Resume GLM development

BojarLab · Dec 15, 2024 · d2c59ca · d2c59ca
1 parent 524fc99
commit d2c59ca
Show file tree

Hide file tree

Showing 14 changed files with 3,721 additions and 36 deletions.
diff --git a/configs/lgi/test.yaml b/configs/lgi/test.yaml
@@ -1,10 +1,10 @@
 seed: 42
-#root_dir: /home/daniel/Data1/roman/GIFFLAR/lgi_data
-#logs_dir: /home/daniel/Data1/roman/GIFFLAR/lgi_logs
-#origin: /home/daniel/Desktop/GIFFLAR/lgi_data_full.pkl
-root_dir: /scratch/SCRATCH_SAS/roman/Gothenburg/GIFFLAR/lgi_data
-logs_dir: /scratch/SCRATCH_SAS/roman/Gothenburg/GIFFLAR/lgi_logs
-origin: /home/rjo21/Desktop/GIFFLAR/lgi_data.pkl
+root_dir: /home/daniel/Data1/roman/GIFFLAR/lgi_data
+logs_dir: /home/daniel/Data1/roman/GIFFLAR/lgi_logs
+origin: /home/daniel/Desktop/GIFFLAR/lgi_data_full.pkl
+#root_dir: /scratch/SCRATCH_SAS/roman/Gothenburg/GIFFLAR/lgi_data
+#logs_dir: /scratch/SCRATCH_SAS/roman/Gothenburg/GIFFLAR/lgi_logs
+#origin: /home/rjo21/Desktop/GIFFLAR/lgi_data.pkl
 model:
   glycan_encoder:
     name: gifflar
@@ -16,7 +16,7 @@ model:
     name: ESM
     layer_num: 33
   batch_size: 256
-  epochs: 5
+  epochs: 100
   learning_rate: 0.001
   optimizer: Adam
 
diff --git a/datasets/glycans_1000.txt b/datasets/glycans_1000.txt
diff --git a/datasets/glyles.txt b/datasets/glyles.txt
@@ -0,0 +1,263 @@
+
+Glc
+Man
+Gal
+Gul
+Alt
+All
+Tal
+Ido
+Qui
+Rha
+Fuc
+Oli
+Tyv 
+Abe
+Par
+Dig
+Col
+Ara
+Lyx
+Xyl
+Rib
+Kdn
+Neu
+Sia
+Pse
+Leg
+Aci
+Bac
+Kdo
+Dha
+Mur
+Api
+Fru
+Tag
+Sor
+Psi
+Ery
+Thre
+Rul
+Xul
+Unk
+Ace
+Aco
+Asc
+Fus
+Ins
+Ko
+Pau
+Per
+Sed
+Sug
+Vio
+Xlu
+Yer
+Erwiniose
+C
+N
+O
+P
+Ceroplastic
+Lacceroic
+3oxoMyr
+Psyllic
+Geddic
+Alloc
+Allyl
+Phthi
+TBDPS
+aLnn
+ClAc
+Coum
+eSte
+Fmoc
+gLnn
+HSer
+Pico
+Prop
+TIPS
+triN
+Troc
+Ach
+Aep
+Ala
+Ang
+Asp
+Beh
+Boc
+But
+Cbz
+Cct
+Cer
+Cet
+Cho
+cHx
+Cin
+Crt
+Cys
+DCA
+Dce
+Dco
+Dec
+Dhp
+DMT
+Dod
+Etg
+Etn
+EtN
+Fer
+Glu
+Gly
+Gro
+Hpo
+Hse
+Hxo
+Lac
+Lau
+Leu
+Lev
+Lin
+Lys
+Mal
+Mar
+Mel
+MMT
+MOM
+Mon
+Myr
+NAP
+Ner
+Nno
+Non
+Oco
+Ole
+oNB
+Orn
+Pam
+Pic
+Piv
+PMB
+PMP
+Poc
+Pro
+Pyr
+Ser
+Sin
+Ste
+TBS
+tBu
+TCA
+TES
+TFA
+THP
+Thr
+Tig
+TMS
+Udo
+Ulo
+ulo
+Und
+Vac
+Ac
+Al
+Am
+Bn
+Br
+Bu
+Bz
+Cl
+Cm
+DD
+DL
+en
+Et
+Fo
+Gc
+Hp
+Hx
+LD
+LL
+Me
+N3
+Nn
+Ns
+Oc
+Pe
+Ph
+Pp
+Pr
+Tf
+Tr
+Ts
+Vl
+A
+F
+I
+S
+Anhydro
+0d
+D
+L
+ulosaric
+ulosonic
+uronic
+onic
+aric
+ol
+Hep
+Hex
+Oct
+Pen
+Suc
+a
+b
+p
+f
+0
+1
+2
+3
+4
+5
+6
+7
+8
+9
+10
+11
+12
+13
+14
+15
+16
+17
+18
+19
+20
+21
+22
+23
+24
+25
+26
+27
+28
+29
+,
+-
+(
+)
+[
+]
+{
+}
+a
+ai
+c
+d
+e
+t
+=
+i
+?