+                            if any(
+                                [
+                                    educt in test_educts
+                                    for educt in reaction_to_educts[str(reaction.uuid)]
+                                ]
+                            ):
                                 overlap += 1
                                 continue
-                            train_reactions.append(reaction)
-                    train_ds = EnviFormerDataset.generate_dataset(train_reactions)
+                            educts = ".".join(
+                                [
+                                    FormatConverter.standardize(smile.smiles, remove_stereo=True)
+                                    for smile in reaction.educts.all()
+                                ]
+                            )
+                            products = ".".join(
+                                [
+                                    FormatConverter.standardize(smile.smiles, remove_stereo=True)
+                                    for smile in reaction.products.all()
+                                ]
+                            )
+                            train_reactions.append(f"{educts}>>{products}")
                     logging.debug(
                         f"{overlap} compounds had to be removed from multigen split due to overlap within pathways"
                     )
-                    model = fine_tune(train_ds.X(), train_ds.y(), s.MODEL_DIR, f"mg_{split_id}")
+                    model = fine_tune(train_reactions, s.MODEL_DIR, f"mg_{split_id}")
                     multi_gen_results.append(evaluate_mg(model, test_pathways, self.threshold))
 
                 self.eval_results.update(

epdb/tasks.py

@@ -172,6 +172,7 @@ def predict(
 
     except Exception as e:
         pw.kv.update({"status": "failed"})
+        pw.kv.update(**{"error": str(e)})
         pw.save()
 
         if JobLog.objects.filter(task_id=self.request.id).exists():

epdb/views.py

@@ -237,7 +237,6 @@ def get_base_context(request, for_user=None) -> Dict[str, Any]:
             "enabled_features": s.FLAGS,
             "debug": s.DEBUG,
             "external_databases": ExternalDatabase.get_databases(),
-            "site_id": s.MATOMO_SITE_ID,
         },
     }
 
@@ -892,7 +891,7 @@ def package_model(request, package_uuid, model_uuid):
                 return JsonResponse(res, safe=False)
 
             else:
-                app_domain_assessment = current_model.app_domain.assess(stand_smiles)
+                app_domain_assessment = current_model.app_domain.assess(stand_smiles)[0]
                 return JsonResponse(app_domain_assessment, safe=False)
 
         context = get_base_context(request)

pyproject.toml

@@ -27,11 +27,10 @@ dependencies = [
     "scikit-learn>=1.6.1",
     "sentry-sdk[django]>=2.32.0",
     "setuptools>=80.8.0",
-    "polars==1.35.1",
 ]
 
 [tool.uv.sources]
-enviformer = { git = "ssh://git@git.envipath.com/enviPath/enviformer.git", rev = "v0.1.4" }
+enviformer = { git = "ssh://git@git.envipath.com/enviPath/enviformer.git", rev = "v0.1.2" }
 envipy-plugins = { git = "ssh://git@git.envipath.com/enviPath/enviPy-plugins.git", rev = "v0.1.0" }
 envipy-additional-information = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git", rev = "v0.1.7"}
 envipy-ambit = { git = "ssh://git@git.envipath.com/enviPath/enviPy-ambit.git" }

templates/framework.html

@@ -56,7 +56,7 @@
             (function () {
                 var u = "//matomo.envipath.com/";
                 _paq.push(['setTrackerUrl', u + 'matomo.php']);
-                _paq.push(['setSiteId', '{{ meta.site_id }}']);
+                _paq.push(['setSiteId', '10']);
                 var d = document, g = d.createElement('script'), s = d.getElementsByTagName('script')[0];
                 g.async = true;
                 g.src = u + 'matomo.js';

tests/test_dataset.py

@@ -1,10 +1,8 @@
-import os.path
-from tempfile import TemporaryDirectory
 from django.test import TestCase
+
 from epdb.logic import PackageManager
-from epdb.models import Reaction, Compound, User, Rule, Package
-from utilities.chem import FormatConverter
-from utilities.ml import RuleBasedDataset, EnviFormerDataset
+from epdb.models import Reaction, Compound, User, Rule
+from utilities.ml import Dataset
 
 
 class DatasetTest(TestCase):
@@ -43,108 +41,12 @@ class DatasetTest(TestCase):
         super(DatasetTest, cls).setUpClass()
         cls.user = User.objects.get(username="anonymous")
         cls.package = PackageManager.create_package(cls.user, "Anon Test Package", "No Desc")
-        cls.BBD_SUBSET = Package.objects.get(name="Fixtures")
 
-    def test_generate_dataset(self):
-        """Test generating dataset does not crash"""
-        self.generate_rule_dataset()
-
-    def test_indexing(self):
-        """Test indexing a few different ways to check for crashes"""
-        ds, reactions, rules = self.generate_rule_dataset()
-        print(ds[5])
-        print(ds[2, 5])
-        print(ds[3:6, 2:8])
-        print(ds[:2, "structure_id"])
-
-    def test_add_rows(self):
-        """Test adding one row and adding multiple rows"""
-        ds, reactions, rules = self.generate_rule_dataset()
-        ds.add_row(list(ds.df.row(1)))
-        ds.add_rows([list(ds.df.row(i)) for i in range(5)])
-
-    def test_times_triggered(self):
-        """Check getting times triggered for a rule id"""
-        ds, reactions, rules = self.generate_rule_dataset()
-        print(ds.times_triggered(rules[0].uuid))
-
-    def test_block_indices(self):
-        """Test the usages of _block_indices"""
-        ds, reactions, rules = self.generate_rule_dataset()
-        print(ds.struct_features())
-        print(ds.triggered())
-        print(ds.observed())
-
-    def test_structure_id(self):
-        """Check getting a structure id from row index"""
-        ds, reactions, rules = self.generate_rule_dataset()
-        print(ds.structure_id(0))
-
-    def test_x(self):
-        """Test getting X portion of the dataframe"""
-        ds, reactions, rules = self.generate_rule_dataset()
-        print(ds.X().df.head())
-
-    def test_trig(self):
-        """Test getting the triggered portion of the dataframe"""
-        ds, reactions, rules = self.generate_rule_dataset()
-        print(ds.trig().df.head())
-
-    def test_y(self):
-        """Test getting the Y portion of the dataframe"""
-        ds, reactions, rules = self.generate_rule_dataset()
-        print(ds.y().df.head())
-
-    def test_classification_dataset(self):
-        """Test making the classification dataset"""
-        ds, reactions, rules = self.generate_rule_dataset()
-        compounds = [c.default_structure for c in Compound.objects.filter(package=self.BBD_SUBSET)]
-        class_ds, products = ds.classification_dataset(compounds, rules)
-        print(class_ds.df.head(5))
-        print(products[:5])
-
-    def test_extra_features(self):
-        reactions = [r for r in Reaction.objects.filter(package=self.BBD_SUBSET)]
-        applicable_rules = [r for r in Rule.objects.filter(package=self.BBD_SUBSET)]
-        ds = RuleBasedDataset.generate_dataset(reactions, applicable_rules, feat_funcs=[FormatConverter.maccs, FormatConverter.morgan])
-        print(ds.shape)
-
-    def test_to_arff(self):
-        """Test exporting the arff version of the dataset"""
-        ds, reactions, rules = self.generate_rule_dataset()
-        ds.to_arff("dataset_arff_test.arff")
-
-    def test_save_load(self):
-        """Test saving and loading dataset"""
-        with TemporaryDirectory() as tmpdir:
-            ds, reactions, rules = self.generate_rule_dataset()
-            ds.save(os.path.join(tmpdir, "save_dataset.pkl"))
-            ds_loaded = RuleBasedDataset.load(os.path.join(tmpdir, "save_dataset.pkl"))
-            self.assertTrue(ds.df.equals(ds_loaded.df))
-
-    def test_dataset_example(self):
-        """Test with a concrete example checking dataset size"""
+    def test_smoke(self):
         reactions = [r for r in Reaction.objects.filter(package=self.package)]
         applicable_rules = [self.rule1]
 
-        ds = RuleBasedDataset.generate_dataset(reactions, applicable_rules)
+        ds = Dataset.generate_dataset(reactions, applicable_rules)
 
         self.assertEqual(len(ds.y()), 1)
-        self.assertEqual(ds.y().df.item(), 1)
-
-    def test_enviformer_dataset(self):
-        ds, reactions = self.generate_enviformer_dataset()
-        print(ds.X().head())
-        print(ds.y().head())
-
-    def generate_rule_dataset(self):
-        """Generate a RuleBasedDataset from test package data"""
-        reactions = [r for r in Reaction.objects.filter(package=self.BBD_SUBSET)]
-        applicable_rules = [r for r in Rule.objects.filter(package=self.BBD_SUBSET)]
-        ds = RuleBasedDataset.generate_dataset(reactions, applicable_rules)
-        return ds, reactions, applicable_rules
-
-    def generate_enviformer_dataset(self):
-        reactions = [r for r in Reaction.objects.filter(package=self.BBD_SUBSET)]
-        ds = EnviFormerDataset.generate_dataset(reactions)
-        return ds, reactions
+        self.assertEqual(sum(ds.y()[0]), 1)

tests/test_enviformer.py

@@ -42,11 +42,13 @@ class EnviFormerTest(TestCase):
                 threshold = float(0.5)
                 data_package_objs = [self.BBD_SUBSET]
                 eval_packages_objs = [self.BBD_SUBSET]
-                mod = EnviFormer.create(self.package, data_package_objs, threshold=threshold)
+                mod = EnviFormer.create(
+                    self.package, data_package_objs, eval_packages_objs, threshold=threshold
+                )
 
                 mod.build_dataset()
                 mod.build_model()
-                mod.evaluate_model(True, eval_packages_objs, n_splits=2)
+                mod.evaluate_model(True, eval_packages_objs)
 
                 mod.predict("CCN(CC)C(=O)C1=CC(=CC=C1)C")
 
@@ -55,9 +57,12 @@ class EnviFormerTest(TestCase):
             with self.settings(MODEL_DIR=tmpdir):
                 threshold = float(0.5)
                 data_package_objs = [self.BBD_SUBSET]
+                eval_packages_objs = [self.BBD_SUBSET]
                 mods = []
                 for _ in range(4):
-                    mod = EnviFormer.create(self.package, data_package_objs, threshold=threshold)
+                    mod = EnviFormer.create(
+                        self.package, data_package_objs, eval_packages_objs, threshold=threshold
+                    )
                     mod.build_dataset()
                     mod.build_model()
                     mods.append(mod)
@@ -68,11 +73,15 @@ class EnviFormerTest(TestCase):
 
                 # Test pathway prediction
                 times = [measure_predict(mods[1], self.BBD_SUBSET.pathways[0].pk) for _ in range(5)]
-                print(f"First pathway prediction took {times[0]} seconds, subsequent ones took {times[1:]}")
+                print(
+                    f"First pathway prediction took {times[0]} seconds, subsequent ones took {times[1:]}"
+                )
 
                 # Test eviction by performing three prediction with every model, twice.
                 times = defaultdict(list)
-                for _ in range(2):  # Eviction should cause the second iteration here to have to reload the models
+                for _ in range(
+                    2
+                ):  # Eviction should cause the second iteration here to have to reload the models
                     for mod in mods:
                         for _ in range(3):
                             times[mod.pk].append(measure_predict(mod))

tests/test_model.py

@@ -4,7 +4,7 @@ import numpy as np
 from django.test import TestCase
 
 from epdb.logic import PackageManager
-from epdb.models import User, MLRelativeReasoning, Package, RuleBasedRelativeReasoning
+from epdb.models import User, MLRelativeReasoning, Package
 
 
 class ModelTest(TestCase):
@@ -17,7 +17,7 @@ class ModelTest(TestCase):
         cls.package = PackageManager.create_package(cls.user, "Anon Test Package", "No Desc")
         cls.BBD_SUBSET = Package.objects.get(name="Fixtures")
 
-    def test_mlrr(self):
+    def test_smoke(self):
         with TemporaryDirectory() as tmpdir:
             with self.settings(MODEL_DIR=tmpdir):
                 threshold = float(0.5)
@@ -35,9 +35,21 @@ class ModelTest(TestCase):
                     description="Created MLRelativeReasoning in Testcase",
                 )
 
+                # mod = RuleBasedRelativeReasoning.create(
+                #     self.package,
+                #     rule_package_objs,
+                #     data_package_objs,
+                #     eval_packages_objs,
+                #     threshold=threshold,
+                #     min_count=5,
+                #     max_count=0,
+                #     name='ECC - BBD - 0.5',
+                #     description='Created MLRelativeReasoning in Testcase',
+                # )
+
                 mod.build_dataset()
                 mod.build_model()
-                mod.evaluate_model(True, eval_packages_objs, n_splits=2)
+                mod.evaluate_model(True, eval_packages_objs)
 
                 results = mod.predict("CCN(CC)C(=O)C1=CC(=CC=C1)C")
 
@@ -58,57 +70,3 @@ class ModelTest(TestCase):
 
                 # from pprint import pprint
                 # pprint(mod.eval_results)
-
-    def test_applicability(self):
-        with TemporaryDirectory() as tmpdir:
-            with self.settings(MODEL_DIR=tmpdir):
-                threshold = float(0.5)
-
-                rule_package_objs = [self.BBD_SUBSET]
-                data_package_objs = [self.BBD_SUBSET]
-                eval_packages_objs = [self.BBD_SUBSET]
-
-                mod = MLRelativeReasoning.create(
-                    self.package,
-                    rule_package_objs,
-                    data_package_objs,
-                    threshold=threshold,
-                    name="ECC - BBD - 0.5",
-                    description="Created MLRelativeReasoning in Testcase",
-                    build_app_domain=True,  # To test the applicability domain this must be True
-                    app_domain_num_neighbours=5,
-                    app_domain_local_compatibility_threshold=0.5,
-                    app_domain_reliability_threshold=0.5,
-                )
-
-                mod.build_dataset()
-                mod.build_model()
-                mod.evaluate_model(True, eval_packages_objs, n_splits=2)
-
-                results = mod.predict("CCN(CC)C(=O)C1=CC(=CC=C1)C")
-
-    def test_rbrr(self):
-        with TemporaryDirectory() as tmpdir:
-            with self.settings(MODEL_DIR=tmpdir):
-                threshold = float(0.5)
-
-                rule_package_objs = [self.BBD_SUBSET]
-                data_package_objs = [self.BBD_SUBSET]
-                eval_packages_objs = [self.BBD_SUBSET]
-
-                mod = RuleBasedRelativeReasoning.create(
-                    self.package,
-                    rule_package_objs,
-                    data_package_objs,
-                    threshold=threshold,
-                    min_count=5,
-                    max_count=0,
-                    name='ECC - BBD - 0.5',
-                    description='Created MLRelativeReasoning in Testcase',
-                )
-
-                mod.build_dataset()
-                mod.build_model()
-                mod.evaluate_model(True, eval_packages_objs, n_splits=2)
-
-                results = mod.predict("CCN(CC)C(=O)C1=CC(=CC=C1)C")

utilities/chem.py

@@ -2,12 +2,13 @@ import logging
 import re
 from abc import ABC
 from collections import defaultdict
-from typing import List, Optional, Dict, TYPE_CHECKING
+from typing import List, Optional, Dict, TYPE_CHECKING, Union
 
 from indigo import Indigo, IndigoException, IndigoObject
 from indigo.renderer import IndigoRenderer
 from rdkit import Chem, rdBase
-from rdkit.Chem import MACCSkeys, Descriptors, rdFingerprintGenerator
+from rdkit.Chem import MACCSkeys, Descriptors
+from rdkit.Chem import rdchem
 from rdkit.Chem import rdChemReactions
 from rdkit.Chem.Draw import rdMolDraw2D
 from rdkit.Chem.MolStandardize import rdMolStandardize
@@ -90,8 +91,15 @@ class FormatConverter(object):
         return Chem.MolToSmiles(mol, canonical=canonical)
 
     @staticmethod
-    def InChIKey(smiles):
-        return Chem.MolToInchiKey(FormatConverter.from_smiles(smiles))
+    def InChIKey(mol_or_smiles: Union[rdchem.Mol | str]):
+        if isinstance(mol_or_smiles, str):
+            mol_or_smiles = mol_or_smiles.replace("~", "")
+            mol_or_smiles = FormatConverter.from_smiles(mol_or_smiles)
+
+        if mol_or_smiles is None:
+            return None
+
+        return Chem.MolToInchiKey(mol_or_smiles)
 
     @staticmethod
     def InChI(smiles):
@@ -107,13 +115,6 @@ class FormatConverter(object):
         bitvec = MACCSkeys.GenMACCSKeys(mol)
         return bitvec.ToList()
 
-    @staticmethod
-    def morgan(smiles, radius=3, fpSize=2048):
-        finger_gen = rdFingerprintGenerator.GetMorganGenerator(radius=radius, fpSize=fpSize)
-        mol = Chem.MolFromSmiles(smiles)
-        fp = finger_gen.GetFingerprint(mol)
-        return fp.ToList()
-
     @staticmethod
     def get_functional_groups(smiles: str) -> List[str]:
         res = list()
@@ -295,7 +296,8 @@ class FormatConverter(object):
                             product = GetMolFrags(product, asMols=True)
                             for p in product:
                                 p = FormatConverter.standardize(
-                                    Chem.MolToSmiles(p), remove_stereo=remove_stereo
+                                    Chem.MolToSmiles(p).replace("~", ""),
+                                    remove_stereo=remove_stereo,
                                 )
                                 prods.append(p)
 

utilities/misc.py

@@ -35,6 +35,7 @@ from epdb.models import (
     RuleBasedRelativeReasoning,
     Scenario,
     SequentialRule,
+    Setting,
     SimpleAmbitRule,
     SimpleRDKitRule,
     SimpleRule,
@@ -1258,3 +1259,46 @@ class PathwayUtils:
                 res[edge.url] = rule_chain
 
         return res
+
+    def _find_intermediates(self, data_pathway, pred_pathway):
+        pass
+
+    def engineer(self, setting: "Setting"):
+        from epdb.logic import SPathway
+
+        # get a fresh copy
+        pw = Pathway.objects.get(id=self.pathway.pk)
+
+        root_nodes = [n.default_node_label.smiles for n in pw.root_nodes]
+
+        if len(root_nodes) != 1:
+            logger.warning(f"Pathway {pw.name} has {len(root_nodes)} root nodes")
+            return
+
+        spw = SPathway(root_nodes[0], None, setting)
+
+        level = 0
+        while not spw.done:
+            spw.predict_step(from_depth=level)
+            level += 1
+
+        # Generate Node / SMILES mapping
+        node_mapping = {}
+        from utilities.chem import FormatConverter
+
+        for node in pw.nodes:
+            for snode in spw.smiles_to_node.values():
+                data_smiles = node.default_node_label.smiles
+                pred_smiles = snode.smiles
+
+                data_key = FormatConverter.InChIKey(data_smiles.replace("~", ""))
+                pred_key = FormatConverter.InChIKey(pred_smiles.replace("~", ""))
+
+                if data_key == pred_key:
+                    node_mapping[snode] = node
+
+        print(node_mapping)
+
+        return spw
+
+        pass

utilities/ml.py

@@ -5,14 +5,11 @@ import logging
 from collections import defaultdict
 from datetime import datetime
 from pathlib import Path
-from typing import List, Dict, Set, Tuple, TYPE_CHECKING, Callable
-from abc import ABC, abstractmethod
+from typing import List, Dict, Set, Tuple, TYPE_CHECKING
 
 import networkx as nx
 import numpy as np
-from envipy_plugins import Descriptor
 from numpy.random import default_rng
-import polars as pl
 from sklearn.base import BaseEstimator, ClassifierMixin
 from sklearn.decomposition import PCA
 from sklearn.dummy import DummyClassifier
@@ -29,281 +26,70 @@ if TYPE_CHECKING:
     from epdb.models import Rule, CompoundStructure, Reaction
 
 
-class Dataset(ABC):
-    def __init__(self, columns: List[str] = None, data: List[List[str | int | float]] | pl.DataFrame = None):
-        if isinstance(data, pl.DataFrame):  # Allows for re-creation of self in cases like indexing with __getitem__
-            self.df = data
+class Dataset:
+    def __init__(
+        self, columns: List[str], num_labels: int, data: List[List[str | int | float]] = None
+    ):
+        self.columns: List[str] = columns
+        self.num_labels: int = num_labels
+
+        if data is None:
+            self.data: List[List[str | int | float]] = list()
         else:
-            # Build either an empty dataframe with columns or fill it with list of list data
-            if data is not None and len(columns) != len(data[0]):
-                raise ValueError(f"Header and Data are not aligned {len(columns)} columns vs. {len(data[0])} columns")
-            if columns is None:
-                raise ValueError("Columns can't be None if data is not already a DataFrame")
-            self.df = pl.DataFrame(data=data, schema=columns, orient="row", infer_schema_length=None)
+            self.data = data
 
-    def add_rows(self, rows: List[List[str | int | float]]):
-        """Add rows to the dataset. Extends the polars dataframe stored in self"""
-        if len(self.columns) != len(rows[0]):
-            raise ValueError(f"Header and Data are not aligned {len(self.columns)} columns vs. {len(rows[0])} columns")
-        new_rows = pl.DataFrame(data=rows, schema=self.columns, orient="row", infer_schema_length=None)
-        self.df.extend(new_rows)
+        self.num_features: int = len(columns) - self.num_labels
+        self._struct_features: Tuple[int, int] = self._block_indices("feature_")
+        self._triggered: Tuple[int, int] = self._block_indices("trig_")
+        self._observed: Tuple[int, int] = self._block_indices("obs_")
 
-    def add_row(self, row: List[str | int | float]):
-        """See add_rows"""
-        self.add_rows([row])
-
-    def block_indices(self, prefix) -> List[int]:
-        """Find the indexes in column labels that has the prefix"""
+    def _block_indices(self, prefix) -> Tuple[int, int]:
         indices: List[int] = []
         for i, feature in enumerate(self.columns):
             if feature.startswith(prefix):
                 indices.append(i)
-        return indices
 
-    @property
-    def columns(self) -> List[str]:
-        """Use the polars dataframe columns"""
-        return self.df.columns
+        return min(indices), max(indices)
 
-    @property
-    def shape(self):
-        return self.df.shape
+    def structure_id(self):
+        return self.data[0][0]
 
-    @abstractmethod
-    def X(self, **kwargs):
-        pass
-
-    @abstractmethod
-    def y(self, **kwargs):
-        pass
-
-    @staticmethod
-    @abstractmethod
-    def generate_dataset(reactions, *args, **kwargs):
-        pass
-
-    def __iter__(self):
-        """Use polars iter_rows for iterating over the dataset"""
-        return self.df.iter_rows()
-
-    def __getitem__(self, item):
-        """Item is passed to polars allowing for advanced indexing.
-        See https://docs.pola.rs/api/python/stable/reference/dataframe/api/polars.DataFrame.__getitem__.html#polars.DataFrame.__getitem__"""
-        res = self.df[item]
-        if isinstance(res, pl.DataFrame):  # If we get a dataframe back from indexing make new self with res dataframe
-            return self.__class__(data=res)
-        else:  # If we don't get a dataframe back (likely base type, int, str, float etc.) return the item
-            return res
-
-    def save(self, path: "Path | str"):
-        import pickle
-
-        with open(path, "wb") as fh:
-            pickle.dump(self, fh)
-
-    @staticmethod
-    def load(path: "str | Path") -> "Dataset":
-        import pickle
-
-        return pickle.load(open(path, "rb"))
-
-    def to_numpy(self):
-        return self.df.to_numpy()
-
-    def __repr__(self):
-        return (
-            f"<{self.__class__.__name__} #rows={len(self.df)} #cols={len(self.columns)}>"
-        )
-
-    def __len__(self):
-        return len(self.df)
-
-    def iter_rows(self, named=False):
-        return self.df.iter_rows(named=named)
-
-    def filter(self, *predicates, **constraints):
-        return self.__class__(data=self.df.filter(*predicates, **constraints))
-
-    def select(self, *exprs, **named_exprs):
-        return self.__class__(data=self.df.select(*exprs, **named_exprs))
-
-    def with_columns(self, *exprs, **name_exprs):
-        return self.__class__(data=self.df.with_columns(*exprs, **name_exprs))
-
-    def sort(self, by, *more_by, descending=False, nulls_last=False, multithreaded=True, maintain_order=False):
-        return self.__class__(data=self.df.sort(by, *more_by, descending=descending, nulls_last=nulls_last,
-                                                multithreaded=multithreaded, maintain_order=maintain_order))
-
-    def item(self, row=None, column=None):
-        return self.df.item(row, column)
-
-    def fill_nan(self, value):
-        return self.__class__(data=self.df.fill_nan(value))
-
-    @property
-    def height(self):
-        return self.df.height
-
-
-class RuleBasedDataset(Dataset):
-    def __init__(self, num_labels=None, columns=None, data=None):
-        super().__init__(columns, data)
-        # Calculating num_labels allows functions like getitem to be in the base Dataset as it unifies the init.
-        self.num_labels: int = num_labels if num_labels else sum([1 for c in self.columns if "obs_" in c])
-        # Pre-calculate the ids of columns for features/labels, useful later in X and y
-        self._struct_features: List[int] = self.block_indices("feature_")
-        self._triggered: List[int] = self.block_indices("trig_")
-        self._observed: List[int] = self.block_indices("obs_")
-        self.feature_cols: List[int] = self._struct_features + self._triggered
-        self.num_features: int = len(self.feature_cols)
-        self.has_probs = False
+    def add_row(self, row: List[str | int | float]):
+        if len(self.columns) != len(row):
+            raise ValueError(f"Header and Data are not aligned {len(self.columns)} vs. {len(row)}")
+        self.data.append(row)
 
     def times_triggered(self, rule_uuid) -> int:
-        """Count how many times a rule is triggered by the number of rows with one in the rules trig column"""
-        return self.df.filter(pl.col(f"trig_{rule_uuid}") == 1).height
+        idx = self.columns.index(f"trig_{rule_uuid}")
 
-    def struct_features(self) -> List[int]:
+        times_triggered = 0
+        for row in self.data:
+            if row[idx] == 1:
+                times_triggered += 1
+
+        return times_triggered
+
+    def struct_features(self) -> Tuple[int, int]:
         return self._struct_features
 
-    def triggered(self) -> List[int]:
+    def triggered(self) -> Tuple[int, int]:
         return self._triggered
 
-    def observed(self) -> List[int]:
+    def observed(self) -> Tuple[int, int]:
         return self._observed
 
-    def structure_id(self, index: int):
-        """Get the UUID of a compound"""
-        return self.item(index, "structure_id")
+    def at(self, position: int) -> Dataset:
+        return Dataset(self.columns, self.num_labels, [self.data[position]])
 
-    def X(self, exclude_id_col=True, na_replacement=0):
-        """Get all the feature and trig columns"""
-        _col_ids = self.feature_cols
-        if not exclude_id_col:
-            _col_ids = [0] + _col_ids
-        res = self[:, _col_ids]
-        if na_replacement is not None:
-            res.df = res.df.fill_null(na_replacement)
-        return res
+    def limit(self, limit: int) -> Dataset:
+        return Dataset(self.columns, self.num_labels, self.data[:limit])
 
-    def trig(self, na_replacement=0):
-        """Get all the trig columns"""
-        res = self[:, self._triggered]
-        if na_replacement is not None:
-            res.df = res.df.fill_null(na_replacement)
-        return res
-
-    def y(self, na_replacement=0):
-        """Get all the obs columns"""
-        res = self[:, self._observed]
-        if na_replacement is not None:
-            res.df = res.df.fill_null(na_replacement)
-        return res
-
-    @staticmethod
-    def generate_dataset(reactions, applicable_rules, educts_only=True, feat_funcs: List["Callable | Descriptor"]=None):
-        if feat_funcs is None:
-            feat_funcs = [FormatConverter.maccs]
-        _structures = set()  # Get all the structures
-        for r in reactions:
-            _structures.update(r.educts.all())
-            if not educts_only:
-                _structures.update(r.products.all())
-
-        compounds = sorted(_structures, key=lambda x: x.url)
-        triggered: Dict[str, Set[str]] = defaultdict(set)
-        observed: Set[str] = set()
-
-        # Apply rules on collected compounds and store tps
-        for i, comp in enumerate(compounds):
-            logger.debug(f"{i + 1}/{len(compounds)}...")
-
-            for rule in applicable_rules:
-                product_sets = rule.apply(comp.smiles)
-                if len(product_sets) == 0:
-                    continue
-
-                key = f"{rule.uuid} + {comp.uuid}"
-                if key in triggered:
-                    logger.info(f"{key} already present. Duplicate reaction?")
-
-                for prod_set in product_sets:
-                    for smi in prod_set:
-                        try:
-                            smi = FormatConverter.standardize(smi, remove_stereo=True)
-                        except Exception:
-                            logger.debug(f"Standardizing SMILES failed for {smi}")
-                        triggered[key].add(smi)
-
-        for i, r in enumerate(reactions):
-            logger.debug(f"{i + 1}/{len(reactions)}...")
-
-            if len(r.educts.all()) != 1:
-                logger.debug(f"Skipping {r.url} as it has {len(r.educts.all())} substrates!")
-                continue
-
-            for comp in r.educts.all():
-                for rule in applicable_rules:
-                    key = f"{rule.uuid} + {comp.uuid}"
-                    if key not in triggered:
-                        continue
-
-                    # standardize products from reactions for comparison
-                    standardized_products = []
-                    for cs in r.products.all():
-                        smi = cs.smiles
-                        try:
-                            smi = FormatConverter.standardize(smi, remove_stereo=True)
-                        except Exception as e:
-                            logger.debug(f"Standardizing SMILES failed for {smi}")
-                        standardized_products.append(smi)
-                    if len(set(standardized_products).difference(triggered[key])) == 0:
-                        observed.add(key)
-        feat_columns = []
-        for feat_func in feat_funcs:
-            if isinstance(feat_func, Descriptor):
-                feats = feat_func.get_molecule_descriptors(compounds[0].smiles)
-            else:
-                feats = feat_func(compounds[0].smiles)
-            start_i = len(feat_columns)
-            feat_columns.extend([f"feature_{start_i + i}" for i, _ in enumerate(feats)])
-        ds_columns = (["structure_id"] +
-                      feat_columns +
-                      [f"trig_{r.uuid}" for r in applicable_rules] +
-                      [f"obs_{r.uuid}" for r in applicable_rules])
-        rows = []
-
-        for i, comp in enumerate(compounds):
-            # Features
-            feats = []
-            for feat_func in feat_funcs:
-                if isinstance(feat_func, Descriptor):
-                    feat = feat_func.get_molecule_descriptors(comp.smiles)
-                else:
-                    feat = feat_func(comp.smiles)
-                feats.extend(feat)
-            trig = []
-            obs = []
-            for rule in applicable_rules:
-                key = f"{rule.uuid} + {comp.uuid}"
-                # Check triggered
-                if key in triggered:
-                    trig.append(1)
-                else:
-                    trig.append(0)
-                # Check obs
-                if key in observed:
-                    obs.append(1)
-                elif key not in triggered:
-                    obs.append(None)
-                else:
-                    obs.append(0)
-            rows.append([str(comp.uuid)] + feats + trig + obs)
-        ds = RuleBasedDataset(len(applicable_rules), ds_columns, data=rows)
-        return ds
+    def __iter__(self):
+        return (self.at(i) for i, _ in enumerate(self.data))
 
     def classification_dataset(
         self, structures: List[str | "CompoundStructure"], applicable_rules: List["Rule"]
-    ) -> Tuple[RuleBasedDataset, List[List[PredictionResult]]]:
+    ) -> Tuple[Dataset, List[List[PredictionResult]]]:
         classify_data = []
         classify_products = []
         for struct in structures:
@@ -327,18 +113,186 @@ class RuleBasedDataset(Dataset):
                 else:
                     trig.append(0)
                     prods.append([])
-            new_row = [struct_id] + features + trig + ([-1] * len(trig))
-            if self.has_probs:
-                new_row += [-1] * len(trig)
-            classify_data.append(new_row)
-            classify_products.append(prods)
-        ds = RuleBasedDataset(len(applicable_rules), self.columns, data=classify_data)
-        return ds, classify_products
 
-    def add_probs(self, probs):
-        col_names = [f"prob_{self.columns[r_id].split('_')[-1]}" for r_id in self._observed]
-        self.df = self.df.with_columns(*[pl.Series(name, probs[:, j]) for j, name in enumerate(col_names)])
-        self.has_probs = True
+            classify_data.append([struct_id] + features + trig + ([-1] * len(trig)))
+            classify_products.append(prods)
+
+        return Dataset(
+            columns=self.columns, num_labels=self.num_labels, data=classify_data
+        ), classify_products
+
+    @staticmethod
+    def generate_dataset(
+        reactions: List["Reaction"], applicable_rules: List["Rule"], educts_only: bool = True
+    ) -> Dataset:
+        _structures = set()
+
+        for r in reactions:
+            for e in r.educts.all():
+                _structures.add(e)
+
+            if not educts_only:
+                for e in r.products:
+                    _structures.add(e)
+
+        compounds = sorted(_structures, key=lambda x: x.url)
+
+        triggered: Dict[str, Set[str]] = defaultdict(set)
+        observed: Set[str] = set()
+
+        # Apply rules on collected compounds and store tps
+        for i, comp in enumerate(compounds):
+            logger.debug(f"{i + 1}/{len(compounds)}...")
+
+            for rule in applicable_rules:
+                product_sets = rule.apply(comp.smiles)
+
+                if len(product_sets) == 0:
+                    continue
+
+                key = f"{rule.uuid} + {comp.uuid}"
+
+                if key in triggered:
+                    logger.info(f"{key} already present. Duplicate reaction?")
+
+                for prod_set in product_sets:
+                    for smi in prod_set:
+                        try:
+                            smi = FormatConverter.standardize(smi, remove_stereo=True)
+                        except Exception:
+                            # :shrug:
+                            logger.debug(f"Standardizing SMILES failed for {smi}")
+                            pass
+
+                        triggered[key].add(smi)
+
+        for i, r in enumerate(reactions):
+            logger.debug(f"{i + 1}/{len(reactions)}...")
+
+            if len(r.educts.all()) != 1:
+                logger.debug(f"Skipping {r.url} as it has {len(r.educts.all())} substrates!")
+                continue
+
+            for comp in r.educts.all():
+                for rule in applicable_rules:
+                    key = f"{rule.uuid} + {comp.uuid}"
+
+                    if key not in triggered:
+                        continue
+
+                    # standardize products from reactions for comparison
+                    standardized_products = []
+                    for cs in r.products.all():
+                        smi = cs.smiles
+
+                        try:
+                            smi = FormatConverter.standardize(smi, remove_stereo=True)
+                        except Exception as e:
+                            # :shrug:
+                            logger.debug(f"Standardizing SMILES failed for {smi}")
+                            pass
+
+                        standardized_products.append(smi)
+
+                    if len(set(standardized_products).difference(triggered[key])) == 0:
+                        observed.add(key)
+                    else:
+                        pass
+
+        ds = None
+
+        for i, comp in enumerate(compounds):
+            # Features
+            feat = FormatConverter.maccs(comp.smiles)
+            trig = []
+            obs = []
+
+            for rule in applicable_rules:
+                key = f"{rule.uuid} + {comp.uuid}"
+
+                # Check triggered
+                if key in triggered:
+                    trig.append(1)
+                else:
+                    trig.append(0)
+
+                # Check obs
+                if key in observed:
+                    obs.append(1)
+                elif key not in triggered:
+                    obs.append(None)
+                else:
+                    obs.append(0)
+
+            if ds is None:
+                header = (
+                    ["structure_id"]
+                    + [f"feature_{i}" for i, _ in enumerate(feat)]
+                    + [f"trig_{r.uuid}" for r in applicable_rules]
+                    + [f"obs_{r.uuid}" for r in applicable_rules]
+                )
+                ds = Dataset(header, len(applicable_rules))
+
+            ds.add_row([str(comp.uuid)] + feat + trig + obs)
+
+        return ds
+
+    def X(self, exclude_id_col=True, na_replacement=0):
+        res = self.__getitem__(
+            (slice(None), slice(1 if exclude_id_col else 0, len(self.columns) - self.num_labels))
+        )
+        if na_replacement is not None:
+            res = [[x if x is not None else na_replacement for x in row] for row in res]
+        return res
+
+    def trig(self, na_replacement=0):
+        res = self.__getitem__((slice(None), slice(self._triggered[0], self._triggered[1])))
+        if na_replacement is not None:
+            res = [[x if x is not None else na_replacement for x in row] for row in res]
+        return res
+
+    def y(self, na_replacement=0):
+        res = self.__getitem__((slice(None), slice(len(self.columns) - self.num_labels, None)))
+        if na_replacement is not None:
+            res = [[x if x is not None else na_replacement for x in row] for row in res]
+        return res
+
+    def __getitem__(self, key):
+        if not isinstance(key, tuple):
+            raise TypeError("Dataset must be indexed with dataset[rows, columns]")
+
+        row_key, col_key = key
+
+        # Normalize rows
+        if isinstance(row_key, int):
+            rows = [self.data[row_key]]
+        else:
+            rows = self.data[row_key]
+
+        # Normalize columns
+        if isinstance(col_key, int):
+            res = [row[col_key] for row in rows]
+        else:
+            res = [
+                [row[i] for i in range(*col_key.indices(len(row)))]
+                if isinstance(col_key, slice)
+                else [row[i] for i in col_key]
+                for row in rows
+            ]
+
+        return res
+
+    def save(self, path: "Path"):
+        import pickle
+
+        with open(path, "wb") as fh:
+            pickle.dump(self, fh)
+
+    @staticmethod
+    def load(path: "Path") -> "Dataset":
+        import pickle
+
+        return pickle.load(open(path, "rb"))
 
     def to_arff(self, path: "Path"):
         arff = f"@relation 'enviPy-dataset: -C {self.num_labels}'\n"
@@ -350,7 +304,7 @@ class RuleBasedDataset(Dataset):
                 arff += f"@attribute {c} {{0,1}}\n"
 
         arff += "\n@data\n"
-        for d in self:
+        for d in self.data:
             ys = ",".join([str(v if v is not None else "?") for v in d[-self.num_labels :]])
             xs = ",".join([str(v if v is not None else "?") for v in d[: self.num_features]])
             arff += f"{ys},{xs}\n"
@@ -359,40 +313,10 @@ class RuleBasedDataset(Dataset):
             fh.write(arff)
             fh.flush()
 
-
-class EnviFormerDataset(Dataset):
-    def __init__(self, columns=None, data=None):
-        super().__init__(columns, data)
-
-    def X(self):
-        """Return the educts"""
-        return self["educts"]
-
-    def y(self):
-        """Return the products"""
-        return self["products"]
-
-    @staticmethod
-    def generate_dataset(reactions, *args, **kwargs):
-        # Standardise reactions for the training data
-        stereo = kwargs.get("stereo", False)
-        rows = []
-        for reaction in reactions:
-            e = ".".join(
-                [
-                    FormatConverter.standardize(smile.smiles, remove_stereo=not stereo)
-                    for smile in reaction.educts.all()
-                ]
-            )
-            p = ".".join(
-                [
-                    FormatConverter.standardize(smile.smiles, remove_stereo=not stereo)
-                    for smile in reaction.products.all()
-                ]
-            )
-            rows.append([e, p])
-        ds = EnviFormerDataset(["educts", "products"], rows)
-        return ds
+    def __repr__(self):
+        return (
+            f"<Dataset #rows={len(self.data)} #cols={len(self.columns)} #labels={self.num_labels}>"
+        )
 
 
 class SparseLabelECC(BaseEstimator, ClassifierMixin):
@@ -574,7 +498,7 @@ class EnsembleClassifierChain:
             self.classifiers = []
 
         if self.num_labels is None:
-            self.num_labels = Y.shape[1]
+            self.num_labels = len(Y[0])
 
         for p in range(self.num_chains):
             logger.debug(f"{datetime.now()} fitting {p + 1}/{self.num_chains}")
@@ -605,7 +529,7 @@ class RelativeReasoning:
 
     def fit(self, X, Y):
         n_instances = len(Y)
-        n_attributes = Y.shape[1]
+        n_attributes = len(Y[0])
 
         for i in range(n_attributes):
             for j in range(n_attributes):
@@ -617,8 +541,8 @@ class RelativeReasoning:
                 countboth = 0
 
                 for k in range(n_instances):
-                    vi = Y[k, i]
-                    vj = Y[k, j]
+                    vi = Y[k][i]
+                    vj = Y[k][j]
 
                     if vi is None or vj is None:
                         continue
@@ -674,7 +598,7 @@ class ApplicabilityDomainPCA(PCA):
         self.min_vals = None
         self.max_vals = None
 
-    def build(self, train_dataset: "RuleBasedDataset"):
+    def build(self, train_dataset: "Dataset"):
         # transform
         X_scaled = self.scaler.fit_transform(train_dataset.X())
         # fit pca
@@ -688,7 +612,7 @@ class ApplicabilityDomainPCA(PCA):
         instances_pca = self.transform(instances_scaled)
         return instances_pca
 
-    def is_applicable(self, classify_instances: "RuleBasedDataset"):
+    def is_applicable(self, classify_instances: "Dataset"):
         instances_pca = self.__transform(classify_instances.X())
 
         is_applicable = []

uv.lock

@@ -1,10 +1,6 @@
 version = 1
-revision = 2
+revision = 3
 requires-python = ">=3.12"
-resolution-markers = [
-    "sys_platform == 'linux' or sys_platform == 'win32'",
-    "sys_platform != 'linux' and sys_platform != 'win32'",
-]
 
 [[package]]
 name = "aiohappyeyeballs"
@@ -180,19 +176,6 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/c9/af/0dcccc7fdcdf170f9a1585e5e96b6fb0ba1749ef6be8c89a6202284759bd/celery-5.5.3-py3-none-any.whl", hash = "sha256:0b5761a07057acee94694464ca482416b959568904c9dfa41ce8413a7d65d525", size = 438775, upload-time = "2025-06-01T11:08:09.94Z" },
 ]
 
-[[package]]
-name = "celery-stubs"
-version = "0.1.3"
-source = { registry = "https://pypi.org/simple" }
-dependencies = [
-    { name = "mypy" },
-    { name = "typing-extensions" },
-]
-sdist = { url = "https://files.pythonhosted.org/packages/98/14/b853ada8706a3a301396566b6dd405d1cbb24bff756236a12a01dbe766a4/celery-stubs-0.1.3.tar.gz", hash = "sha256:0fb5345820f8a2bd14e6ffcbef2d10181e12e40f8369f551d7acc99d8d514919", size = 46583, upload-time = "2023-02-10T02:20:11.837Z" }
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/1c/7a/4ab2347d13f1f59d10a7337feb9beb002664119f286036785284c6bec150/celery_stubs-0.1.3-py3-none-any.whl", hash = "sha256:dfb9ad27614a8af028b2055bb4a4ae99ca5e9a8d871428a506646d62153218d7", size = 89085, upload-time = "2023-02-10T02:20:09.409Z" },
-]
-
 [[package]]
 name = "certifi"
 version = "2025.10.5"
@@ -542,14 +525,13 @@ wheels = [
 [[package]]
 name = "enviformer"
 version = "0.1.0"
-source = { git = "ssh://git@git.envipath.com/enviPath/enviformer.git?rev=v0.1.4#7094be5767748fd63d4a84a5d71f06cf02ba07f3" }
+source = { git = "ssh://git@git.envipath.com/enviPath/enviformer.git?rev=v0.1.2#3f28f60cfa1df814cf7559303b5130933efa40ae" }
 dependencies = [
     { name = "joblib" },
     { name = "lightning" },
     { name = "pytorch-lightning" },
     { name = "scikit-learn" },
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+    { name = "torch" },
 ]
 
 [[package]]
@@ -564,6 +546,7 @@ dependencies = [
     { name = "django-ninja" },
     { name = "django-oauth-toolkit" },
     { name = "django-polymorphic" },
+    { name = "django-stubs" },
     { name = "enviformer" },
     { name = "envipy-additional-information" },
     { name = "envipy-ambit" },
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     { name = "python-dotenv" },
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